RECOMBINANT NEWCASTLE DISEASE VIRUSES AND IMMUNOGENIC COMPOSITIONS FOR USE IN IMMUNIZING AGAINST SARS-COV-2 OMICRON VARIANT

SEQUENCE LISTING

This application contains a computer readable Sequence Listing which has been submitted in XML file format with this application, the entire content of which is incorporated by reference herein in its entirety. The Sequence Listing XML file submitted with this application is entitled “06923-398-228_SEQLISTING.xml”, was created on Mar. 30, 2023 and is 380,403 bytes in size.

1. INTRODUCTION

In one aspect, described herein are recombinant Newcastle disease virus (“NDV”) comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a protein comprising a spike protein of an Omicron variant of a severe acute respiratory syndrome coronavirus 2 (“SARS-CoV-2”) or a portion thereof (e.g., ectodomain or receptor binding domain of SARS-CoV-2 spike protein). In a specific embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene comprising a codon-optimized nucleic acid sequence encoding a protein comprising a spike protein of an Omicron variant of a SARS-CoV-2 or portion thereof (e.g., ectodomain or receptor binding domain of SARS-CoV-2 spike protein). In a specific embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a chimeric F protein, wherein the chimeric F protein comprises a spike protein ectodomain of an Omicron variant of a SARS-CoV-2 and NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a spike protein ectodomain of an Omicron variant of a SARS-CoV-2 and NDV F protein transmembrane and cytoplasmic domains. Also described herein are compositions comprising such recombinant NDV(s) and the use of such recombinant NDV(s) as well as compositions to induce an immune response to SARS-CoV-2 an Omicron variant of spike protein, and in immunoassays to detect the presence of antibody that binds to SARS-CoV-2 spike protein. Further, provided herein are immunogenic compositions comprising recombinant NDVs and the use of such immunogenic compositions to immunize against SARS-CoV-2 as well as prevent COVID-19.

2. BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19). Since the beginning of the pandemic, the emergence of new variants of concern (VOC) has threatened the protection conferred by vaccination using the original strain (Carreno et al., 2021. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. EBioMedicine 73:103626). In December 2020, the Alpha variant (B.1.1.7) and Beta variant (B.1.351) were declared VOC and spread over the world, followed by the Gamma strain (P.1) that was declared VOC in January 2021. Both Beta and Gamma variants exhibited notable resistance to neutralizing antibodies raised against the original strain in humans (Carreno et al., 2021. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. EBioMedicine 73:103626; Garcia-Beltran et al., 2021. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 184:2372-2383 e9). In May 2021, a huge epidemic in India gave rise to a new VOC: the Delta variant (B.1.617.2). This new VOC harbored different mutations in the spike from other variants that also significantly reduced its sensitivity to neutralizing antibodies, and increased transmissibility quickly replacing the previous variants worldwide (Carreno et al., 2021. Evidence for retained spike-binding and neutralizing activity against emerging SARS-CoV-2 variants in serum of COVID-19 mRNA vaccine recipients. EBioMedicine 73:103626; Planas et al., 2021. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 596:276-280). In November 2021, a new VOC named Omicron appeared in South Africa. Since that moment, Omicron has taken over worldwide replacing the Delta variant (Holder J. 2022. Tracking Coranavirus Vaccination Around the World, on The New York Times. https://www.nytimes.com/interactive/2021/world/covid-vaccinations-tracker.html. Accessed 5 Feb. 2022). Compared to the previous VOC, Omicron presents the highest number of mutations in the spike protein and has shown the highest drop-in neutralization activity (Carreño et al., 2021. Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron. Nature doi: 10.1038/d41586-021-03846-z; Hannah Ritchie et. al., 2020. Coronavirus Pandemic (COVID-19), on Our World Data. https://ourworldindata.org/covid-vaccinations. Accessed 05-Febraury-2022). Currently, the Omicron sub-linage BA.2, also known as the “stealth” Omicron seems to show even more immune evasion and transmissibility (Mahase E. 2022. Omicron sub-lineage BA.2 may have “substantial growth advantage,” UKHSA reports. BMJ 376:0263; Li et al., 2021. Omicron and S-gene target failure cases in the highest COVID-19 case rate region in Canada-December 2021. J Med Virol doi: 10.1002/jmv.27562; ECDC/WHO. 2021. Methods for the detection and characterisation of SARS-CoV-2 variants-first update. 20 Dec. 2021. Stockholm/Copenhagen).

Despite of the unprecedentedly rapid development of COVID-19 vaccines, only a 63.1% of the global population are fully vaccinated (Hannah Ritchie et. al., 2020. Coronavirus Pandemic (COVID-19), on Our World Data. https://ourworldindata.org/covid-vaccinations. Accessed 05-Febraury-2022). Hence, there is still a need for COVID-19 vaccines that can be produced locally in low- and middle-income countries (LMICs), where the vaccination rates are the lowest worldwide (id.).

3. SUMMARY

In one aspect, described herein are nucleotide sequences comprising severe acute respiratory syndrome coronavirus 2 (“SARS-CoV-2”) Omicron spike protein or a portion thereof (e.g., ectodomain or receptor binding domain of SARS-CoV-2 Omicron spike protein), or a derivative thereof. In a specific embodiment, encoding a chimeric F protein, wherein the chimeric F protein comprises an SARS-CoV-2 Omicron spike protein ectodomain or a derivative thereof and NDV F protein transmembrane and cytoplasmic domains.

In some embodiments, provided herein are nucleic acid sequences comprising a nucleotide sequence set forth in Table 3, infra. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:6, 10, 14, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:6, 10, 14, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98 without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 66, 80, 86, 92, or 98 without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:7, 11, or 15. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:36, 48, or 60, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 66, 80, 92, or 98. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 66, 80, 92, or 98 without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of an ectodomain set forth in Table 3. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of an ectodomain set forth in Table 3, and the nucleotide sequence encoding NDV F protein transmembrane and cytoplasmic domains. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO: 18, 20, 22, 34, 40, 46, 52, 58, 64, 70, 78, 84, 90, 96, or 102, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:34, 46, 58, 84, 90, 96, or 102, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:32, 34, 44, 46, 56, 58, 68, or 70, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence of SEQ ID NO:32, 44, 56, 82, 88, 94, or 102, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein.

In some embodiments, provided herein are nucleic acid sequences encoding an amino acid sequence set forth in Table 3, infra. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:8, 12, 16, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 99. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:8, 12, 16, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 31, 43, 55, 81, 87, 93, or 99. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 31, 43, 55, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:9, 13, or 17. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:37, 49, or 61. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:37, 49, or 61, without the signal peptide. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:31, 43, 55, 61, 67, 81, or 87. In some embodiments, provided herein is a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:31, 43, 55, 61, 67, 81, or 87, without the signal peptide. In some embodiments, provided herein is a nucleic acid sequence encoding the amino acid sequence of an ectodomain set forth in Table 3. In some embodiments, provided herein is a nucleic acid sequence encoding the amino acid sequence of an ectodomain set forth in Table 3, and the nucleotide sequence encoding NDV F protein transmembrane and cytoplasmic domains. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 19, 21, 23, 39, 41, 51, 53, 63, or 65, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 19, 21, 23, 35, 41, 47, 53, 59, 65, 71, 79, 85, 91, 97, or 103, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 35, 47, 59, 85, 91, 97, or 103, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95, or 101, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein is a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 33, 45, 57, 83, 89, 95, or 101, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, provided herein a nucleic acid sequence comprising the nucleotide sequence encoding the amino acid sequence of SEQ ID NO:33, 35, 45, 47, 57, 59, 69, or 71, and the nucleotide sequence encoding the transmembrane and cytoplasmic domains of NDV F protein.

In some embodiments, provided herein is a recombinant protein comprising a SARS-CoV-2 Omicron spike protein ectodomain or portion thereof described herein. The SARS-CoV-2 Omicron spike protein ectodomain or portion thereof may be any one described herein in the context of a transgene. In some embodiments, provided herein is a recombinant protein comprising a derivative of a SARS-CoV-2 Omicron spike protein ectodomain described herein. The derivative of the SARS-CoV-2 Omicron spike protein ectodomain may be any one described herein in the context of a transgene. In some embodiments, provided herein is a recombinant protein comprising a derivative of a SARS-CoV-2 Omicron spike protein ectodomain, wherein the derivative comprises the ectodomain of the amino acid sequence of SEQ ID NO:104 without the signal peptide and with amino acid modifications, wherein the amino acid modifications comprise: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of SEQ ID NO:104 to a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of SEQ ID NO: 104: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) two or more amino acid modifications to the amino acid sequence of the ectodomain of SEQ ID NO: 104 to amino acid residues found at the corresponding amino acid positions in the Omicron spike protein ectodomain, wherein the two or more amino acid modifications comprise two or more amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and/or N969K. In some embodiments, the two or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371 and 375 in SEQ ID NO:104. In some embodiments, the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371, 373, and 375 in SEQ ID NO:104. In some embodiments, the two or more amino acid modifications does not comprise amino acid modifications does not include amino acid modification at the amino acid position corresponding to amino acid position of 452 in SEQ ID NO:104. In some embodiments, the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371, 375, and 452 in SEQ ID NO: 104. In some embodiments, the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371, 373, 375, and 452 in SEQ ID NO: 104. In some embodiments, the two or more amino acid modifications further comprises the following amino acid modification at the amino acid position corresponding to the indicated amino acid positions of SEQ ID NO: 104: G339D or G339H.

In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 5. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 6. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 7. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 8. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 9. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 10. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the amino acid modifications of a construct in Table 11.

In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, the two or more amino acid modifications further comprise one or more (e.g., 1, 2, 3, 4, 5, or more) of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), T376A, D405N, R408S, and/or Q498R. In some embodiments, the two or more amino acid modifications further comprise one or more of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), T376A, D405N, R408S, and Q498R. In some embodiments, the two or more amino acid modifications further comprise the following amino acid modification at the amino acid position corresponding to the indicated amino acid position of SEQ ID NO:104: V213G or V213E. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more amino acid modifications comprise the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO:104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more amino acid modifications does not include amino acid modification at the amino acid position corresponding to amino acid position of 452 in SEQ ID NO:104. In some embodiments, the two or more amino acid modifications comprise two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, or more) or all of the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70(HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

In some embodiments, provided herein is a recombinant protein comprising a derivative of a SARS-CoV-2 Omicron spike protein ectodomain, wherein the derivative comprises the ectodomain of the amino acid sequence of SEQ ID NO: 104 without the signal peptide and with amino acid modifications, wherein the amino acid modifications comprise: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of SEQ ID NO:104 to a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of SEQ ID NO:104: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications to the amino acid sequence of the ectodomain of SEQ ID NO: 104 to amino acid residues found at the corresponding amino acid positions in the Omicron spike protein ectodomain. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications do not include amino acid modifications at the amino acid positions corresponding to the amino acid positions 371 and 375 of SEQ ID NO:104. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications do not include amino acid modifications at the amino acid positions corresponding to the amino acid positions 371, 373, and 375 of SEQ ID NO: 104.

In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) amino acid modifications two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or more) or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

In some embodiments, the two or more amino acid modifications are 18 or more amino acid modifications. In some embodiments, the two or more amino acid modifications are 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28 amino acid modifications.

In some embodiments, a recombinant protein described herein further comprises a trimerization domain (e.g., a T4 foldon trimerization domain). In some embodiments, a recombinant protein described herein further comprises NDV F protein transmembrane and cytoplasmic domains.

In some embodiments, the derivative of the ectodomain comprises the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the ectodomain comprises the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97.

In some embodiments, provided herein is a recombinant protein comprising a derivative of the ectodomain of a SARS-CoV-2 variant, wherein the ectodomain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, 79, 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95 or 101. In some embodiments, provided herein is a recombinant protein comprising a derivative of the ectodomain of a SARS-CoV-2 variant, wherein the ectodomain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97. In some embodiments, the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO:104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO: 104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K. In some embodiments, the ectodomain comprises the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, 79, 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95 or 101.

In some embodiments, the protein further comprises a signal peptide. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO:29.

In some embodiments, the protein further comprises the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, the protein further comprises a linker and the transmembrane and cytoplasmic domains of NDV F protein. In some embodiments, the transmembrane and cytoplasmic domains of NDV F protein comprises the amino acid sequence of SEQ ID NO: 5.

In some embodiments, provided herein is a polynucleotide comprising a nucleotide sequence encoding a protein described herein (e.g., a recombinant protein described herein). In some embodiments, the nucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74. In some embodiments, the nucleotide sequence comprises the nucleotide sequence SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, the nucleotide sequence comprises the nucleotide sequence SEQ ID NO: 32, 82, 100, 88, or 94. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 35, 85, 91, 97, 103, 59, 19, 21, 23, 41, 47, 53, 65, 71, 79, 33, 83, 89, 95, 101, 57, 39, 45, 51, 63, 69, or 77. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 35, 85, 91, 97, 103, or 59. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 33, 83, 89, 95, 101, or 57. In some embodiments, the nucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, the nucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60, or 74. In some embodiments, the nucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 6, 11, or 15. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, without the signal peptide. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 9, 13, 17.

In some embodiments, provided herein is a vector comprising a polynucleotide described herein. In some embodiments, the vector is a plasmid or a viral vector.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99, without the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, or 99.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 8, 12, 16, 37, 49, 61, or 75, or an amino acid sequence that is at least 90% identical to SEQ ID NO: 88, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 8, 12, 16, 37, 49, 61, or 75.

In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74. In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, 78, 32, 38, 44, 50, 56, 62, 68, 76, 82, 88, 94, or 100. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, or 58. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, 78, 32, 38, 44, 50, 56, 62, 68, 76, 82, 88, 94, or 100. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, or 58. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 60, 80, 86, 92, or 98.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, or 58. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76. In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, or 56. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, or 59. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, or 59. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, or 59. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, or 57. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77. In some embodiments, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, or 57. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 35, 45, 47, 57, 59, 69, 83, 85, 89, 91, 95, 97, 103, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 35, 45, 47, 57, or 59. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 36, 48, or 60, or a nucleotide sequence that is at least 80% identical to SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises a nucleotide sequence that is at least 80% identical to SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises the nucleotide sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60.

In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 80, 86, 92, 98, or 66, or a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66. In some embodiments, the transgene comprises a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66. In some embodiments, the transgene comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66. In some embodiments, the transgene comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, or 66.

In some embodiments, provided herein is a transgene comprising the nucleotide sequence of SEQ ID NO:30, 42, 54, 80, 86, 92, 98, or 66, without the signal peptide, or a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66, without the signal peptide. In some embodiments, the transgene comprises a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66, without the signal peptide. In some embodiments, the transgene comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66, without the signal peptide. In some embodiments, the transgene comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 80, 86, 92, 98, or 66, without the signal peptide.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO:32, 34, 82, 84, 88, 90, 94, 96, 100, 102, 44, 46, 56, 58, 68, or 70, or a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 32, 34, 82, 84, 88, 90, 94, 96, 100, 102, 44, 46, 56, 58, 68, or 70. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 32, 34, 82, 84, 88, 90, 94, 96, 100, 102, 44, 46, 56, 58, 68, or 70. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 32, 34, 82, 84, 88, 90, 94, 96, 100, 102, 44, 46, 56, 58, 68, or 70. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 32, 34, 82, 84, 88, 90, 94, 96, 100, 102, 44, 46, 56, 58, 68, or 70. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 36, 48, or 60, or a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 36, 48, or 60.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, or a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

In some embodiments, provided herein is a transgene comprising an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the signal peptide, or a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the signal peptide. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the signal peptide. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the signal peptide. In some embodiments, the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74, without the signal peptide.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78, or a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, provided herein is a transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76, or a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76. In some embodiments, the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the linker comprises the amino acid sequence of SEQ ID NO:24.

In some embodiments, the transgene further comprises a Newcastle Disease Virus (NDV) gene start sequence (e.g., SEQ ID NO:27). In some embodiments, the transgene further comprises a Newcastle Disease Virus (NDV) gene end sequence (e.g., SEQ ID NO: 26). In some embodiments, the transgene further comprises SEQ ID NO:26 and 27. In some embodiments, the transgene further comprises SEQ ID NO: 25 or SEQ ID NO:28. In some embodiments, the transgene further comprises SEQ ID NOS: 25 and 28.

In some embodiments, provided herein is a vector comprising a transgene described herein (e.g., in Section 5.1 or 6). The vector may be a plasmid or a viral vector.

In some embodiments, provided herein is a nucleotide sequence comprising a transgene described herein, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit. In some embodiments, provided herein is a nucleotide sequence comprising a transgene described herein, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit, wherein the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain. In some embodiments, provided herein is a vector comprising a nucleotide sequence described herein. The vector may be a plasmid or a viral vector.

In another aspect, described herein are recombinant Newcastle disease virus (“NDV”) comprising a packaged genome, wherein the packaged genome comprises a transgene encoding severe acute respiratory syndrome coronavirus 2 (“SARS-CoV-2”) Omicron spike protein or a portion thereof (e.g., ectodomain or receptor binding domain of SARS-CoV-2 Omicron spike protein), or a derivative thereof. In a specific embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene comprising a codon-optimized nucleic acid sequence encoding SARS-CoV-2 Omicron spike protein or portion thereof (e.g., ectodomain or receptor binding domain of SARS-CoV-2 Omicron spike protein), or a derivative thereof. In a specific embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a chimeric F protein, wherein the chimeric F protein comprises an SARS-CoV-2 Omicron spike protein ectodomain or a derivative thereof and NDV F protein transmembrane and cytoplasmic domains. In some embodiments, the ectodomain of the SARS-CoV-2 Omicron spike protein or derivative thereof is encoded by a codon-optimized nucleic acid sequence.

In some embodiments, provided herein is a recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene described herein (e.g., in Section 5.1 or 6). In some embodiments, the NDV virion comprises the chimeric F protein. In some embodiments, provided herein is a recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene, wherein the transgene encodes a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene, wherein the transgene encodes a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene, wherein the transgene encodes a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene, wherein the transgene encodes a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95% (e.g., at least 96%, at least 97%, at least 98%, or at least 99%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO: 104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO: 104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K. In some embodiments, the genome comprises a NDV F transcription unit, a NDV NP transcription unit, a NDV M transcription unit, a NDV L transcription unit, a NDV P transcription unit, and a NDV HN transcription unit. In some embodiments, the genome comprises a NDV F transcription unit, a NDV NP transcription unit, a NDV M transcription unit, a NDV L transcription unit, a NDV P transcription unit, and a NDV HN transcription unit, and wherein the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain. In some embodiments, the transgene is between two NDV transcription units of the packaged genome. In some embodiments, the two transcription units of the packaged genome are the transcription units for the NDV P gene and the NDV M gene. In some embodiments, the two transcription units of the packaged genome are the transcription units for the NDV NP gene and the NDV P gene. In some embodiments, a chimeric F protein or protein encoded by the transgene is incorporated into the NDV virion.

In some embodiments, provided herein is a recombinant NDV comprising a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO:31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises an amino acid sequence that is at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises an amino acid sequence that is at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75. In some embodiments, the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

In some embodiments, provided herein is a recombinant NDV comprising a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

In some embodiments, provided herein is a recombinant NDV comprising a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence SEQ ID NO:33, 45, 57, 83, 89, 95, 101, 39, 51, 63, 69, or 77. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 33, 45, 57, 83, 89, 95, 101, 39, 51, 63, 69, or 77. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 33, 45, 57, 83, 89, 95, 101, 39, 51, 63, 69, or 77. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 45, 57, 83, 89, 95, 101, 39, 51, 63, 69, or 77.

In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, 103, 45, 47, 57, 59, 69, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, 103, 45, 47, 57, 59, 69, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, or 103. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, 103, 45, 47, 57, 59, 69, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, or 103. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, 103, 45, 47, 57, 59, 69, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 33, 35, 83, 85, 89, 91, 95, 97, 101, or 103. In some embodiments, the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

In some embodiments, provided herein is a recombinant NDV comprising a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant NDV comprising a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 80% (e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant NDV comprising a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% (e.g., at least 91%, at least 92%, at least 93%, or at least 94%) identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, provided herein is a recombinant NDV comprising a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79. In some embodiments, the derivative of the ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, and wherein the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO:104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO: 104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K

In some embodiments, the recombinant NDV comprises an NDV backbone which is lentogenic. In some embodiments, the recombinant NDV comprises an NDV backbone of LaSota strain. In some embodiments, the recombinant NDV comprises an NDV backbone of Hitchner B1 strain.

In another aspect, provided herein are compositions (e.g., immunogenic compositions) comprising a recombinant NDV described herein. The composition (e.g., immunogenic composition) may be monovalent, bivalent, or multivalent. In some embodiments, the immunogenic composition is monovalent. In some embodiments, the recombinant NDV described herein is inactivated. In some embodiments, an immunogenic composition described herein further comprises an adjuvant (e.g., an adjuvant described herein). The immunogenic composition may be used to induce an immune response, immunize a subject against SARS-CoV-2, and/or the prevent of COVID-19.

In some embodiments, provided herein is an immunogenic composition comprising a polynucleotide described herein. In some embodiments, the immunogenic composition described herein further comprises an adjuvant (e.g., an adjuvant described herein). The polynucleotide may be RNA, DNA, or a combination thereof. The polynucleotide may comprise naturally occurring nucleotides or analogs thereof. The immunogenic composition may be used to induce an immune response, immunize a subject against SARS-CoV-2, and/or the prevent of COVID-19.

In some embodiments, provided herein is an immunogenic composition comprising a recombinant protein described herein. In some embodiments, the immunogenic composition described herein further comprises an adjuvant (e.g., an adjuvant described herein). The immunogenic composition may be used to induce an immune response, immunize a subject against SARS-CoV-2, and/or the prevent of COVID-19.

In some embodiments, provided herein is an immunogenic composition comprising a vector described herein. In some embodiments, the immunogenic composition described herein further comprises an adjuvant (e.g., an adjuvant described herein). The immunogenic composition may be used to induce an immune response, immunize a subject against SARS-CoV-2, and/or the prevent of COVID-19.

In another aspect, the recombinant NDV described herein and the immunogenic compositions described herein are for use in inducing an immune response, immunizing a subject against SARS-CoV-2, and/or the prevention of COVID-19. In some embodiments, the recombinant NDV described herein and the immunogenic compositions described herein are for use in preventing moderate or severe COVID-19. In some embodiments, provided herein is a method for inducing an immune response to SARS-CoV-2 Omicron spike protein, comprising administering an immunogenic composition described herein to a subject. In some embodiments, provided herein is a method for preventing COVID-19, comprising administering an immunogenic composition described herein to a subject. In some embodiments, provided herein is a method for preventing severe COVID-19, comprising administering an immunogenic composition described herein to a subject. In some embodiments, provided herein is a method for immunizing a subject against SARS-CoV-2, comprising administering an immunogenic composition described herein to a subject. In specific embodiments, the composition is administered to the subject intranasally or intramuscularly. In a specific embodiment, the subject is a human. In some embodiments, the subject has been previously vaccinated with a COVID-19 vaccine. In some embodiments, the subject is administered at least one booster of the immunogenic composition.

In another aspect, provided herein are kits. In some embodiments, provided herein is a kit comprising a transgene described herein. In some embodiments, provided herein is a kit comprising a polynucleotide described herein. In some embodiments, provided herein is a kit comprising a nucleotide sequence described herein. In some embodiments, provided herein is a vector described herein. In some embodiments, provided herein is a kit comprising a recombinant protein described herein. In some embodiments, provided herein is a recombinant NDV described herein. In some embodiments, provided herein is a kit comprising an immunogenic composition described herein.

In another aspect, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., a chicken embryonated egg) comprising a transgene described herein, a polynucleotide described herein, or a nucleotide sequence described herein. In some embodiments, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., a chicken embryonated egg) comprising a transgene described herein. In some embodiments, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., a chicken embryonated egg) comprising a polynucleotide described herein. In another aspect, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., embryonated chicken egg) comprising a vector described herein. In another aspect, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., chicken embryonated egg) comprising a recombinant NDV described herein. In another aspect, provided herein is a cell(s) (e.g., a cell line) or an embryonated egg (e.g., a chicken embryonated egg) expressing a protein described herein. In some embodiments, the cell(s) is in vitro or ex vivo.

In another aspect, provided herein is a method for propagating a recombinant NDV described herein, the method comprising culturing a cell(s) (e.g., cell line) or an embryonated egg described herein. In some embodiments, the method further comprises isolating the recombinant NDV from the cell(s) (e.g., cell line) or embryonated egg.

In another aspect, provided herein is a method for detecting the presence of antibody specific to SARS-CoV-2 Omicron spike protein, comprising contacting a specimen with a recombinant NDV described herein in an immunoassay. In another aspect, provided herein is a method for detecting the presence of antibody specific to SARS-CoV-2 Omicron spike protein, comprising contacting a specimen with a recombinant protein described herein in an immunoassay. In another aspect, provided herein is a method for detecting the presence of antibody specific to SARS-CoV-2 Omicron spike protein, comprising contacting a specimen with a vector expressing a protein described herein in an immunoassay. In some embodiments, the specimen is a biological specimen. In some embodiments, the biological specimen is blood, plasma or sera from a subject. In some embodiments, the subject is human. In some embodiments, the specimen is an antibody or antisera.

3.1 Terminology

As used herein, the term “about” or “approximately” when used in conjunction with a number refers to any number within 1, 5 or 10% of the referenced number, including the referenced number.

The phrase “amino acid modifications” includes amino acid substitutions, amino acid deletions, and/or amino acid insertions.

As used herein, the terms “antibody” and “antibodies” refer to molecules that contain an antigen binding site, e.g., immunoglobulins. Antibodies include, but are not limited to, monoclonal antibodies, bispecific antibodies, multispecific antibodies, human antibodies, humanized antibodies, synthetic antibodies, chimeric antibodies, polyclonal antibodies, single domain antibodies, camelized antibodies, single-chain Fvs (scFv), single chain antibodies, Fab fragments, F(ab′) fragments, disulfide-linked bispecific Fvs (sdFv), intrabodies, and anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id and anti-anti-Id antibodies to antibodies), and epitope-binding fragments of any of the above. In particular, antibodies include immunoglobulin molecules and immunologically active fragments of immunoglobulin molecules. Immunoglobulin molecules can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass.

As used herein, the term “elderly human” refers to a human 65 years or older.

As used herein, the term “human adult” refers to a human that is 18 years or older.

As used herein, the term “human child” refers to a human that is 1 year to 18 years old.

As used herein, the term “human toddler” refers to a human that is 1 year to 3 years old.

As used herein, the term “human infant” refers to a newborn to 1 year old year human.

As used herein, the phrases “IFN deficient systems” or “IFN-deficient substrates” refer to systems, e.g., cells, cell lines and animals, such as mice, chickens, turkeys, rabbits, rats, horses etc., which do not produce one, two or more types of IFN, or do not produce any type of IFN, or produce low levels of one, two or more types of IFN, or produce low levels of any IFN (i.e., a reduction in any IFN expression of 5-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90% or more when compared to IFN-competent systems under the same conditions), do not respond or respond less efficiently to one, two or more types of IFN, or do not respond to any type of IFN, have a delayed response to one, two or more types of IFN, are deficient in the activity of antiviral genes induced by one, two or more types of IFN, or induced by any type of IFN, or any combination thereof.

As used herein, the terms “subject” or “patient” are used interchangeably. As used herein, the terms “subject” and “subjects” refers to an animal. In some embodiments, the subject is a mammal including a non-primate (e.g., a camel, donkey, zebra, bovine, horse, horse, cat, dog, rat, and mouse) and a primate (e.g., a monkey, chimpanzee, and a human). In some embodiments, the subject is a non-human mammal. In certain embodiments, the subject is a pet (e.g., dog or cat) or farm animal (e.g., a horse, pig or cow). In specific embodiments, the subject is a human. In certain embodiments, the mammal (e.g., human) is 4 to 6 months old, 6 to 12 months old, 1 to 5 years old, 5 to 10 years old, 10 to 15 years old, 15 to 20 years old, 20 to 25 years old, 25 to 30 years old, 30 to 35 years old, 35 to 40 years old, 40 to 45 years old, 45 to 50 years old, 50 to 55 years old, 55 to 60 years old, 60 to 65 years old, 65 to 70 years old, 70 to 75 years old, 75 to 80 years old, 80 to 85 years old, 85 to 90 years old, 90 to 95 years old or 95 to 100 years old. In specific embodiments, the subject is an animal that is not avian.

As used herein, the term “in combination” in the context of the administration of a therapy(ies) to a subject, refers to the use of more than one therapy. The use of the term “in combination” does not restrict the order in which therapies are administered to a subject. A first therapy can be administered prior to, concomitantly with, or subsequent to the administration of a second therapy to a subject.

As used herein, the terms “SARS-CoV-2 spike protein” and “spike protein of SARS-CoV-2” includes a SARS-CoV-2 spike protein known to those of skill in the art. See, e.g., GenBank Accession Nos. MN908947.3, MT447160, MT44636, MT446360, MT444593, MT444529, MT370887, and MT334558 for examples of amino acid sequences of SARS-CoV-2 spike protein and nucleotide sequences encoding SARS-CoV-2 spike protein. A typical spike protein comprises domains known to those of skill in the art including an S1 domain, a receptor binding domain, an S2 domain, a transmembrane domain and a cytoplasmic domain. See, e.g., Wrapp et al., 2020, Science 367:1260-1263 and Duan et al., 2020, Front. Immunol., Vol. 11, Article 576622 for a description of SARS-CoV-2 spike protein (in particular, the structure of such protein). The spike protein may be characterized has having a signal peptide, a receptor binding domain, an ectodomain, an S1 domain, an S2 domain, and a transmembrane and endodomain (or cytoplasmic).

As used herein, the terms “spike protein of an Omicron variant of a SARS-CoV-2”, “SARS-CoV-2 Omicron spike protein”, “SARS-CoV-2 Omicron variant spike protein” and “spike protein of SARS-CoV-2 Omicron variant” includes a SARS-CoV-2 Omicron variant spike protein known to those of skill in the art. See, e.g., GISAID Accession Numbers EPI_ISL_6640917, EPI_ISL_6640916, EPI_ISL_6640919, EPI_ISL_7580387, and EPI_ISL_12920491. In specific embodiments, the Omicron variant is of the BA. 1 lineage. In specific embodiments, the Omicron variant is of the BA.2 lineage. In specific embodiments, the Omicron variant is of the BA.4/5 lineage. In specific embodiments, the Omicron variant is of the BA.5 lineage. In specific embodiments, the spike protein of BA.5 comprises the amino acid sequence of the spike protein of the BA.5 strain hCoV-19/Albania/280808/2022 found at GISAID Accession ID: EPI_ISL_17295779. In specific embodiments, the Omicron variant is of the BQ.1.1 lineage. In specific embodiments, the spike protein of BQ.1.1 comprises the amino acid sequence of the spike protein of the BQ.1.1 strain hCoV-19/Canada/QC-L00595284001/2023 found at GISAID Accession ID: EPI_ISL_17321793. In specific embodiments, the Omicron variant is of the XBB.1.5 lineage. In specific embodiments, the spike protein of XBB.1.5 comprises the amino acid sequence of the spike protein of the XBB. 1.5 strain hCoV-19/Spain/CT-HUB07938/2023 found at GISAID Accession ID: EPI_ISL_17321709.

As used herein, the term “Wuhan strain” refers to the SARS-CoV-2 strain referred to by one of skill in the art as the Wuhan strain. See, e.g., GenBank Accession No. MN908947.3. In specific embodiments, the spike protein of the Wuhan strain comprises the amino acid sequence of the spike protein found at GenBank Accession No. MN908947.3. SEQ ID NO: 104 reproduces the spike protein found at GenBank Accession No. MN908947.3. SEQ ID NO: 105 reproduces the spike protein found at found at GenBank Accession No. MN908947.3, without the signal peptide.

As used herein, the terms “therapies” and “therapy” can refer to any protocol(s), method(s), agent(s) or a combination thereof that can be used in the treatment or prevention of COVID-19, or vaccination. In certain embodiments, the term “therapy” refers to a recombinant NDV described herein. In other embodiments, the term “therapy” refers to an agent that is not a recombinant NDV described herein.

The term “and/or” as a phrase such as “A and/or B” herein is intended to include both A and B; A or B; A (alone); and B (alone). Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

Examples of conservative amino acid substitutions include, e.g., replacement of an amino acid of one class with another amino acid of the same class. In a particular embodiment, a conservative substitution does not alter the structure or function, or both, of a polypeptide. Classes of amino acids may include hydrophobic (Met, Ala, Val, Leu, Ile), neutral hydrophilic (Cys, Ser, Thr), acidic (Asp, Glu), basic (Asn, Gln, His, Lys, Arg), conformation disruptors (Gly, Pro) and aromatic (Trp, Tyr, Phe).

4. BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1B. Characterization of NDV-HXP-S variants. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 1A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1. FIG. 1B shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1 (H655_delCSV687I). H655: In the Omicron spike protein 655Y was changed back to H655. delCSV687I: Deletion of 679KSHRRARS686 and changed V687 to 687I.

FIGS. 2A-2C. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 2A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1. FIG. 2B shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S Omicron BA.1 (H655_delCSV687I).

FIG. 3. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody.

FIGS. 4A-4B. Characterization of NDV-HXP-S variants. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 4A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.2. FIG. 4B shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.2 SSS (S371, S372, and S375).

FIGS. 5A-5C. Characterization of NDV-HXP-S variants. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 5A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan), NDV-HXP-S Omicron BA.5 SSS (S371, S372, and S375), or NDV-HXP-S Omicron BA.5. FIG. 5B shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan), NDV-HXP-S Omicron BA.5 SSS (S371, S372, S375, and G446), NDV-HXP-S Omicron BA.5 SSS (S371, S372, S375, and F486), NDV-HXP-S Omicron BA.5 SSS (S371, S372, S375, and Add69-70), NDV-HXP-S Omicron BA.5 SSS L452 (S371, S372, S375, and L452). FIG. 5C shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan), NDV-HXP-S Omicron BA.5 SSS L452 (S371, S372, S375, and L452).

FIGS. 6A-6C. Characterization of NDV-HXP-S variants. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 6A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BQ1.1. FIG. 6B shows a Coomassie Blue staining of purified virus from allanotic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BQ1.1. FIG. 6C shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron XBB1.5.

FIGS. 7A-7C. NDV-HXP-S variants were rescued by reverse genetics as previously described (Ayllon et al., 2013, J Vis Exp. (80): 50830). Cells were co-transfected with the expression plasmid required for replication and transcription of the NDV viral genome (NP, P, and L), together with the full-length NDV cDNA. After 1 day, transfected cells were co-cultured with DF-1 cells. After 2 or 3 days, the co-culture cell supernatants were inoculated into eight- or nine-day-old specific pathogen free (SPF) embryonated chicken eggs. Antigen identity was confirmed by biochemical methods and sequencing. The genetic stability of the recombinant viruses was evaluated across multiples passages on ten days old-SPF embryonated chicken eggs. The spike protein in the allantoic fluid were detected by western blot using an anti-spike 2B3E5 mouse monoclonal antibody. FIG. 7A shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1. FIG. 7B shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1 (S371, S373, S375). FIG. 7C shows the western blot results of allantoic fluid from embryonated eggs infected with NDV-HXP-S (Wuhan) or NDV-HXP-S Omicron BA.1 (S371, S375).

FIGS. 8A-8C. Immunization studies in mice to compare the immunogenicity of the cleaved BA.1 WT spike and the stabilized BA.1 SSS spike. Female BALB/c mice were immunized intranasally with live vaccine of NDV-HXP-S (Wuhan), NDV-HXP-S (BA.1 WT), and NDV-HXP-S (BA.1 SSS) twice with a 4-week interval (FIG. 8A). Four weeks after the first and second dose, serum IgG against ancestral spike protein, ancestral RBD protein, BA. 1 spike protein, BA. 1 RBD protein, BA.4/5 spike protein, and BA.4/5 RBD protein were measured by ELISAs (FIGS. 8B and 8C).

FIGS. 9A-9C. Immunization studies in mice to investigate humoral responses using NDV-HXP-S ancestral and BA.1 SSS as a booster vaccine. Female BALB/c mice were vaccinated with NDV-HXP-S Wuhan strain twice with a 3-week interval between the first and second dose. Approximately 5 months later, a third booster with either the same ancestral NDV-HXP-S Wuhan vaccine or the NDV-HXP-S BA.1 SSS vaccine was given. Each vaccination was administered intranasally at the same dose to each mouse. Antibodies induced by the following vaccinations were measured: two vaccinations of the NDV-HXP-S Wuhan (2×NDV-HXP-S), three vaccinations of NDV-HXP-S Wuhan (3×NDV-HXP-S), two vaccinations of NDV-HXP-S Wuhan followed by NDV-HXP-S BA.1 SSS booster, and two vaccinations of the vector (2×NDV WT) (FIG. 9A). Serum IgG titers were measured for all four conditions against the Wuhan spike, BA. 1 spike, Wuhan RBD, BA.1 RBD as well as the vector (inactivated whole virion of NDV WT) by ELISAs (FIGS. 9B and 9C).

5. DETAILED DESCRIPTION

Provided herein are transgenes encoding a chimeric F protein, recombinant NDV comprising such a transgene, and recombinant NDV comprising such a chimeric F protein, wherein the chimeric F protein comprises a SARS-CoV-2 Omicron spike protein ectodomain or a derivative thereof, and NDV F protein transmembrane and cytoplasmic domains. The disclosure is based, in part, upon the surprising discovery that maintaining certain amino acid residues corresponding to certain amino acid residues of the spike protein of GenBank Accession No. MN908947.3 in a derivative of the Omicron spike protein variant BA. 1 ectodomain prevents cleavage of the spike protein. For example, the disclosure is based, in part, upon the surprising discovery that maintaining serines at amino acid positions corresponding to amino acid residues 371 and 375 (or amino acid residues 371, 373, and 373) of the spike protein of GenBank Accession No. MN908947.3 in a derivative of the Omicron spike protein variant BA. 1 ectodomain prevents cleavage of the spike protein. See, e.g., Examples 2 and 5. The disclosure is also based, in part, upon the surprising discovery that maintaining serines at amino acid positions corresponding to amino acid residues 371, 373, and 373 of the spike protein of GenBank Accession No. MN908947.3 in a derivative of the Omicron spike protein variant BA.2 ectodomain prevents cleavage of the spike protein. See, e.g., Examples 3 and 4. The disclosure is also based, in part, upon the surprising discovery that maintaining serines at amino acid positions corresponding to amino acid residues 371, 373, and 375 of the spike protein of GenBank Accession No. MN908947.3, and maintaining leucine at the amino acid position corresponding to 452 of the spike protein of GenBank Accession No. MN908947.3 in a derivative of the Omicron spike protein variant BA. 1 ectodomain prevents cleavage of the spike protein. See, e.g., Examples 4. Thus, in some embodiments, a derivative of a SARS-CoV-2 Omicron spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371 and 375 of SEQ ID NO: 104, or a serine at amino acid positions corresponding to amino acid positions 371, 373, and 375 of SEQ ID NO:104. In some embodiments, a derivative of a SARS-CoV-2 Omicron spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to amino acid position 452 of SEQ ID NO:104.

5.1 Recombinant Newcastle Disease Virus

In one aspect, provided herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a SARS-CoV-2 Omicron spike protein ectodomain or a derivative thereof, and NDV F protein transmembrane and cytoplasmic domains. The recombinant NDV may be administered as a live virus or an inactivated virus.

5.1.1 NDV

Newcastle disease virus (NDV) is a member of the Avulavirus genus in the Paramyxoviridae family, which has been shown to infect a number of avian species (Alexander, DJ (1988). Newcastle disease, Newcastle disease virus—an avian paramyxovirus. Kluwer Academic Publishers: Dordrecht, The Netherlands. pp 1-22). NDV possesses a single-stranded RNA genome in negative sense and does not undergo recombination with the host genome or with other viruses (Alexander, DJ (1988). Newcastle disease, Newcastle disease virus—an avian paramyxovirus. Kluwer Academic Publishers: Dordrecht, The Netherlands. pp 1-22). The genomic RNA contains genes in the order of 3′-NP-P-M-F-HN-L-5′. Two additional proteins, V and W, are produced by NDV from the P gene by alternative mRNAs that are generated by RNA editing. The genomic RNA also contains a leader sequence at the 3′ end.

The structural elements of the virion include the virus envelope which is a lipid bilayer derived from the cell plasma membrane. The glycoprotein, hemagglutinin-neuraminidase (HN) protrudes from the envelope allowing the virus to contain both hemagglutinin (e.g., receptor binding/fusogenic) and neuraminidase activities. The fusion glycoprotein (F), which also interacts with the viral membrane, is first produced as an inactive precursor, then cleaved post-translationally to produce two disulfide linked polypeptides. The active F protein is involved in penetration of NDV into host cells by facilitating fusion of the viral envelope with the host cell plasma membrane. The matrix protein (M), is involved with viral assembly, and interacts with both the viral membrane as well as the nucleocapsid proteins.

The main protein subunit of the nucleocapsid is the nucleocapsid protein (NP) which confers helical symmetry on the capsid. In association with the nucleocapsid are the P and L proteins. The phosphoprotein (P), which is subject to phosphorylation, is thought to play a regulatory role in transcription, and may also be involved in methylation, phosphorylation and polyadenylation. The L gene, which encodes an RNA-dependent RNA polymerase, is required for viral RNA synthesis together with the P protein. The L protein, which takes up nearly half of the coding capacity of the viral genome is the largest of the viral proteins, and plays an important role in both transcription and replication.

Any NDV type or strain may be serve as the “backbone” that is engineered to comprise a transgene described herein, including, but not limited to, naturally-occurring strains, variants or mutants, mutagenized viruses, reassortants and/or genetically engineered viruses. See, e.g., Section 5.1.2 and Section 6 for examples of transgenes. In a specific embodiment, a transgene described herein is incorporated into the genome of a lentogenic NDV. In another specific embodiment, a transgene described herein is incorporated into the genome of NDV strain LaSota. In another embodiment, a transgene described herein is incorporated into the genome of NDV Hitchner B1 strain. In some embodiments, a lentogenic strain other than NDV Hitchner B1 strain is used as the backbone into which a nucleotide sequence may be incorporated. The transgene may be incorporated into the NDV genome between two transcription units (e.g., between the NDV M and P transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units).

In a specific embodiment, a NDV that is engineered to comprise a transgene described herein is a naturally-occurring strain. Specific examples of NDV strains include, but are not limited to, Hitchner B1 strain (see, e.g., GenBank No. AF309418 or NC_002617) and LaSota strain (see, e.g., GenBank Nos. AY845400, AF07761.1 and JF950510.1 and GI No. 56799463). In a specific embodiment, the NDV that is engineered to comprises a transgene described herein is the Hitchner B1 strain. In another embodiment, the NDV that is engineered to comprise a transgene described herein is a B1 strain as identified by GenBank No. AF309418 or NC_002617. In a specific embodiment, the nucleotide sequence of the Hitchner B1 genome comprises an RNA sequence corresponding to the negative sense of the cDNA sequence set forth in SEQ ID NO:2. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein is the LaSota strain. In another embodiment, the NDV that is engineered to comprise a transgene described herein is a LaSota strain as identified by AY845400, AF07761.1 or JF950510.1. In a specific embodiment, the nucleotide sequence of the LaSota genome comprises an RNA sequence corresponding to the negative sense of the cDNA sequence set forth in SEQ ID NO:1. In another specific embodiment, the nucleotide sequence of the LaSota genome comprises an RNA sequence corresponding to the negative sense of the cDNA sequence set forth in SEQ ID NO: 3. One skilled in the art will understand that the NDV genomic RNA sequence is an RNA sequence corresponding to the negative sense of a cDNA sequence encoding the NDV genome. Thus, any program that generates converts a nucleotide sequence to its reverse complement sequence may be utilized to convert a cDNA sequence encoding an NDV genome into the genomic RNA sequence (see, e.g., www.bioinformatics.org/sms/rev_comp.html, www.fr33.net/seqedit.php, and DNAStar). Accordingly, the nucleotide sequences provided in Tables 1-4, infra, may be readily converted to the negative-sense RNA sequence of the NDV genome by one of skill in the art.

In a specific embodiment, the NDV that is engineered to comprise a transgene described herein comprises a genome encoding an NDV F protein in which a leucine amino acid residue at amino acid position 289 of NDV F protein is substituted for alanine (as described by, e.g., Sergel et al., 2000, Journal of Virology 74:5101-5107). In another specific embodiment, the NDV that is engineered to comprise a transgene described herein comprises a genome encoding an NDV F protein in which a leucine amino acid residue at amino acid position 289 of NDV F protein (as counted by the LaSota strain F protein) is substituted for alanine. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein comprises a nucleotide sequence encoding an NDV F protein in which leucine at the amino acid position corresponding to amino acid residue 289 of LaSota NDV F protein is substituted for alanine. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein comprises a nucleotide sequence encoding an NDV F protein in which leucine at the amino acid residue 289 of LaSota NDV F protein is substituted for alanine. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein is of the LaSota strain (e.g., GenBank Accession Nos. AY845400, AF07761.1 or JF950510.1) and the genome of the LaSota strain encodes an NDV F protein in which a leucine amino acid residue at amino acid position 289 of NDV F protein is substituted for alanine. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein is of the LaSota strain (e.g., GenBank Accession Nos. AY845400, AF07761.1 or JF950510.1) and the genome of the LaSota strain comprises a nucleotide sequence encoding LaSota NDV F protein in which leucine at amino acid residue 289 of the NDV F protein (as counted by the LaSota strain F protein) is substituted for alanine. In another specific embodiment, the NDV that is engineered to comprise a transgene described herein is of the Hitchner B1 strain (e.g., GenBank No. AF309418 or NC_002617) and the genome of the Hitchner B1 strain encodes an NDV F protein in which a leucine amino acid residue at amino acid position 289 of NDV F protein (as counted by the LaSota strain F protein) is substituted for alanine.

In some embodiments, the NDV that is engineered to comprise a transgene described herein is of the Fuller strain. In certain embodiments, the NDV genome that is engineered to comprise a transgene described herein is of the Ulster strain. In some embodiments, the NDV that is engineered to comprise a transgene described herein is of the Roakin strain. In certain embodiments, the NDV that is engineered to comprise a transgene described herein is of the Komarov strain. In some embodiments, the NDV that is engineered to comprise a transgene described herein is of the Roakin strain. In certain embodiments, the NDV that is engineered to comprise a transgene described herein is of the r73T-RI 16 virus.

In specific embodiments, the NDV that is engineered to comprise a transgene described herein is not pathogenic in birds as assessed by a technique known to one of skill. In certain specific embodiments, the NDV that is engineered to comprise a transgene described herein is not pathogenic as assessed by intracranial injection of 1-day-old chicks with the virus, and disease development and death as scored for 8 days. In some embodiments, the NDV that is engineered to comprise a transgene described herein has an intracranial pathogenicity index of less than 0.7, less than 0.6, less than 0.5, less than 0.4, less than 0.3, less than 0.2 or less than 0.1. In certain embodiments, the NDV that is engineered to comprise a transgene described herein has an intracranial pathogenicity index of zero. See, e.g., OIE Terrestrial Manual 2012, Chapter 2.3.14, entitled “Newcastle Disease (Infection With Newcastle Disease Virus) for a description of this assay, which is found at the following website www.oie.int/fileadmin/Home/eng/Health_standards/tahm/2.03.14 NEWCASTLE_DIS.pdf, which is incorporated herein by reference in its entirety.

In certain embodiments, the NDV that is engineered to comprise a transgene described herein is a mesogenic strain that has been genetically engineered so as not be a considered pathogenic in birds as assessed by techniques known to one skilled in the art.

In preferred embodiments, the NDV that is engineered to comprise a transgene described herein is non-pathogenic in humans. In preferred embodiments, the NDV that is engineered to comprise a transgene described herein is non-pathogenic in human and avians. In certain embodiments, the NDV that is engineered to comprise a transgene described herein is attenuated such that the NDV remains, at least partially, infectious and can replicate in vivo, but only generate low titers resulting in subclinical levels of infection that are non-pathogenic (see, e.g., Khattar et al., 2009, J. Virol. 83:7779-7782). Such attenuated NDVs may be especially suited for embodiments wherein the virus is administered to a subject in order to act as an immunogen, e.g., a live vaccine. The viruses may be attenuated by any method known in the art. In a specific embodiment, the genome of NDV comprises sequences necessary for infection and replication of the virus such that progeny is produced and the infection level is subclinical. In certain embodiments, NDV is attenuated by introducing one, two, or more mutations (e.g., amino acid substitutions) in the NDV V protein.

In some embodiments, provided herein is a recombinant NDV comprising a genome comprising a nucleotide sequence described herein or polynucleotide sequence described herein.

In a specific embodiment, provided herein is a nucleotide sequence comprising: (1) an NDV F transcription unit, (2) an NDV NP transcription unit, (3) an NDV P transcription unit, (4) an NDV M transcription unit, (5) an NDV HN transcription unit, (6) an NDV L transcription unit, and (7) a transgene described herein. In certain embodiments, the NDV transcription units are LaSota NDV transcription units. In a specific embodiment, provided herein is a nucleotide sequence comprising: (1) an NDV F transcription unit, (2) an NDV NP transcription unit, (3) an NDV P transcription unit, (4) an NDV M transcription unit, (5) an NDV HN transcription unit, (6) an NDV L transcription unit, and (7) a transgene described herein, wherein the NDV F transcription unit encodes an NDV F protein with an amino acid substitution of leucine to alanine at the amino acid residue corresponding to amino acid position 289 of LaSota NDV F protein. In another specific embodiment, provided herein is a nucleotide sequence comprising (1) an NDV F transcription unit, (2) an NDV NP transcription unit, (3) an NDV P transcription unit, (4) an NDV M transcription unit, (5) an NDV HN transcription unit, (6) an NDV L transcription unit, and (7) a transgene described herein, wherein the NDV F transcription unit encodes an NDV F protein with an amino acid substitution of leucine to alanine at amino acid position 289 of LaSota NDV F protein. In certain embodiments, the NDV transcription units are LaSota NDV transcription units. In certain embodiments, the nucleotide sequence is part of a vector (e.g., a plasmid). In specific embodiments, the nucleotide sequence is isolated.

In a specific embodiment, provided herein is a polynucleotide sequence comprising: (1) a nucleotide sequence encoding NDV F, (2) a nucleotide sequence encoding NDV NP, (3) a nucleotide sequence encoding NDV P, (4) a nucleotide sequence encoding NDV M, (5) a nucleotide sequence encoding NDV HN, (6) a nucleotide sequence encoding NDV L, and (7) a transgene described herein. In another specific embodiment, provided herein is a polynucleotide sequence comprising: (1) a nucleotide sequence encoding NDV F, (2) a nucleotide sequence encoding NDV NP, (3) a nucleotide sequence encoding NDV P, (4) a nucleotide sequence encoding NDV M, (5) a nucleotide sequence encoding NDV HN, (6) a nucleotide sequence encoding NDV L, and (7) a transgene described herein, wherein the NDV F comprises an amino acid substitution of leucine to alanine at the amino acid position corresponding to amino acid residue 289 of LaSota NDV F. In another specific embodiment, provided herein is a polynucleotide sequence comprising: (1) a nucleotide sequence encoding NDV F, (2) a nucleotide sequence encoding NDV NP, (3) a nucleotide sequence encoding NDV P, (4) a nucleotide sequence encoding NDV M, (5) a nucleotide sequence encoding NDV HN, (6) a nucleotide sequence encoding NDV L, and (7) a transgene described herein, wherein the NDV F comprises an amino acid substitution of leucine to alanine at the amino acid position 289 of LaSota NDV F. In certain embodiments, the NDV proteins are LaSota NDV proteins. In another specific embodiment, provided herein is a polynucleotide sequence comprising a nucleotide sequence of an NDV genome known in the art or described (see, e.g., Section 5.1 or the Example below; see also SEQ ID NO: 1, 2 or 3) and a transgene described herein. In certain embodiments, the nucleic acid sequence is part of a vector (e.g., a plasmid). In a specific embodiment, the polynucleotide sequence is isolated.

In specific embodiments, a polynucleotide sequence described herein, a nucleic acid sequence described herein, or nucleotide sequence described herein is a recombinant polynucleotide sequence described herein, recombinant nucleic acid sequence described herein, or recombinant nucleotide sequence. In certain embodiments, a polynucleotide sequence described herein, a nucleotide sequence described herein, or nucleic acid sequence described herein may be a DNA molecule (e.g., cDNA), an RNA molecule (e.g., mRNA), or a combination of a DNA and RNA molecule. In some embodiments, a polynucleotide sequence described herein, nucleotide sequence described herein, or nucleic acid sequence described herein may comprise analogs of DNA or RNA molecules. Such analogs can be generated using, for example, nucleotide analogs, which include, but are not limited to, inosine, methylcytosine, pseudouridine, or tritylated bases. Such analogs can also comprise DNA or RNA molecules comprising modified backbones that lend beneficial attributes to the molecules such as, for example, nuclease resistance or an increased ability to cross cellular membranes. The polynucleotide sequences, nucleic acid sequences, or nucleotide sequences can be single-stranded, double-stranded, may contain both single-stranded and double-stranded portions, and may contain triple-stranded portions. In a specific embodiment, a polynucleotide sequence described herein, nucleotide sequence described herein, or nucleic acid sequence described herein is a negative sense single-stranded RNA. In another specific embodiment, a polynucleotide sequence described herein, a nucleotide sequence described herein, or nucleic acid sequence described herein is a positive sense single-stranded RNA. In another specific embodiment, a polynucleotide sequence described herein, nucleotide sequence described herein, or nucleic acid sequence described herein is a cDNA.

5.1.2 SARS-CoV-2 Variant Spike Protein/Chimeric F Protein with the SARS-CoV-2 Variant Spike Protein Ectodomain or Derivative Thereof

In a specific embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising a SARS-CoV-2 Omicron spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron spike protein). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) may inserted into any NDV type or strain (e.g., NDV LaSota strain). In a specific embodiment, a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). In a specific embodiment, the SARS-CoV-2 Omicron variant is of the BA.1 sublineage. In a specific embodiment, the SARS-CoV-2 Omicron variant is of the BA.2 sublineage. In a specific embodiment, the SARS-CoV-2 Omicron variant is of the BA.4/5 sublineage. In a specific embodiment, the SARS-CoV-2 Omicron variant is of the BQ1.1. In a specific embodiment, the SARS-CoV-2 Omicron variant is of the XBB1.5. See, e.g., Section 3.1 for exemplary sequences for SARS-CoV-2 Omicron variant spike proteins or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) and exemplary nucleic acid sequences encoding SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein). One of skill in the art would be able to use such sequence information to produce a transgene for incorporation into the genome of any NDV type or strain. Given the degeneracy of the nucleic acid code, there are a number of different polynucleotide sequences that may encode the same SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein). In a specific embodiment, a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In certain embodiments, the transgene encoding a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein) without the SARS-CoV-2 Omicron variant spike protein signal peptide. The transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the HN and L transcription units).

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues to N-terminus of the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues N-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein, 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein, or 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the receptor binding domain of SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein.

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues to N-terminus of the S1 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues N-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain of the SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein, 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein, or 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S1 domain of SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S1 domain of the SARS-CoV-Omicron variant spike protein.

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S2 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S2 domain of the SARS-CoV-2 spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues to N-terminus of the S2 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues N-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S2 domain of the SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein, 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein, or 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S2 domain of SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein.

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain and S2 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain and S2 domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues to N-terminus of the S1 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues N-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the S1 domain and S2 domain of the SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S1 domain of the SARS-CoV-2 Omicron variant spike protein, 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S2 domain of the SARS-CoV-2 Omicron variant spike protein, or 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the S1 domain of SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the S2 domain of the SARS-CoV-Omicron variant spike protein.

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the ectodomain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the ectodomain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues to N-terminus of the ectodomain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein, or 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues N-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein and 5, 10, 15, 20, 30, 40, 50, 75 or more amino acid residues C-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises the ectodomain of the SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein, 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein, or 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues N-terminus to the ectodomain of SARS-CoV-2 Omicron variant spike protein and 5 to 25, 5 to 50, 25 to 50, 25 to 75, or 50 to 75 amino acid residues C-terminus to the ectodomain of the SARS-CoV-2 Omicron variant spike protein.

In certain embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises 200, 220, 222, 250, 300, 350, 400, or more amino acid residues. In some embodiments, a portion of a SARS-CoV-2 Omicron variant spike protein comprises 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200 or more amino acid residues. In specific embodiments, the amino acid residues are contiguous.

In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a full-length SARS-CoV-2 Omicron variant spike protein or a fragment thereof. In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a portion of a SARS-CoV-2 Omicron variant spike protein. In certain embodiments, the protein further comprises a domain(s) that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In certain embodiments, a fragment of the SARS-CoV-2 Omicron variant spike protein is at least 1000, 1025, 1075, 1100, 1125, 1150, 1200 or 1215 amino acid residues in length.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of a SAR-CoV-2 Omicron variant spike protein, or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or a receptor binding domain), or a fragment thereof. In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of a SAR-CoV-2 Omicron variant spike protein, or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or a receptor binding domain), or a fragment thereof. In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of a SAR-CoV-2 Omicron variant spike protein, or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or a receptor binding domain), or a fragment thereof. Methods/techniques known in the art may be used to determine sequence identity (see, e.g., “Best Fit” or “Gap” program of the Sequence Analysis Software Package, version 10; Genetics Computer Group, Inc.). In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus or N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO: 72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72). In certain embodiments, a fragment of the SARS-CoV-2 spike protein is at least 250, at least 500, at least 750, at least 1000, at least 1025, at least 1075, at least 1100, at least 1125, at least 1150, at least 1175, at least 1200, or at least 1215 amino acid residues in length.

Techniques known to one of skill in the art can be used to determine the percent identity between two amino acid sequences or between two nucleotide sequences. Generally, to determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total number of positions X 100%). In one embodiment, the two sequences are the same length. In a certain embodiment, the percent identity is determined over the entire length of an amino acid sequence or nucleotide sequence. In some embodiments, the length of sequence identity comparison may be over the full-length of the two sequences being compared (e.g., the full-length of a gene coding sequence, or a fragment thereof). In some embodiments, a fragment of a nucleotide sequence is at least 25, at least 50, at least 75, or at least 100 nucleotides. Similarly, “percent sequence identity” may be readily determined for amino acid sequences, over the full-length of a protein, or a fragment thereof. In some embodiments, a fragment of a protein comprises at least 20, at least 30, at least 40, at least 50 or more contiguous amino acids of the protein. In certain embodiments, a fragment of a protein comprises at least 75, at least 100, at least 125, at least 150 or more contiguous amino acids of the protein.

The determination of percent identity between two sequences (e.g., amino acid sequences or nucleic acid sequences) can be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. U.S.A. 87:2264 2268, modified as in Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. U.S.A. 90:5873 5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990, J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to nucleic acid molecules described herein. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score 50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res. 25:3389 3402. Alternatively, PSI BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., National Center for Biotechnology Information (NCBI) on the worldwide web, ncbi.nlm.nih.gov). Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:11 17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used.

The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acids substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus substituted with another amino acid (e.g., a conservative amino acid substitution) and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus substituted with another amino acid (e.g., a conservative amino acid substitution). In a specific embodiment, the N-terminus is the first 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In a specific embodiment, the C-terminus is the last 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In specific embodiments, the SARS-CoV-2 Omicron variant spike protein is the mature form of the protein. In other embodiments, the SARS-CoV-2 Omicron variant spike protein is the immature form of the protein. In certain embodiments, the protein further comprise one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus or N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the C-terminus. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the N-terminus. In a specific embodiment, the N-terminus is the first 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In a specific embodiment, the C-terminus is the last 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In specific embodiments, the SARS-CoV-2 Omicron variant spike protein is the mature form of the protein. In other embodiments, the SARS-CoV-2 Omicron variant spike protein is the immature form of the protein. In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus or N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations (e.g., amino acid substitutions, amino acid deletions, amino acid additions, or a combination thereof). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 amino acid substitutions. In a specific embodiment, the N-terminus is the first 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In a specific embodiment, the C-terminus is the last 100 amino acid residues of the SARS-CoV-2 Omicron variant spike protein. In specific embodiments, the SARS-CoV-2 Omicron variant spike protein is the mature form of the protein. In other embodiments, the SARS-CoV-2 Omicron variant spike protein is the immature form of the protein. In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or the C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72).

In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) the receptor binding domain of a SARS-CoV-2 Omicron variant spike protein. In certain embodiments, protein further comprise one or more polypeptide domains. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In a specific embodiment, a protein comprises or consists of the receptor binding domain of a SARS-CoV-2 Omicron variant spike protein and a His tag (e.g., a (His) n, where n is 6 (SEQ ID NO:72)). In certain embodiments, a protein comprising (or consisting) of the receptor binding domain of a SARS-CoV-2 Omicron variant spike protein is a secreted polypeptide. In a specific embodiment, when designing a protein comprising SARS-CoV-2 Omicron variant spike protein receptor binding domain, care is taken to maintain the stability of the resulting protein.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein receptor binding domain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein receptor binding domain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus of the receptor binding domain substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein receptor binding domain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus of the receptor binding domain substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein receptor binding domain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus of the receptor binding domain substituted with another amino acid (e.g., a conservative amino acid substitution) and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus of the receptor binding domain substituted with another amino acid (e.g., a conservative amino acid substitution). In a specific embodiment, the N-terminus is the first 25 amino acid residues of the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein. In a specific embodiment, the C-terminus is the last 25 amino acid residues of the receptor binding domain of the SARS-CoV-2 Omicron variant spike protein. In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO: 72).

In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) the ectodomain of a SARS-CoV-2 Omicron variant spike protein. In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative lacks the polybasic cleavage site of the ectodomain (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) the ectodomain of a SARS-CoV-2 Omicron variant spike protein with amino acid substitutions to proline at amino acid residues corresponding to amino acid residues 817, 892, 899, 942, 986, and 987 of the spike protein of GenBank Accession No. MN908947.3. In another embodiment, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) the ectodomain of a SARS-CoV-2 Omicron variant spike protein with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine, and amino acid substitutions to proline at amino acid residues corresponding to amino acid residues 817, 892, 899, 942, 986, and 987 of the spike protein of GenBank Accession No. MN908947.3. In certain embodiments, protein further comprises one or more polypeptide domains. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In a specific embodiment, a protein comprises or consists of the ectodomain of a SARS-CoV-2 Omicron variant spike protein and a His tag (e.g., a (His) n, where n is 6 (SEQ ID NO:72)). In some embodiments, a protein comprises or consists of a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein and a His tag (e.g., a (His) n, where n is 6 (SEQ ID NO:72)). In certain embodiments, a protein comprising (or consisting) of the ectodomain of a SARS-CoV-2 Omicron variant spike protein or a derivative thereof is a secreted polypeptide. In certain embodiments, a protein comprises the ectodomain of a SARS-CoV-2 Omicron variant spike protein or a derivative thereof comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag). In a specific embodiment, when designing a protein comprising SARS-CoV-2 Omicron variant spike protein ectodomain or a derivative thereof, care is taken to maintain the stability of the resulting protein.

In some embodiments, described herein is a transgene comprising a polynucleotide sequence encoding a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the polynucleotide sequence comprises a nucleotide sequence at least 80%, at least 85%, or at least 90% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, 70, 76, 78, 82, 84, 88, 90, 94, 96, 100, or 102. In some embodiments, described herein is a transgene comprising a polynucleotide sequence encoding a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the polynucleotide sequence comprises a nucleotide sequence at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, 70, 76, 78, 82, 84, 88, 90, 94, 96, 100, or 102. In some embodiments, described herein is a transgene comprising a polynucleotide sequence encoding a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the polynucleotide sequence comprises the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, 70, 76, 78, 82, 84, 88, 90, 94, 96, 100, or 102.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 substituted with a single alanine, and amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 of the following positions of the spike protein of GenBank Accession No. MN908947.3 substituted: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 substituted with a single alanine, and amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 of the following positions of the spike protein of GenBank Accession No. MN908947.3 substituted: A67V, T95I, G142D, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, V687I, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 substituted with a single alanine, and amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 of the following positions of the spike protein of GenBank Accession No. MN908947.3 substituted: L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 substituted with a single alanine, the amino acid residues at amino acid positions corresponding to amino acid positions 817, 892, 899, 942, 986, and 987 of the spike protein found at the spike protein of GenBank Accession No. MN908947.3 substituted with prolines, and amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or more of the positions of the spike protein of GenBank Accession No. MN908947.3 mutated as indicated for one of the constructs in Table 6, 7, 8, 9, 10, or 11. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 substituted with a single alanine, the amino acid residues at amino acid positions corresponding to amino acid positions 817, 892, 899, 942, 986, and 987 of the spike protein found at the spike protein of GenBank Accession No. MN908947.3 substituted with prolines, and amino acid residues corresponding to the positions of the spike protein of GenBank Accession No. MN908947.3 mutated as indicated for one of the constructs in Table 6, 7, 8, 9, 10, or 11. In some embodiments, the derivative of the ectodomain comprises two or more (e.g., 3, 4, 5, 6, or 7), or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and/or N969K. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, or 375 of SEQ ID NO: 104. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371 or 373 of SEQ ID NO: 104. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and 375 of SEQ ID NO:104. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, or 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to 452 of SEQ ID NO: 104. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371 or 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to 452 of SEQ ID NO: 104. In some embodiments, the derivative of the ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to 452 of SEQ ID NO: 104.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, NSPRRARS 679-686 deletion, V687I, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) amino acid mutations at amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, or more of the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F; and (4) one or two of the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371L, S373P, and S375F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F; and (4) one, two, or three amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371, S373, and S375, wherein the amino acid substitutions are not S371L, S373P, and S375F.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P. A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K; and (4) one or two of the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371F, S373P, and S375F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K; and (4) one, two, or three amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371, S373, and S375, wherein the amino acid substitutions are not S371F, S373P, and S375F.

In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K; and (4) one or two of the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371F, S373P, S375F. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein, wherein the derivative comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3 with (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; (3) the following mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K; and (4) one, two, or three amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: S371, S373, and S375, wherein the amino acid substitutions are not S371F, S373P, and S375F.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution) and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution). In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In a specific embodiment, the C-terminus of the ectodomain is the last 100 amino acid residues. In a specific embodiment, the N-terminus of the ectodomain is the first 100 amino acid residues. In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72). In certain embodiments, a protein comprising (or consisting) of the ectodomain of a SARS-CoV-2 Omicron variant spike protein is a secreted polypeptide. In certain embodiments, a protein comprises the ectodomain of a SARS-CoV-2 Omicron variant spike polypeptide comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) an amino acid sequence at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) an amino acid sequence at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In certain embodiments, the protein further comprises one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72). In certain embodiments, the protein is a secreted polypeptide. In some embodiments, a protein comprises further comprises NDV F protein transmembrane and cytoplasmic domains. In some embodiments, a protein comprises further comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acid substitutions and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the C-terminus. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the N-terminus. In certain embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., amino acid residues 682 to 685 (RRAR) are substituted with a single alanine). In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain comprises the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In a specific embodiment, the SARS-CoV-2 Omicron variant spike protein ectodomain comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO:19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain comprises two or more (e.g., 3, 4, 5, 6, or 7), or all of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and/or N969K. In some embodiments, the SARS-CoV-2 spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO:104. In some embodiments, the SARS-CoV-2 spike protein ectodomain includes a leucine at the amino acid position corresponding to amino acid position 452 of SEQ ID NO:104. In a specific embodiment, the C-terminus of the ectodomain is the last 100 amino acid residues. In a specific embodiment, the N-terminus of the ectodomain is the first 100 amino acid residues. In certain embodiments, the protein further comprise one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO: 72). In some embodiments, a protein comprises further comprises NDV F protein transmembrane and cytoplasmic domains. In some embodiments, a protein that comprises the ectodomain of a SARS-CoV-2 Omicron variant spike protein further comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the C-terminus. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the N-terminus. In certain embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, amino acid substitutions corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3 are substituted: F817P, A892P, A899P, A942P, K986P, and V987P. In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In certain embodiments, the protein further comprise one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In one embodiment, the His tag has the sequence (His) n, wherein n is 6 (SEQ ID NO:72). In some embodiments, a protein comprises further comprises NDV F protein transmembrane and cytoplasmic domains. In certain embodiments, a protein that comprises the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 mutations (e.g., amino acid substitutions, amino acid deletions, amino acid additions, or a combination thereof). In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acid substitutions and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted. In certain embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, amino acid substitutions corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3 are substituted: F817P, A892P, A899P, A942P, K986P, and V987P. In some embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In certain embodiments, the protein further comprise one or more polypeptide domains. The one or more polypeptide domains may be at the C-terminus, N-terminus, or C-terminus and N-terminus. In a specific embodiment, the one or more polypeptide domains are at the C-terminus. Useful polypeptide domains include domains that facilitate purification, folding and cleavage of portions of a polypeptide. For example, a His tag (His-His-His-His-His-His (SEQ ID NO:72)), FLAG epitope or other purification tag can facilitate purification of the protein provided herein. In some embodiments, the His tag has the sequence, (His) n, wherein n is 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or greater. In some embodiments, a protein comprises further comprises NDV F protein transmembrane and cytoplasmic domains. In certain embodiments, a protein that comprises the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises one or more trimerization domains known to one of skill in the art (e.g., a T4 foldon trimerization domain), and optionally a tag (e.g., a His tag or Flag tag).

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein, wherein the protein comprises a spike protein ectodomain that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein, wherein the protein comprises a spike protein ectodomain that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a protein, wherein the protein comprises a spike protein ectodomain that is at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. Methods/techniques known in the art may be used to determine sequence identity (see, e.g., “Best Fit” or “Gap” program of the Sequence Analysis Software Package, version 10; Genetics Computer Group, Inc.).

In another embodiment, a SARS-CoV-2 spike protein ectodomain or a derivative thereof comprises an amino acid sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, a SARS-CoV-2 spike protein ectodomain or a derivative thereof comprises an amino acid sequence that is at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. In another embodiment, a SARS-CoV-2 spike protein ectodomain or a derivative thereof comprises an amino acid sequence that is at least 97%, at least 98%, at least 99%, or at least 99.5% identical to the nucleotide sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 91, 95, 97, 101, or 103. Methods/techniques known in the art may be used to determine sequence identity (see, e.g., “Best Fit” or “Gap” program of the Sequence Analysis Software Package, version 10; Genetics Computer Group, Inc.).

In another embodiment, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a SARS-CoV-2 Omicron variant spike protein ectodomain described herein and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of SARS-CoV-2 Omicron variant spike protein ectodomain described herein and NDV F protein transmembrane and cytoplasmic domains. In specific embodiments, the entire NDV F protein transmembrane and cytoplasmic domains is included in a chimeric F protein. In a specific embodiment, the NDV F protein transmembrane and cytoplasmic domains comprise the amino acid sequence of SEQ ID NO: 5. In some embodiments, the entire NDV F protein transmembrane and cytoplasmic domains is not included in a chimeric F protein. For example, a few amino acid residues (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 1-5, 1-10, or 5-15 amino acid residues) upstream to the NDV F protein transmembrane may be included in a chimeric F protein and/or a few amino acid residues (e.g., 1-5, 1-10, or 5-15 amino acid residues) downstream of the NDV F protein cytoplasmic domain may be included in a chimeric F protein. For example, a few amino acid residues (e.g., 1, 2, 3, 4, 5, or 1-5 amino acid residues) less than the entire NDV F protein transmembrane may be included in a chimeric F protein and/or a few amino acid residues (e.g., 1, 2, 3, 4, 5, or 1-5 amino acid residues) less than the entire NDV F protein cytoplasmic domain may be included. In specific embodiments, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a SARS-CoV-2 spike protein ectodomain described herein, a NDV F protein transmembrane domain plus or minus 1, 2, 3, 4, or 5 amino acid residues, and a NDV F protein cytoplasmic domain plus or minus 1, 2, 3, 4, or 5 amino acid residues. In specific embodiments, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 spike protein ectodomain described herein, a NDV F protein transmembrane domain plus or minus 1, 2, 3, 4, or 5 amino acid residues, and a NDV F protein cytoplasmic domain plus or minus 1, 2, 3, 4, or 5 amino acid residues. In specific embodiments, the entire transmembrane and cytoplasmic domains of the SARS-CoV-2 spike protein are not present in the chimeric F protein. In some embodiments, 1, 2, or 3 amino acid residues of the transmembrane domain and/or cytoplasmic domain of the SARS-CoV-2 spike protein are present in the chimeric F protein. The ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 spike protein and NDV F protein may be determined using techniques known to one of skill in the art. For example, published information, GenBank or websites such as VIPR virus pathogen website (www.viprbrc.org), DTU Bioinformatics domain website (www.cbs.dtu.dk/services/TMHMM/) or programs available to determine the transmembrane domain may be used to determine the ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 spike protein and NDV F protein. See, e.g., Table 2, infra, with the transmembrane and cytoplasmic domains of NDV F protein indicated. In specific embodiments, the SARS-CoV-2 spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In some embodiments, the NDV F protein transmembrane and cytoplasmic domains are fused directly to the SARS-CoV-2 spike protein ectodomain. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization.

In specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises the nucleotide sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the nucleotides sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the nucleotides sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98. In some embodiments, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the transgene comprises a nucleotide sequence that is at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the nucleotides sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, or 98, without the nucleotide sequence encoding the signal peptide. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NDV NP and P transcription units or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103, and NDV F protein transmembrane and cytoplasmic domains. In another specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 33, 35, 45, 47, 57, 83, 85, 89, 91, 95, 97, 101, or 103, and NDV F protein transmembrane and cytoplasmic domains. In another specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 81, 87, 93, or 99, without the signal peptide. In another specific embodiment, described herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 81, 87, 93, or 99. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a preferred embodiment, a transgene comprises a codon-optimized version of a nucleic acid sequence encoding the chimeric F protein. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NDV NP and P transcription units or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In certain embodiments, a transgene comprises a codon-optimized version of a nucleic acid sequence encoding the derivative of the ectodomain of the SARS-CoV-2 spike protein. In a specific embodiment, a transgene described herein comprises a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO:8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 81, 87, 93, or 99. In a specific embodiment, a transgene described herein comprises a nucleotide sequence encoding an amino acid sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence set forth in SEQ ID NO:8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 81, 87, 93, or 99. In another specific embodiment, a transgene described herein comprises the nucleotide sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98, or an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NDV NP and P transcription units or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a SARS-CoV-2 Omicron variant spike protein ectodomain plus or minus 1, 2, 3, 4, 5, 6, 7, 8 or more amino acid residues at C-terminus of the ectodomain and NDV F protein transmembrane and cytoplasmic domains. In other words, the portion of the SARS-CoV-2 Omicron variant spike protein encoded by the chimeric F protein does not include the entire SARS-CoV-2 Omicron variant spike protein transmembrane and cytoplasmic domains. The ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 Omicron spike protein and NDV F protein may be determined using techniques known to one of skill in the art. For example, published information, GenBank or websites such as VIPR virus pathogen website (www.viprbrc.org), DTU Bioinformatics domain website (www.cbs.dtu.dk/services/TMHMM/) or programs available to determine the transmembrane domain may be used to determine the ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 spike protein and NDV F protein. See, e.g., Table 2, infra, with the transmembrane and cytoplasmic domains of NDV F protein indicated (SEQ ID NO:5). In specific embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In some embodiments, the NDV F protein transmembrane and cytoplasmic domains are fused to directly to the SARS-CoV-2 Omicron variant spike protein ectodomain. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NDV NP and P transcription units or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, described herein are transgenes comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises plus or minus 1, 2, 3, 4, 5, 6, 7, 8 or more amino acid residues at C-terminus of the ectodomain. In other words, the portion of the SARS-CoV-2 Omicron variant spike protein encoded by the chimeric F protein does not include the entire SARS-CoV-2 spike protein transmembrane and cytoplasmic domains. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, the derivative comprises the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In some embodiments, the derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 19, 21, 23, 35, 41, 47, 53, 59, 65, 71, 79, 85, 91, 97, or 103. In some embodiments, the derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95, or 101. The ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 Omicron variant spike protein and NDV F protein may be determined using techniques known to one of skill in the art. For example, published information, GenBank or websites such as VIPR virus pathogen website (www.viprbrc.org), DTU Bioinformatics domain website (www.cbs.dtu.dk/services/TMHMM/) or programs available to determine the transmembrane domain may be used to determine the ectodomain, transmembrane and cytoplasmic domains of the SARS-CoV-2 Omicron variant spike protein and NDV F protein. See, e.g., Table 2, infra, with the transmembrane and cytoplasmic domains of NDV F protein indicated. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO: 73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In some embodiments, the NDV F protein transmembrane and cytoplasmic domains are fused directly to the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NDV NP and P transcription units or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids substituted with another amino acid (e.g., a conservative amino acid substitution) and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution) and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus of the ectodomain substituted with another amino acid (e.g., a conservative amino acid substitution) and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the N-terminus substituted with another amino acid (e.g., a conservative amino acid substitution) and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids at the C-terminus substituted with another amino acid (e.g., a conservative amino acid substitution), and NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, the C-terminus of the ectodomain is the last 100 amino acid residues. In a specific embodiment, the N-terminus of the ectodomain is the first 100 amino acid residues. In some embodiments, the derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, or 71. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises (or consists of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 amino acids substituted with another amino acid (e.g., a conservative amino acid substitution) and NDV F protein transmembrane and cytoplasmic domains. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. In a specific embodiment, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain comprises amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, the derivative comprises the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In specific embodiments, the derivative of the SARS-CoV-2 spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 spike protein ectodomain is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted, and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the C-terminus, and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the N-terminus, and NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, the C-terminus of the ectodomain is the last 100 amino acid residues. In a specific embodiment, the N-terminus of the ectodomain is the first 100 amino acid residues. In specific embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted, and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the C-terminus, and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted from the N-terminus, and NDV F protein transmembrane and cytoplasmic domains. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In some embodiments, the derivative comprises the following amino acid substitutions at amino acid residues corresponding to at amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, V687I, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine, and amino acid substitutions at amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or more of the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, V687I, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) amino acid substitutions at amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or more of the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5. In specific embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). In some embodiments, the derivative of the SARS-CoV-2 spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104. In some embodiments, the SARS-CoV-2 spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to amino acid position 452 of SEQ ID NO: 104. The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO: 24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the mutations at amino acid residues corresponding to the amino acid residues of one of the constructs set forth in Table 6, 7, 8, 9, 10, or 11. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the SARS-CoV-2 spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104. In some embodiments, the SARS-CoV-2 spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO:104, and a leucine at the amino acid position corresponding to amino acid position 452. In specific embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations (e.g., amino acid substitutions, amino acid deletions, amino acid additions, or a combination thereof), and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acid substitutions and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted, and NDV F protein transmembrane and cytoplasmic domains. In specific embodiments, the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO: 73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more mutations (e.g., amino acid substitutions, amino acid deletions, amino acid additions, or a combination thereof), and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acid substitutions and 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted, and NDV F protein transmembrane and cytoplasmic domains. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain lacks the polybasic cleavage site (e.g., one, two or more residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted for other amino acid residues). In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. In a specific embodiment, amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 are substituted with a single alanine. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, NSPRRARS 679-686 deletion, V687I, N764K, D796Y, N856K, Q954H, N969K, L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the following mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) amino acid substitutions at amino acid residues corresponding to 1, 2, 3, 4, 5, 6, 7, 8, or more of the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5, 6, 7, 8, 9, 10, or 11. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the mutations at amino acid residues corresponding to the amino acid residues of one of the constructs set forth in Table 6, 7, 8, 9, 10, or 11. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104. In some embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO:104, and a leucine at the amino position corresponding to amino acid position 452 of SEQ ID NO:104. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of SEQ ID NO:6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, or 66. In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, or 66. In another embodiment, provided herein is a transgene comprising a nucleotide sequence that is at least 97%, at least 98% or at least 99% identical to the nucleotide sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, or 66. Methods/techniques known in the art may be used to determine sequence identity (see, e.g., “Best Fit” or “Gap” program of the Sequence Analysis Software Package, version 10; Genetics Computer Group, Inc.). In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises (or consists of) a SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains. In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises a SARS-CoV-2 Omicron spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 amino acids substituted with another amino acid (e.g., a conservative amino acid substitution) and lacks a polybasic cleavage site (e.g., as a result of one, two, or more amino acid substitutions in polybasic cleavage site), and wherein amino acid residues corresponding to amino acid residues 817, 892, 899, 942, 986, and 987 of the spike protein found at the spike protein of GenBank Accession No. MN908947.3 are substituted with prolines. The SARS-CoV-2 Omicron variant spike protein ectodomain may lack the polybasic cleavage site as a result of a substitution of amino acid residues RRAR to A at amino acid residues corresponding to amino acid residues 682 to 685 of the spike protein of GenBank Accession No. MN908947.3. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, or 71. In specific embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)).

In certain embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, or 71. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain comprises an amino acid sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, or 71. In some embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises two or more (e.g., 1, 2, 3, 4, 5, 6, or 7), or all of the amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and/or N969K. In certain embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is encoded by nucleotide sequence that is at least 80%, at least 85%, or at least 90% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, or 70. In certain embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is encoded by a nucleotide sequence that is at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, or 70. In certain embodiments, the derivative of the SARS-CoV-2 Omicron spike protein ectodomain is encoded by the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, or 70. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid substitutions at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid substitutions at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, V687I, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid substitutions at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, T95I, G142D, L212I, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of GenBank Accession No. MN908947.3; and (3) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more of the amino acid substitutions at the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5, 6, 7, 8, 9, 10, or 11. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid mutations at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid mutations at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, NSPRRARS 679-686 deletion, V687I, N764K, D796Y, N856K, Q954H, N969K, L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) the following amino acid mutations at the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493, G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F. In some embodiments, a derivative of the SARS-CoV-2 Omicron spike protein ectodomain comprises the amino acid sequence of the spike protein of GenBank Accession No. MN908947.3, with (1) an amino acid substitution at amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues F817P, A892P, A899P, A942P, K986P, and V987P of the spike protein of GenBank Accession No. MN908947.3; and (3) 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more of the amino acid mutations at the amino acid residues of the spike protein of GenBank Accession No. MN908947.3 set forth in Table 5, 6, 7, 8, 9, 10, or 11. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) the mutations at amino acid residues corresponding to the amino acid residues of one of the constructs set forth in Table 6, 7, 8, 9, 10, or 11. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K. In a specific embodiment, the derivative comprises: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the spike protein of GenBank Accession No. MN908947.3 with a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) mutations at amino acid residues corresponding to the following amino acid residues of the spike protein of GenBank Accession No. MN908947.3: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K. In some embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104. In some embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain includes a serine at amino acid positions corresponding to amino acid positions 371, 373, and/or 375 of SEQ ID NO: 104, and a leucine at the amino acid position corresponding to 452 of SEQ ID NO: 104.

In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused directly to the NDV F protein transmembrane and cytoplasmic domains.

In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises a SARS-CoV-2 spike protein ectodomain with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acids deleted and lacks a polybasic cleavage site (e.g., as a result of one, two, or more amino acid substitutions in polybasic cleavage site), and wherein amino acid residues corresponding to amino acid residues 817, 892, 899, 942, 986, and 987 of the spike protein found at GenBank Accession No. MN908947.3 are substituted with prolines. In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. The derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain may lack the polybasic cleavage site as a result of a substitution of amino acid residues RRAR to A at amino acid residues corresponding to amino acid residues 682 to 685 of the spike protein of GenBank Accession No. MN908947.3. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO: 24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another specific embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein chimeric F protein comprises a derivative of SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, wherein the derivative of SARS-CoV-2 Omicron variant spike protein ectodomain is encoded by a nucleotide sequence that can hybridize under high, moderate or typical stringency hybridization conditions to the nucleic acid sequence set forth in SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, 70, 76, 78, 84, 94, 96, 100, or 102. Hybridization conditions are known to one of skill in the art (see, e.g., U.S. Patent Application No. 2005/0048549 at, e.g., paragraphs 72 and 73). In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene comprising a nucleotide sequence encoding a chimeric F protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises a SARS-CoV-2 Omicron variant spike protein with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 mutations (e.g. amino acid substitutions, amino acid additions, amino acid deletions or a combination thereof) and lacks a polybasic cleavage site (e.g., as a result of one, two, or more amino acid substitutions in polybasic cleavage site), and wherein amino acid residues corresponding to amino acid residues 817, 892, 899, 942, 986, and 987 of the spike protein found at GenBank Accession No. MN908947.3 are substituted with prolines. In specific embodiments, the lack of a polybasic cleavage means that the polybasic site is altered such that it cannot be cleaved by, e.g., furin. The derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain may lack the polybasic cleavage site as a result of a substitution of amino acid residues RRAR to A at amino acid residues corresponding to amino acid residues 682 to 685 of the spike protein of GenBank Accession No. MN908947.3. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain comprises an amino acid sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103. In certain embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103 . . . . In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In other embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein is fused directly to the NDV F protein transmembrane and cytoplasmic domains. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another specific embodiment, provided herein is a transgene comprising a nucleotide sequence that can hybridize under high, moderate or typical stringency hybridization conditions to the nucleic acid sequence set forth in SEQ ID NO:6, 7, 10, 11, 14 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. Hybridization conditions are known to one of skill in the art (see, e.g., U.S. Patent Application No. 2005/0048549 at, e.g., paragraphs 72 and 73). In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between NP and P transcription units, or between the NDV HN and L transcription units). In specific embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from the same NDV strain as the transcription units of the NDV genome. In other embodiments, the NDV F protein transmembrane and cytoplasmic domains of the chimeric F protein are from a different NDV strain than the transcription units of the NDV genome. In a specific embodiment, the NDV genome is of the LaSota strain.

In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and an NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises the amino acid sequence set forth in SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103 . . . . In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and an NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises an amino acid sequence that is at least 85%, at least 90%, or at least 95%, identical to the amino acid sequence set forth in SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103 . . . . In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and an NDV F protein transmembrane and cytoplasmic domains, wherein the derivative comprises an amino acid sequence that is at least 96%, at least 97%, or at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence set forth in SEQ ID NO: 19, 21, 23, 33, 35, 39, 41, 45, 47, 51, 53, 57, 59, 63, 65, 69, 71, 77, 79, 83, 85, 89, 91, 95, 97, 101, or 103 . . . . See, e.g., Table 2, infra, with the transmembrane and cytoplasmic domains of NDV F protein indicated. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO:73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In some embodiments, the NDV F protein transmembrane and cytoplasmic domains are fused directly to the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units).

In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and an NDV F protein transmembrane and cytoplasmic domains, wherein the derivative is encoded by a nucleotide sequence that is at least 80%, at least 85%, or at least 90% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, 70, 76, 78, 82, 85, 88, 90, 94, 97, 100, or 102. In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron variant spike protein ectodomain and an NDV F protein transmembrane and cytoplasmic domains, wherein the derivative is encoded by a nucleotide sequence that is at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 18, 20, 22, 32, 34, 38, 40, 44, 46, 50, 52, 56, 58, 62, 64, 68, or 70. See, e.g., Table 2, infra, with the transmembrane and cytoplasmic domains of NDV F protein indicated. In specific embodiments, the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain is fused to the NDV F protein transmembrane and cytoplasmic domains via a linker (e.g., GGGGS (SEQ ID NO:24)). The linker may be any linker that does not interfere with folding of the ectodomain, function of the ectodomain or both. In some embodiments, the linker is an amino acid sequence (e.g., a peptide) that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more amino acids long. In some embodiments, the linker is a glycine (G) linker or glycine and serine (GS) linker. For example, the linker may comprise the sequence of (GGGGS)_n(SEQ ID NO: 73), wherein n is 1, 2, 3, 4, 5 or more. In another example, the linker may comprise (G)_n, wherein n is 3, 4, 5, 6, 7, 8 or more. In a specific embodiment, the linker comprises the sequence GGGGS (SEQ ID NO:24). In some embodiments, the NDV F protein transmembrane and cytoplasmic domains are fused directly to the derivative of the SARS-CoV-2 Omicron variant spike protein ectodomain. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units).

In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO:8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 99. In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 85%, at least 90%, or at least 95%, identical to the amino acid sequence set forth in SEQ ID NO: 8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 99. In another embodiment, provided herein is a transgene that comprises a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises an amino acid sequence that is at least 96%, at least 97%, or at least 98%, at least 99%, or at least 99.5% identical to the amino acid sequence set forth in SEQ ID NO: 8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 99. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units).

In another embodiment, provided herein is a transgene that comprises a nucleotide sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In another embodiment, provided herein is a transgene that comprises a nucleotide sequence that is at least 85%, at least 90%, or at least 95%, identical to the nucleotide sequence of SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, or 66. In another embodiment, provided herein is a transgene that comprises a nucleotide sequence comprises an nucleotide sequence that is at least 96%, at least 97%, or at least 98%, at least 99%, or at least 99.5% identical to the nucleotide sequence set forth in SEQ ID NO: 6, 7, 10, 11, 14, 15, 30, 36, 42, 48, 54, 60, 66, 74, 80, 86, 92, or 98. In certain embodiments, the transgene encoding the chimeric F protein is codon optimized. See, e.g., Section 5.1.4, infra, for a discussion regarding codon optimization. In a specific embodiment, a transgene encoding a chimeric F protein is incorporated into the genome of any NDV type or strain (e.g., NDV LaSota strain). See, e.g., Section 5.1.1, supra, for types and strains of NDV that may be used. The transgene encoding a chimeric F protein may be incorporated between any two NDV transcription units (e.g., between the NDV P and M transcription units, between the NDV NP and P transcription units, or between the NDV HN and L transcription units).

In a specific embodiment, a transgene encodes a protein described herein. In a specific embodiment, a transgene encoding a chimeric F protein is one described in the Example (Section 6), infra. In a specific embodiment, a transgene comprises a nucleotide sequence encoding the ectodomain of a chimeric F protein described in the Example (Section 6), infra. In a specific embodiment, a transgene comprises a nucleotide sequence described in Table 3, infra. In a specific embodiment, a transgene encodes a protein comprising an amino acid sequence described in Table 3, infra. In a specific embodiment, a transgene encodes a chimeric F protein comprising an amino acid sequence described in Table 3, infra. In some embodiments, a protein (e.g., a chimeric F protein) is one encoded by a transgene described herein. In some embodiments, provided herein is a recombinant protein encoded by a transgene described herein, a polynucleotide described herein, nucleic acid sequence described herein, or nucleotide sequence described herein. In a specific embodiment, a chimeric F protein is one described in Section 6, infra. In some embodiments, provided herein is a recombinant protein comprising (or consisting of) an amino acid described herein (e.g., in Table 3, infra). In a specific embodiment, a chimeric F protein comprises an amino acid sequence described in Table 3, infra.

In specific embodiments, NDV F protein transmembrane and cytoplasmic domains of a chimeric F protein may be from any NDV strain known in the art or described herein. For example, NDV F protein transmembrane and cytoplasmic domains of a chimeric F protein may be from the NDV F protein of LaSota strain, Hitchner B1 strain, Fuller strain, Ulster strain, Roakin strain, or Komarov strain. In some embodiments, the NDV F protein transmembrane and cytoplasmic domains comprise the amino acid sequence of SEQ ID NO: 5.

In certain embodiments, a transgene encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron spike protein) comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences) and Kozak sequences. In some embodiments, a transgene encoding a protein comprising (or consisting of) the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences) and Kozak sequences. In certain embodiments, a transgene encoding a protein comprising (or consisting of) a derivative of SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein) comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences) and Kozak sequences. In some embodiments, a transgene encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences) and Kozak sequences. In certain embodiments, a transgene encoding a chimeric F protein comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences) and Kozak sequences. In some embodiments, a transgene encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences), Kozak sequences and restriction sites to facilitate cloning. In some embodiments, a transgene encoding a protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein) comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences), Kozak sequences and restriction sites to facilitate cloning. In some embodiments, a transgene encoding a chimeric F protein comprises NDV regulatory signals (e.g., gene end, intergenic, and gene start sequences), Kozak sequences and restriction sites to facilitate cloning. In certain embodiments, a transgene encoding a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein) comprises NDV regulatory signals (gene end, intergenic and gene start sequences), Kozak sequences, restriction sites to facilitate cloning, and additional nucleotides in the non-coding region to ensure compliance with the rule of six. In some embodiments, a transgene encoding a protein comprising (or consisting of) the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises NDV regulatory signals (gene end, intergenic and gene start sequences), Kozak sequences, restriction sites to facilitate cloning, and additional nucleotides in the non-coding region to ensure compliance with the rule of six. In certain embodiments, a transgene encoding a protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron spike protein) comprises NDV regulatory signals (gene end, intergenic and gene start sequences), Kozak sequences, restriction sites to facilitate cloning, and additional nucleotides in the non-coding region to ensure compliance with the rule of six. In some embodiments, a transgene encoding a protein comprising (or consisting of) a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein comprises NDV regulatory signals (gene end, intergenic and gene start sequences), Kozak sequences, restriction sites to facilitate cloning, and additional nucleotides in the non-coding region to ensure compliance with the rule of six. In certain embodiments, a transgene encoding a protein comprising (or consisting of) a chimeric F protein comprises NDV regulatory signals (gene end, intergenic and gene start sequences), Kozak sequences, restriction sites to facilitate cloning, and additional nucleotides in the non-coding region to ensure compliance with the rule of six. See, e.g., SEQ ID NOS: 25-28 for examples of a restriction sequence (SacII), a gene end sequence, a gene start sequence and a Kozak sequence that may be used. In a preferred embodiment, the transgene complies with the rule of six.

In some embodiments, provided herein is a vector (e.g., a plasmid or viral vector) comprising a transgene, or nucleic acid described herein, nucleotide sequence described herein, or polynucleotide sequence described herein.

In a specific embodiment, a transgene described herein is isolated. In specific embodiments, a polynucleotide or nucleic acid sequence described herein is isolated. In certain embodiments, an “isolated” nucleic acid sequence or polynucleotide refers to a nucleic acid molecule which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. In other words, the isolated nucleic acid sequence or polynucleotide can comprise heterologous nucleic acids that are not associated with it in nature. In other embodiments, an “isolated” nucleic acid sequence or polynucleotide, such as a cDNA or RNA sequence, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. The term “substantially free of cellular material” includes preparations of nucleic acid sequences or polynucleotides in which the nucleic acid sequence or polynucleotide is separated from cellular components of the cells from which it is isolated or recombinantly produced. Thus, a nucleic acid sequence or polynucleotide that is substantially free of cellular material includes preparations of nucleic acid sequence or polynucleotide having less than about 30%, 20%, 10%, or 5% (by dry weight) of other nucleic acids. The term “substantially free of culture medium” includes preparations of nucleic acid sequence or polynucleotide in which the culture medium represents less than about 50%, 20%, 10%, or 5% of the volume of the preparation. The term “substantially free of chemical precursors or other chemicals” includes preparations in which the nucleic acid sequence or polynucleotide is separated from chemical precursors or other chemicals which are involved in the synthesis of the nucleic acid sequence or polynucleotide. In specific embodiments, such preparations of the nucleic acid sequence or polynucleotide have less than about 50%, 30%, 20%, 10%, 5% (by dry weight) of chemical precursors or compounds other than the nucleic acid sequence of interest or polynucleotide of interest.

Also, provided herein is a protein (e.g., a recombinant protein) encoded by a polynucleotide described herein, a nucleic acid sequence described herein, a nucleotide sequence described herein, or a transgene described herein. A protein described herein may be isolated from a cell (e.g., a cell line or primary cell) or embryonated egg (e.g., embryonated chicken egg). An “isolated” protein is a protein which is substantially separated from other proteins.

In specific embodiments, a protein described herein comprising a SARS-CoV-2 ectodomain or a derivative thereof has a pre-fusion conformation of a SARS-CoV-2 spike protein. In some embodiments, a chimeric F protein described herein comprising a SARS-CoV-2 ectodomain or a derivative thereof has a post-fusion conformation of a SARS-CoV-2 spike protein.

An “isolated” protein is one which is separated from other proteins which are present in the natural source of the protein. Moreover, an “isolated” protein can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.

5.1.3 Recombinant NDV Encoding a SARS-CoV-2 Spike Protein or a Chimeric F Protein with a SARS-CoV-2 Spike Protein Ectodomain

In one aspect, presented herein are recombinant Newcastle disease virus (“NDV”) comprising a packaged genome, wherein the packaged genome comprises a transgene described herein. In one embodiment, a recombinant NDV comprises a packaged genome, wherein the packaged genome comprises a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof. See, e.g., Sections 5.1.2 and 6 for transgenes encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein) which the packaged genome may comprise. In a specific embodiment, the transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron spike protein), or derivative thereof is one described in Section 5.1.2, supra. In a specific embodiment, the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof is expressed by cells infected with the recombinant NDV. In certain embodiments, the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron spike protein) is incorporated into the NDV virion.

In another embodiment, a recombinant NDV comprises a packaged genome, wherein the packaged genome comprises a transgene encoding a protein comprising a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof. See, e.g., Sections 5.1.2 and 6 for transgenes encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof which the packaged genome may comprise. In a specific embodiment, the transgene is one described in Section 5.1.2 or 6. In a specific embodiment, the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof is expressed by cells infected with the recombinant NDV. In certain embodiments, the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof is incorporated into the NDV virion.

In another embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a protein described herein. In another embodiment, described herein are recombinant NDV comprising a packaged genome, wherein the packaged genome comprises a transgene encoding a chimeric F protein described herein. In a specific embodiment, the chimeric F protein is expressed by cells infected with the recombinant NDV. In another specific embodiment, the chimeric F protein is incorporated into the NDV virion. In another specific embodiment, the chimeric F protein is expressed by cells infected with the recombinant NDV and the chimeric F protein is incorporated into the NDV virion.

In a specific embodiment, a recombinant NDV is one described in the Example (Section 6), infra. In specific embodiments, a recombinant NDV described herein is replication competent. In other embodiments, a recombinant NDV described herein has been inactivated.

In some embodiments, the genome of the recombinant NDV comprises a heterologous sequence encoding a heterologous protein in addition to nucleotide sequence encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof. In some embodiments, the genome of the recombinant NDV comprises a heterologous sequence encoding a heterologous protein in addition to nucleotide sequence encoding a chimeric F protein.

In certain embodiments, the genome of the recombinant NDV does not comprise a heterologous sequence encoding a heterologous protein other than a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof. In some embodiments, the genome of the recombinant NDV does not comprise a transgene other than a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof. In a specific embodiment, a heterologous sequence encodes a protein that is not found associated with naturally-occurring NDV. In certain embodiments, a recombinant NDV described herein comprises a packaged genome, wherein the genome comprises the genes found in NDV and a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof. In other words, the recombinant NDV encodes for both NDV F protein and the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or derivative thereof. In some embodiments, a recombinant NDV described herein comprises a packaged genome, wherein the genome comprises the genes found in NDV and a transgene encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain, S1 domain, S2 domain or receptor binding domain of SARS-CoV-2 Omicron variant spike protein), or a derivative thereof but does not include any other transgenes.

In some embodiments, the packaged genome of recombinant NDV encodes a chimeric F protein described herein. In certain embodiment, the genome of the recombinant NDV does not comprise a heterologous sequence encoding a heterologous protein other than the chimeric F protein. In a specific embodiment, a heterologous sequence encodes a protein that is not found associated with naturally-occurring NDV. In some embodiments, the genome of the recombinant NDV does not comprise a transgene other than a transgene encoding a chimeric F protein described herein. In preferred embodiments, a recombinant NDV described herein comprises a packaged genome, wherein the genome comprises the genes found in NDV and a transgene encoding a chimeric F protein. In other words, the recombinant NDV encodes for both NDV F protein and the chimeric F protein. In some embodiments, a recombinant NDV described herein comprises a packaged genome, wherein the genome comprises the genes found in NDV and a transgene encoding a chimeric F protein, but does not include any other transgenes.

In a specific embodiment, provided herein is a NDV virion comprising a protein comprising (or consisting of) a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof) described herein (e.g., a SARS-CoV-2 Omicron variant spike protein or portion thereof encoded by a transgene described herein), or a derivative thereof. See, e.g., Section 5.1.2 for examples of such a protein that may incorporated into the virion of a recombinant NDV. In a specific embodiment, the protein is one described in Section 5.1.2, supra. In specific embodiments, the NDV virion is recombinantly produced.

In a specific embodiment, provided herein is a NDV virion comprising a protein comprising (or consisting of) a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof) described herein. See, e.g., Section 5.1.2 for examples of such a protein that may incorporated into the virion of a recombinant NDV. In a specific embodiment, the protein is one described in Section 5.1.2, supra. In specific embodiments, the NDV virion is recombinantly produced.

In a specific embodiment, provided herein is a NDV virion comprising a chimeric F protein described herein (e.g., a chimeric F protein encoded by a transgene described herein). See, e.g., Section 5.1.2 and the Example (e.g., Section 6) for examples of a chimeric F protein that may incorporated into the virion of a recombinant NDV. In a specific embodiment, the chimeric F protein comprises an amino acid sequence that is at least 80%, at least 85%, or at least 90% identical to the amino acid sequence of SEQ ID NO: 8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 94. In a specific embodiment, the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 94. In a specific embodiment, the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 8, 9, 12, 13, 16, 17, 31, 37, 43, 49, 55, 61, 67, 75, 81, 87, 93, or 94. In a specific embodiment, the chimeric F protein is one described in Section 5.1.2 or 6. In specific embodiments, the NDV virion is recombinantly produced.

In a specific embodiment, provided herein is a NDV virion comprising a chimeric F protein described in Section 5.1.2 or 6.

In a specific embodiment, a chimeric F protein described herein is in a pre-fusion conformation. In some embodiments, a chimeric F protein described herein is in a post-fusion conformation.

As shown in FIGS. 2A, 2B, 3, 4A, 5A, 5B, 5C, and 7A, certain chimeric F protein expressed by recombinant NDV described in Section 6 undergo proteolysis. Also, as shown in FIG. 2C, 4B, 5B, 6A, 6C, 7B, or 7C, proteolysis of the certain chimeric F protein expressed by certain recombinant NDV described in Section 6 prevented. In specific embodiments, a chimeric F protein described herein does not undergo proteolysis such as shown in FIG. 2A, 2B, 3, 4A, 5A, 5B, 5C, or 7A. In some embodiments, a chimeric F protein described herein that does not undergo proteolysis such as shown in FIG. 2A, 2B, 3, 4A, 5A, 5B, 5C, or 7A, maintains a conformation similar to the ectodomain of the spike protein of a SARS-CoV-2 Omicron variant. In some embodiments, a chimeric F protein described herein that does not undergo proteolysis such as shown in FIG. 2A, 2B, 3, 4A, 5A, 5B, 5C, or 7A yields antibodies that bind to the spike protein of a SARS-CoV-2 Omicron variant in an immunoassay. In some embodiments, a chimeric F protein described herein that does not undergo proteolysis such as shown in FIG. 2A, 2B, 3, 4A, 5A, 5B, 5C, or 7A induces antibodies in a subject that neutralize a SARS-CoV-2 Omicron variant.

5.1.4 Codon Optimization

Any codon optimization technique known to one of skill in the art may be used to codon optimize a nucleic acid sequence encoding a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), or a chimeric F protein. Methods of codon optimization are known in the art, e.g., the OptimumGene™ (GenScript®) protocol and Genewiz® protocol, which are incorporated by reference herein in its entirety. See also U.S. Pat. No. 8,326,547 for methods for codon optimization, which is incorporated herein by reference in its entirety.

As an exemplary method for codon optimization, each codon in the open frame of the nucleic acid sequence encoding a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), or a chimeric F protein is replaced by the codon most frequently used in mammalian proteins. This may be done using a web-based program (www.encorbio.com/protocols/Codon.htm) that uses the Codon Usage Database, maintained by the Department of Plant Gene Research in Kazusa, Japan. This nucleic acid sequence optimized for mammalian expression may be inspected for: (1) the presence of stretches of 5xA or more that may act as transcription terminators; (2) the presence of restriction sites that may interfere with subcloning; (3) compliance with the rule of six. Following inspection, (1) stretches of 5xA or more that may act as transcription terminators may be replaced by synonymous mutations; (2) restriction sites that may interfere with subcloning may be replaced by synonymous mutations; (3) NDV regulatory signals (gene end, intergenic and gene start sequences), and Kozak sequences for optimal protein expression may be added; and (4) nucleotides may be added in the non-coding region to ensure compliance with the rule of six. Synonymous mutations are typically nucleotide changes that do not change the amino acid encoded. For example, in the case of a stretch of 6 As (AAAAAA), which sequence encodes Lys-Lys, a synonymous sequence would be AAGAAG, which sequence also encodes Lys-Lys.

5.2 Construction of NDVS

The recombinant NDVs described herein (see, e.g., Sections 5.1 and 6) can be generated using the reverse genetics technique. The reverse genetics technique involves the preparation of synthetic recombinant viral RNAs that contain the non-coding regions of the negative-strand, viral RNA which are essential for the recognition by viral polymerases and for packaging signals necessary to generate a mature virion. The recombinant RNAs are synthesized from a recombinant DNA template and reconstituted in vitro with purified viral polymerase complex to form recombinant ribonucleoproteins (RNPs) which can be used to transfect cells. A more efficient transfection is achieved if the viral polymerase proteins are present during transcription of the synthetic RNAs either in vitro or in vivo. The synthetic recombinant RNPs can be rescued into infectious virus particles. The foregoing techniques are described in U.S. Pat. No. 5,166,057 issued Nov. 24, 1992; in U.S. Pat. No. 5,854,037 issued Dec. 29, 1998; in U.S. Pat. No. 6,146,642 issued Nov. 14, 2000; in European Patent Publication EP 0702085A1, published Feb. 20, 1996; in U.S. patent application Ser. No. 09/152,845; in International Patent Publications PCT WO 97/12032 published Apr. 3, 1997; WO 96/34625 published Nov. 7, 1996; in European Patent Publication EP A780475; WO 99/02657 published Jan. 21, 1999; WO 98/53078 published Nov. 26, 1998; WO 98/02530 published Jan. 22, 1998; WO 99/15672 published Apr. 1, 1999; WO 98/13501 published Apr. 2, 1998; WO 97/06270 published Feb. 20, 1997; and EPO 780 475A1 published Jun. 25, 1997, each of which is incorporated by reference herein in its entirety.

The helper-free plasmid technology can also be utilized to engineer a NDV described herein. Briefly, a complete cDNA of a NDV (e.g., the Hitchner B1 strain or LaSota strain) is constructed, inserted into a plasmid vector and engineered to contain a unique restriction site between two transcription units (e.g., the NDV P and M genes; the NDV NP and P genes; or the NDV HN and L genes). A nucleotide sequence encoding a heterologous amino acid sequence (e.g., a transgene or other sequence described herein such as, e.g., a nucleotide sequence encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), or a chimeric F protein) may be inserted into the viral genome at the unique restriction site. Alternatively, a nucleotide sequence encoding a heterologous amino acid sequence (e.g., a transgene or other sequence described herein such as, e.g., a nucleotide sequence encoding SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), or a chimeric F protein) may be engineered into a NDV transcription unit so long as the insertion does not affect the ability of the virus to infect and replicate. The single segment is positioned between a T7 promoter and the hepatitis delta virus ribozyme to produce an exact negative or positive transcript from the T7 polymerase. The plasmid vector and expression vectors comprising the necessary viral proteins are transfected into cells leading to production of recombinant viral particles (see, e.g., International Publication No. WO 01/04333; U.S. Pat. Nos. 7,442,379, 6,146,642, 6,649,372, 6,544,785 and 7,384,774; Swayne et al. (2003). Avian Dis. 47:1047-1050; and Swayne et al. (2001). J. Virol. 11868-11873, each of which is incorporated by reference in its entirety).

Bicistronic techniques to produce multiple proteins from a single mRNA are known to one of skill in the art. Bicistronic techniques allow the engineering of coding sequences of multiple proteins into a single mRNA through the use of IRES sequences. IRES sequences direct the internal recruitment of ribosomes to the RNA molecule and allow downstream translation in a cap independent manner. Briefly, a coding region of one protein is inserted downstream of the ORF of a second protein. The insertion is flanked by an IRES and any untranslated signal sequences necessary for proper expression and/or function. The insertion must not disrupt the open reading frame, polyadenylation or transcriptional promoters of the second protein (see, e.g., Garcia-Sastre et al., 1994, J. Virol. 68:6254-6261 and Garcia-Sastre et al., 1994 Dev. Biol. Stand. 82:237-246, each of which are incorporated by reference herein in their entirety).

Methods for cloning recombinant NDV to encode a transgene and express a heterologous protein encoded by the transgene (e.g., a transgene comprises a nucleotide sequence encoding SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein), or a derivative thereof, a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain thereof), or a chimeric F protein) are known to one skilled in the art, such as, e.g., insertion of the transgene into a restriction site that has been engineered into the NDV genome, inclusion an appropriate signals in the transgene for recognition by the NDV RNA-dependent-RNA polymerase (e.g., sequences upstream of the open reading frame of the transgene that allow for the NDV polymerase to recognize the end of the previous gene and the beginning of the transgene, which may be, e.g., spaced by a single nucleotide intergenic sequence), inclusion of a valid Kozak sequence (e.g., to improve eukaryotic ribosomal translation); incorporation of a transgene that satisfies the “rule of six” for NDV cloning; and inclusion of silent mutations to remove extraneous gene end and/or gene start sequences within the transgene. See, e.g., SEQ ID NO:25-28 for examples of a restriction site sequence, gene end sequence, gene start sequence, and Kozak sequence. Regarding the rule of six, one skilled in the art will understand that efficient replication of NDV (and more generally, most members of the paramyxoviridae family) is dependent on the genome length being a multiple of six, known as the “rule of six” (see, e.g., Calain, P. & Roux, L. The rule of six, a basic feature of efficient replication of Sendai virus defective interfering RNA. J. Virol. 67, 4822-4830 (1993)). Thus, when constructing a recombinant NDV described herein, care should be taken to satisfy the “Rule of Six” for NDV cloning. Methods known to one skilled in the art to satisfy the Rule of Six for NDV cloning may be used, such as, e.g., addition of nucleotides downstream of the transgene. See, e.g., Ayllon et al., Rescue of Recombinant Newcastle Disease Virus from cDNA. J. Vis. Exp. (80), e50830, doi: 10.3791/50830 (2013) for a discussion of methods for cloning and rescuing of NDV (e.g., recombinant NDV), which is incorporated by reference herein in its entirety.

In a specific embodiment, an NDV described herein (see, e.g., Section 5.1, and 6) may be generated according to a method described in Section 6, infra.

In a specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) described herein comprises a LaSota strain backbone. In another specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) described herein comprises a LaSota strain backbone. In a specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO: 1. In a specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO:3. As the skilled person will appreciate, the genome of NDV is negative-sense and single stranded. SEQ ID NOS: 1 and 3 provide cDNA sequences.

In a specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) described herein comprises a LaSota strain backbone. In another specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., ectodomain, S1 domain, S2 domain, or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein) described herein comprises a LaSota strain backbone. In a specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO:1. In a specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO:3. As the skilled person will appreciate, the genome of NDV is negative-sense and single stranded. SEQ ID NOS: 1 and 3 provide cDNA sequences.

In a specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene encoding a chimeric F protein described herein comprises a LaSota strain backbone. In a specific embodiment, a recombinant NDV comprising a packaged genome comprising a transgene encoding a chimeric F protein described herein comprises a LaSota strain backbone. In a specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO:1. In another specific embodiment, the genomic sequence of the LaSota strain backbone (i.e., without the transgene) is as set forth in SEQ ID NO:3. As the skilled person will appreciate, the genome of NDV is negative-sense and single stranded. SEQ ID NOS: 1 and 3 provide cDNA sequences.

Techniques and procedures described or referenced herein include those that are generally well understood and/or commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized methodologies described in, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (3d ed. 2001); Current Protocols in Molecular Biology (Ausubel et al. eds., 2003). Conventional methodologies well understood and/or commonly employed by those of skill in the art may be used to produced a protein described herein.

5.3 Propagation of NDVS

The recombinant NDVs described herein (e.g., Sections 5.1 and 6) can be propagated in any substrate that allows the virus to grow to titers that permit the uses of the viruses described herein. In one embodiment, the substrate allows the recombinant NDVs described herein to grow to titers comparable to those determined for the corresponding wild-type viruses.

The recombinant NDVs described herein (e.g., Sections 5.1 and 6) may be grown in cells (e.g., avian cells, chicken cells, etc.) that are susceptible to infection by the viruses, embryonated eggs (e.g., chicken eggs or quail eggs) or animals (e.g., birds). Such methods are well known to those skilled in the art. In a specific embodiment, the recombinant NDVs described herein may be propagated in cancer cells, e.g., carcinoma cells (e.g., breast cancer cells and prostate cancer cells), sarcoma cells, leukemia cells, lymphoma cells, and germ cell tumor cells (e.g., testicular cancer cells and ovarian cancer cells). In another specific embodiment, the recombinant NDVs described herein may be propagated in cell lines, e.g., cancer cell lines such as HeLa cells, MCF7 cells, THP-1 cells, U87 cells, DU145 cells, Lncap cells, and T47D cells. In certain embodiments, the cells or cell lines (e.g., cancer cells or cancer cell lines) are obtained, derived, or obtained and derived from a human(s). In another embodiment, the recombinant NDVs described herein are propagated in interferon deficient systems or interferon (IFN) deficient substrates, such as, e.g., IFN deficient cells (e.g., IFN deficient cell lines) or IFN deficient embryonated eggs. In another embodiment, the recombinant NDVs described herein are propagated in chicken cells or embryonated chicken eggs. Representative chicken cells include, but are not limited to, chicken embryo fibroblasts and chicken embryo kidney cells. In a specific embodiment, the recombinant NDVs described herein are propagated in Vero cells. In another specific embodiment, the recombinant NDVs described herein are propagated in chicken eggs or quail eggs. In certain embodiments, a recombinant NDV virus described herein is first propagated in embryonated eggs and then propagated in cells (e.g., a cell line). In another specific embodiment, the recombinant NDVs described herein are propagated as described in Section 6, infra.

The recombinant NDVs described herein may be propagated in embryonated eggs (e.g. chicken embryonated eggs), e.g., from 6 to 14 days old, 6 to 12 days old, 6 to 10 days old, 6 to 9 days old, 6 to 8 days old, 8 to 10 day old, 9 to 11 days old, or 10 to 12 days old. In a specific embodiment, 10 day old embryonated chicken eggs are used to propagate the recombinant NDVs described herein. Young or immature embryonated eggs (e.g. chicken embryonated eggs) can be used to propagate the recombinant NDVs described herein. Immature embryonated eggs encompass eggs which are less than ten day old eggs, e.g., eggs 6 to 9 days old or 6 to 8 days old that are IFN-deficient. Immature embryonated eggs also encompass eggs which artificially mimic immature eggs up to, but less than ten day old, as a result of alterations to the growth conditions, e.g., changes in incubation temperatures; treating with drugs; or any other alteration which results in an egg with a retarded development, such that the IFN system is not fully developed as compared with ten to twelve day old eggs. The recombinant NDVs described herein can be propagated in different locations of the embryonated egg, e.g., the allantoic cavity (such as, e.g., the allantoic cavity of chicken embryonated eggs). For a detailed discussion on the growth and propagation viruses, see, e.g., U.S. Pat. Nos. 6,852,522 and 7,494,808, both of which are hereby incorporated by reference in their entireties.

In a specific embodiment, a virus is propagated as described in the Example below (e.g., Section 6).

For virus isolation, the recombinant NDVs described herein can be removed from embryonated eggs or cell culture and separated from cellular components, typically by well-known clarification procedures, e.g., such as centrifugation, depth filtration, and microfiltration, and may be further purified as desired using procedures well known to those skilled in the art, e.g., tangential flow filtration (TFF), density gradient centrifugation, differential extraction, or chromatography.

In a specific embodiment, virus isolation from allantoic fluid of an infected egg (e.g., a chicken egg) begins with harvesting allantoic fluid, which is clarified using a filtration system to remove cells and other large debris.

In a specific embodiment, provided herein is a cell (e.g., a cell line) or embryonated egg (e.g., a chicken embryonated egg) comprising a recombinant NDV described herein. In another specific embodiment, provided herein is a method for propagating a recombinant NDV described herein, the method comprising culturing a cell (e.g., a cell line) or embryonated egg (e.g., a chicken embryonated egg) infected with the recombinant NDV. In some embodiments, the method may further comprise isolating or purifying the recombinant NDV from the cell or embryonated egg. In a specific embodiment, provided herein is a method for propagating a recombinant NDV described herein, the method comprising (a) culturing a cell (e.g., a cell line) or embryonated egg infected with a recombinant NDV described herein; and (b) isolating the recombinant NDV from the cell or embryonated egg. The cell or embryonated egg may be one described herein or known to one of skill in the art. In some embodiments, the cell or embryonated egg is IFN deficient. The cell may be one described herein. In specific embodiments, the cell is in vitro or ex vivo. In specific embodiments, the cell(s) is isolated.

In a specific embodiment, provided herein is a method for producing a pharmaceutical composition (e.g., an immunogenic composition) comprising a recombinant NDV described herein, the method comprising (a) propagating a recombinant NDV described herein a cell (e.g., a cell line) or embryonated egg; and (b) isolating the recombinant NDV from the cell or embryonated egg. The method may further comprise adding the recombinant NDV to a container along with a pharmaceutically acceptable carrier.

In some embodiments, provided herein are cells (e.g., cell line) comprising a transgene described herein, polynucleotide described herein, nucleic acid sequence described herein, vector described herein, or nucleotide sequence described herein. The cells may be transfected, transformed, or transduced with the transgene described herein, polynucleotide described herein, nucleic acid sequence described herein, vector described herein, or nucleotide sequence described herein. In some embodiments, provided herein are cells (e.g., cell line) expressing a protein (e.g., a chimeric F protein) described herein. In specific embodiments, the cells are isolated. The cell(s) may be one described herein. In specific embodiments, the cell(s) is in vitro or ex vivo.

5.4 Compositions and Routes of Administration

Provided herein are compositions comprising a recombinant NDV described herein (e.g., Section 5.1, or 6). In a specific embodiment, the compositions are pharmaceutical compositions, such as immunogenic compositions (e.g., vaccine compositions). In some embodiments provided herein are compositions (e.g., immunogenic compositions) comprising a transgene described herein, a polynucleotide described herein, a nucleotide sequence described herein, a vector described herein, or a recombinant protein described herein (e.g., Section 5.1, or 6). In some embodiments provided herein are compositions (e.g., immunogenic compositions) comprising a transgene described herein, a polynucleotide described herein, or nucleotide sequence described herein. In some embodiments provided herein are compositions (e.g., immunogenic compositions) comprising a vector described herein. In some embodiments provided herein are compositions (e.g., immunogenic compositions) comprising a recombinant protein described herein (e.g., Section 5.1, or 6). In a specific embodiment, provided herein are immunogenic compositions comprising a recombinant NDV described herein (e.g., Section 5.1, or 6). The compositions may be include a carrier or excipient. For example, the compositions may comprise a pharmaceutically acceptable carrier. The compositions may include an adjuvant (e.g., an adjuvant described herein) or be administered in combination with an adjuvant. The compositions may be used in methods of inducing an immune response to SARS-CoV-2 spike protein. The compositions may or may not include one or more additional prophylactic or therapeutic agents. The compositions may be used in methods for inducing an immune response to SARS-CoV-2 Omicron variant or immunizing against SARS-CoV-2. The compositions may be used in methods for immunizing against COVID-19. The compositions may be used in methods for preventing COVID-19, such as, e.g., preventing severe or moderate COVID-19.

In one embodiment, an immunogenic composition comprises a recombinant NDV described herein (e.g., Section 5.1, or 6), in an admixture with a pharmaceutically acceptable carrier. In some embodiments, the immunogenic composition further comprises one or more additional prophylactic or therapeutic agents. In a specific embodiment, an immunogenic composition comprises an effective amount of a recombinant NDV described herein (e.g., Section 5.1, or 6), and optionally one or more additional prophylactic or therapeutic agents, in a pharmaceutically acceptable carrier. In some embodiments, the recombinant NDV (e.g., Section 5.1, or 6) is the only active ingredient included in the immunogenic composition. In some embodiments, the immunogenic composition is bivalent or multivalent. In some embodiments, the immunogenic composition is monovalent. In a particular embodiment, the immunogenic composition is a vaccine.

In a specific embodiment, administration of an immunogenic composition described herein to a subject (e.g., a human) generates neutralizing antibody (e.g., anti-SARS-CoV-2 spike protein IgG). In certain embodiments, administration of an immunogenic composition described herein to a subject (e.g., a human) generates an immune response that provides some level of protection against developing COVID-19.

In a specific embodiment, the recombinant NDV included in an immunogenic composition described herein is a live virus. In particular, embodiment, the recombinant NDV included in a pharmaceutical composition described herein is an attenuated live virus. In some embodiments, the recombinant NDV included in an immunogenic composition described herein is inactivated. Any technique known to one of skill in the art may be used to inactivate a recombinant NDV described herein. For example, formalin or beta-propiolactone may be used to inactivate a recombinant NDV described herein. In a specific embodiment, the recombinant NDV included in a composition described herein is inactivated using 0.05% to 2% (e.g., 0.05%, 0.1%, 0.5%, 1%, or 2%) beta-Propiolactone, or another technique known to one of skill in the art. For example, in certain embodiments, to prepare inactivated concentrated recombinant NDV, 1 part of 0.5 M disodium phosphate (DSP) may be mixed with 38 parts of the allantoic fluid of an embryonated egg infected with the virus to stabilize the pH, one part of 2% beta-Propiolactone (BPL) is added dropwise to the mixture during shaking, and incubated on ice for 30 min, the mixture is then placed in a 37° C. water bath for approximately 1 to 3 hours shaken every 5-30 min. In another example, recombinant NDV in allantoic fluid is inactivated in 0.05% beta-propiolactone. The inactivated allantoic fluid may be clarified by centrifugation at 4,000 rpm for 20-40 minutes (e.g., about 30 minutes). The clarified allantoic fluids may be laid on top of a 20% sucrose cushion in PBS and ultracentrifuged at 25,000 rpm for about 2 hours at 4° C. using, e.g., a Beckman L7-65 ultracentrifuge with a Beckman SW28 rotor, to pellet the virus through the sucrose cushion to remove soluble egg protein. The virus may then be resuspended in PBS at, e.g., about pH 7 to about 7.6 (such as, e.g., pH 7.4). In specific embodiments, the total protein is determined using the bicinchoninic acid (BCA) assay, or another assay known to one of skill in the art. In a specific embodiment, a chimeric F protein is stable in an inactivated recombinant NDV described herein for a period of time (e.g., for 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, or longer), as assessed by the ability of the inactivated recombinant NDV to induce anti-SARS-CoV-2 spike protein antibodies.

In specific embodiments, an immunogenic composition described herein or a recombinant NDV described herein does not require frozen storage, which makes it difficult to transport and store in low-income countries. In specific embodiments, an immunogenic composition described herein or a recombinant NDV described herein may be stored at about 2° C. to about 8° C. (e.g., 4° C.).

The immunogenic compositions provided herein can be in any form that allows for the composition to be administered to a subject. In a specific embodiment, the pharmaceutical compositions are suitable for veterinary administration, human administration, or both. As used herein, the term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the pharmaceutical composition is administered. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin. The formulation should suit the mode of administration.

In a specific embodiment, the immunogenic compositions are formulated to be suitable for the intended route of administration to a subject. For example, an immunogenic composition may be formulated to be suitable for parenteral, intravenous, intraarterial, intrapleural, inhalation, intranasal, intraperitoneal, oral, intradermal, colorectal, intraperitoneal, and intracranial administration. In one embodiment, an immunogenic composition may be formulated for intravenous, intraarterial, oral, intraperitoneal, intranasal, intratracheal, intrapleural, intracranial, subcutaneous, intramuscular, topical, or pulmonary administration. In a specific embodiment, an immunogenic composition may be formulated for intranasal administration. In certain embodiments, an immunogenic composition is formulated for a nasal spray. In another embodiment, an immunogenic composition may be formulated for intramuscular administration.

In a specific embodiment, an immunogenic composition comprising a recombinant NDV described herein (see, e.g., Sections 5.1 and 6) is formulated to be suitable for intranasal administration to the subject (e.g., human subject).

In a specific embodiment, an immunogenic composition comprising an inactivated recombinant NDV described herein may comprise an adjuvant. In some embodiments, an immunogenic composition comprising a polynucleotide described herein, nucleotide sequence described herein, a vector described herein, or a recombinant protein described herein may comprise an adjuvant. In certain embodiments, the compositions described herein comprise, or are administered in combination with, an adjuvant. The adjuvant for administration in combination with a composition described herein may be administered before, concomitantly with, or after administration of the composition. In specific embodiments, an inactivated virus immunogenic composition described herein comprises one or more adjuvants. In some embodiments, the term “adjuvant” refers to a compound that when administered in conjunction with or as part of a composition described herein augments, enhances and/or boosts the immune response to a recombinant NDV, but when the compound is administered alone does not generate an immune response to the virus. In some embodiments, the adjuvant generates an immune response to a recombinant NDV and does not produce an allergy or other adverse reaction. Adjuvants can enhance an immune response by several mechanisms including, e.g., lymphocyte recruitment, stimulation of B and/or T cells, and stimulation of macrophages. Specific examples of adjuvants include, but are not limited to, aluminum salts (alum) (such as aluminum hydroxide, aluminum phosphate, and aluminum sulfate), 3 De-O-acylated monophosphoryl lipid A (MPL) (see GB 2220211), MF59 (Novartis), AS03 (GlaxoSmithKline), AS04 (GlaxoSmithKline), polysorbate 80 (Tween 80; ICL Americas, Inc.), imidazopyridine compounds (see International Application No. PCT/US2007/064857, published as International Publication No. WO2007/109812), imidazoquinoxaline compounds (see International Application No. PCT/US2007/064858, published as International Publication No. WO2007/109813) and saponins, such as QS21 (see Kensil et al., in Vaccine Design: The Subunit and Adjuvant Approach (eds. Powell & Newman, Plenum Press, NY, 1995); U.S. Pat. No. 5,057,540). In some embodiments, the adjuvant is Freund's adjuvant (complete or incomplete). Other adjuvants are oil in water emulsions (such as squalene or peanut oil), optionally in combination with immune stimulants, such as monophosphoryl lipid A (see Stoute et al, N. Engl. J. Med. 336, 86-91 (1997)). Another adjuvant is CpG (Bioworld Today, Nov. 15, 1998). Such adjuvants can be used with or without other specific immunostimulating agents such as MPL or 3-DMP, QS21, polymeric or monomeric amino acids such as poly glutamic acid or polylysine. In certain embodiments, the adjuvant is a liposomal suspension adjuvant (R-enantiomer of the cationic lipid DOTAP, R-DOTAP) or an MF-59 like oil-in-water emulsion adjuvant (AddaVax). The adjuvant may be a toll-like receptor (TLR) agonist (e.g., a TLR7 agonist, TLR8 agonist, TLR7/8 agonist, or TLR9 agonist). In some embodiments, the adjuvant is a toll-like receptor 9 (TLR9) agonist adjuvant. In certain embodiments, the adjuvant is CpG 1018. In some embodiments, a composition described herein (e.g., a live recombinant NDV composition) does not contain an adjuvant.

In certain embodiments, an immunogenic composition described herein comprises an effective amount of a recombinant NDV described herein. In specific embodiments, an effective amount of a recombinant NDV described herein is an amount of recombinant NDV to generate an immune response in a subject or a population of subjects. In specific embodiments, an effective amount of a recombinant NDV described herein is 10⁴to 10¹²PFU or EID50. In some embodiments, an effective amount comprises 1 to 15 micrograms of a recombinant protein described herein. In some embodiments, an effective amount comprises 1 to 15 micrograms of a SARS-CoV-2 spike protein or a portion thereof (e.g., an ectodomain), a derivative of a SARS-CoV-2 spike protein or a portion thereof (e.g., an ectodomain), or a chimeric F protein expressed by a recombinant NDV described herein.

In certain embodiments, an immunogenic composition described herein comprises 10⁴to 10¹²EID50 of a recombinant NDV described herein. In some embodiments, an immunogenic composition described herein comprises 1 to 15 micrograms of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., an ectodomain), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., an ectodomain), or a chimeric F protein expressed by a recombinant NDV described herein. In some embodiments, an immunogenic composition described herein comprises 1 to 15 micrograms of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., an ectodomain), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., an ectodomain), or a chimeric F protein expressed by a recombinant NDV described herein. In some embodiments, pharmaceutical composition (e.g., an immunogenic composition) described herein comprises 1 to 15 micrograms per ml of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., an ectodomain), a derivative of a SARS-CoV-2 spike protein or a portion thereof (e.g., an ectodomain), or a chimeric F protein expressed by a recombinant NDV described herein.

In some embodiments, an immunogenic composition described herein comprises 1 to 15 micrograms of inactivated recombinant NDV described herein.

In a specific embodiment, an immunogenic composition described herein may be stored at 2° to 8° C. (e.g., 4° C.). In certain embodiments, an immunogenic composition described herein is stable for at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, at least 9 months or at least 1 year at 2° to 8° C. In some embodiments, an immunogenic composition described herein is stable for 3-6 months, 3-9 months, 6-12 months, or 9-12 months at 2° to 8° C. (e.g., 4° C.). In certain embodiments, the stability is assessed by protein denaturation assays, immunoassays or a combination thereof.

5.5 Uses of a Recombinant NDV
5.5.1 Prevention of COVID-19

The recombinant NDV(s) described herein or an immunogenic composition described herein may be used to immunize a subject against SARS-CoV-2, induce an immune response to SARS-CoV-2 spike protein, or prevent COVID-19. In a specific aspect, the recombinant NDV(s) described herein may be used to immunize a subject against a SARS-CoV-2 Omicron variant, induce an immune response to a SARS-CoV-2 Omicron variant spike protein, or prevent COVID-19 caused by or associated with a SARS-CoV-2 Omicron variant. In another specific aspect, an immunogenic composition described herein may be used to immunize a subject against a SARS-CoV-2 Omicron variant, induce an immune response to a SARS-CoV-2 Omicron variant spike protein, or prevent COVID-19 caused by or associated with a SARS-CoV-2 Omicron variant.

In one aspect, presented herein are methods for inducing an immune response in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein or an immunogenic composition comprising a recombinant NDV described herein. In one embodiment, presented herein is a method for inducing an immune response to a SARS-CoV-2 spike protein in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein or an immunogenic composition described herein, such as described in Section 5.4. In another embodiment, presented herein is a method for inducing an immune response to a SARS-CoV-2 spike protein in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) an effective amount of a recombinant NDV described herein or an immunogenic composition described herein. See, e.g., Section 5.1 and 6 for recombinant NDV and Section 5.4 or 6 for immunogenic compositions. In a specific embodiment, the recombinant NDV is one described in Section 5.1 or 6, and the immunogenic composition is one described in Section 5.4 or 6.

In a specific embodiment, presented herein is a method for inducing an immune response to a SARS-CoV-2 Omicron variant spike protein in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein, or an immunogenic composition described herein. In another specific embodiment, presented herein is a method for inducing an immune response to a SARS-CoV-2 Omicron variant spike protein in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) an effective amount of a recombinant NDV described herein, or an immunogenic composition described herein. In a specific embodiment, the immunogenic composition is one described in Section 5.4 or 6.

In another aspect, presented herein are methods for immunizing a subject (e.g., a human subject) against SARS-CoV-2 (e.g., a SARS-CoV-2 Omicron variant) comprising administering the subject (e.g., a human subject) a recombinant NDV described herein or an immunogenic composition comprising a recombinant NDV described herein. In one embodiment, presented herein is a method for immunizing a subject (e.g., a human subject) against SARS-CoV-2 (e.g., a SARS-CoV-2 Omicron variant), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein, or an immunogenic composition described herein. In another embodiment, presented herein is a method for immunizing a subject (e.g., a human subject) against SARS-CoV-2 (e.g., a SARS-CoV-2 Omicron variant), comprising administering the subject (e.g., a human subject) an effective amount of a recombinant NDV described herein, or an immunogenic composition described herein. See, e.g., Section 5.1 and 6 for recombinant NDV and Section 5.4 and 6 for compositions. In a specific embodiment, the recombinant NDV is one described in Section 5.1 or 6, and the immunogenic composition is one described in Section 5.4 or 6.

In another aspect, presented herein are methods for preventing COVID-19 in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein, or an immunogenic composition comprising a recombinant NDV described herein. In one embodiment, presented herein is a method for preventing COVID-19 in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) a recombinant NDV described herein or an immunogenic composition described herein. In another embodiment, presented herein is a method for preventing COVID-19 in a subject (e.g., a human subject), comprising administering the subject (e.g., a human subject) an effective amount of a recombinant NDV described herein or an immunogenic composition described herein. In some embodiments, moderate COVID-19 is prevented. In some embodiments, severe COVID-19 is prevented. In a specific embodiment, the recombinant NDV is one described in Section 5.1 or 6, and the immunogenic composition is one described in Section 5.4 or 6. The COVID-19 may be caused by or associated with a SARS-CoV-2 Omicron variant.

The recombinant NDV described herein may be administered to a subject in combination with one or more other therapies. The recombinant NDV and one or more other therapies may be administered by the same or different routes of administration to the subject. In a specific embodiment, the recombinant NDV is administered to a subject intranasally. See, e.g., Sections 5.1, and 6, infra for information regarding recombinant NDV, Section 5.5.3 for information regarding other therapies, and Section 5.4, infra, for information regarding compositions and routes of administration.

The recombinant NDV and one or more additional therapies may be administered concurrently or sequentially to the subject. In certain embodiments, the recombinant NDV and one or more additional therapies are administered in the same composition. In other embodiments, the recombinant NDV and one or more additional therapies are administered in different compositions. The recombinant NDV and one or more other therapies may be administered by the same or different routes of administration to the subject. Any route known to one of skill in the art or described herein may be used to administer the recombinant NDV and one or more other therapies. In a specific embodiment, the recombinant NDV is administered intranasally or intramuscularly and the one or more other therapies are administered by the same or a different route. In a specific embodiment, the recombinant NDV is administered intranasally and the one or more other therapies is administered intravenously.

In some embodiments, two immunogenic compositions described herein are administered concurrently or sequentially to the subject. In some embodiments, three immunogenic compositions described herein are administered concurrently or sequentially to the subject. In some embodiments, three immunogenic compositions described herein are administered concurrently or sequentially to the subject. In some embodiments, four immunogenic compositions described herein are administered concurrently or sequentially to the subject.

In certain embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously vaccinated with a COVID-19 vaccine. In some embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously vaccinated with a COVID-19 vaccine other than a NDV-based COVID-19 vaccine. The COVID-19 vaccine may be a protein subunit vaccine, vector vaccine, or an mRNA vaccine. The COVID-19 vaccine may be Pfizer's COVID-19 vaccine, Pfizer-BioNTech bivalent COVID-19 vaccine, Moderna's COVID-19 vaccine, Moderna's bivalent COVID-19 vaccine, AstraZeneca's COVID-19 vaccine, Johnson & Johnson's COVID-19, Novavax COVID-19 Vaccine, Adjuvanted, SinoVac's COVID-19 vaccine, SinoPharm's COVID-19 vaccine, Bharat's COVID-19 vaccine, Cansino's COVID-19 vaccine, or another COVID-19 vaccine. In certain embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously vaccinated with an immunogenic composition other than one described herein. In certain embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously infected with SARS-CoV-2. In some embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously diagnosed with a SARS-CoV-2 infection. In some embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously experiencing symptoms of COVID-19. In certain embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered to a subject previously diagnosed with COVID-19.

In a specific embodiment, the immune response resulting from administration of a recombinant NDV described herein, or an immunogenic composition described herein provides some protection against COVID-19 caused by or associated with a SARS-CoV-2 Omicron variant. In another specific embodiment, an antibody induced by a recombinant NDV described herein, or an immunogenic composition described herein binds to a SARS-CoV-2 spike protein Omicron variant. In another specific embodiment, an antibody induced by a recombinant NDV described herein, or an immunogenic composition described herein may neutralize a SARS-CoV-2 Omicron variant, as assessed by an assay described herein or known to one of skill in the art. In some embodiments, the immune response resulting from administration of a recombinant NDV described herein, or an immunogenic composition described herein provides some protection against COVID-19 caused by or associated a SARS-CoV-2 Omicron variant, as assessed by an assay described herein or known to one of skill in the art.

In some embodiments, a recombinant NDV described herein or an immunogenic composition described herein, or a combination therapy described herein is administered to a patient to prevent the onset of one, two or more symptoms of COVID-19. In a specific embodiment, the administration of a recombinant NDV described herein or an immunogenic composition described herein, or a combination therapy described herein to a subject prevents the onset or development of one, two or more symptoms of COVID-19, or reduces the severity of one, two or more symptoms of COVID-19. In a specific embodiment, the administration of a recombinant NDV described herein or an immunogenic composition described herein, or a combination therapy described herein to a subject prevents the onset or development of one, two or more symptoms of COVID-19 and reduces the severity of one, two or more symptoms of COVID-19. Symptoms of COVID-19 include congested or runny nose, cough, fever, sore throat, fatigue, headache, wheezing, rapid or shallow breathing or difficulty breathing, bluish color the skin due to lack of oxygen, chills, muscle pain, loss of taste and/or smell, nausea, vomiting, and diarrhea.

In one embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents the spread of SARS-CoV-2 infection. In a specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents the spread of SARS-CoV-2 Omicron variant virus infection. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents hospitalization. In another specific embodiment, the administration of a recombinant NDV described herein or an immunogenic composition described herein, or a combination therapy described herein to a subject prevents COVID-19. In another specific embodiment, the administration of a recombinant NDV described herein or an immunogenic composition described herein, or a combination therapy described herein to a subject prevents moderate or severe COVID-19. In another embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject reduces the length of hospitalization. In another embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject reduces the likelihood of intubation. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents recurring SARS-CoV-2 infections. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents recurring SARS-CoV-2 Omicron virus infections. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents asymptomatic SARS-CoV-2 infection. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject prevents asymptomatic SARS-CoV-2 Omicron variant virus infection.

In another specific embodiment, the administration of a recombinant NDV described herein, or an immunogenic composition described herein induces antibodies to SARS-CoV-2 spike protein. In another specific embodiment, the administration of a recombinant NDV described herein, or an immunogenic composition described herein induces antibodies specific to SARS-CoV-2 spike protein. An antibody (ies) may specifically bind to a SARS-CoV-2 Omicron variant spike protein if it binds to the SARS-CoV-2 Omicron variant spike protein with a higher affinity than a spike protein that is not a SARS-CoV-2 Omicron variant spike protein, or other unrelated protein. For example, an antibody (ies) specific for SARS-CoV-2 Omicron variant spike protein may bind to a SARS-CoV-2 Omicron variant spike protein with a 10 fold higher for affinity than the antibody (ies) binds to a spike protein that is not a SARS-CoV-2 Omicron spike protein, or other unrelated protein. In some embodiments, the administration of a recombinant NDV described herein, or an immunogenic composition induces a higher concentration of antibody (ies) that specifically bind to a SARS-CoV-2 Omicron variant spike protein than the administration of a recombinant NDV comprising a chimeric F protein comprising the ectodomain of SEQ ID NO: 104, and the transmembrane and cytoplasmic domains of NDV F protein, such as described in Example 5.

In another specific embodiment, the administration of a recombinant NDV described herein, or an immunogenic composition described herein induces both mucosal and systemic antibodies to SARS-CoV-2 Omicron spike protein (e.g., neutralizing antibodies). In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject induces neutralizing IgG antibody to SARS-CoV-2 Omicron variant spike protein. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject induces IgG antibody to SARS-CoV-2 Omicron variant spike protein at a level that is considerate moderate to high in an ELISA approved by the FDA for measuring antibody in a patient specimen.

In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject induces neutralizing antibody to SARS-CoV-2 spike protein. In another specific embodiment, the administration of a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein to a subject induces neutralizing antibody to SARS-CoV-2 Omicron variant spike protein.

In some embodiments, a recombinant NDV described herein or a composition thereof, or a combination therapy described herein is administered to a subject predisposed or susceptible to COVID-19.

In certain embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to a human. In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to a human infant. In another specific embodiment, the subject is a human infant six months old or older. In other embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to a human toddler. In other embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to a human child. In other embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to a human adult. In yet other embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to an elderly human.

In a specific embodiment, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) in close contact with an individual with increased risk of COVID-19 or SARS-CoV-2 infection (e.g., a SARS-CoV-2 Omicron variant infection). In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) with a condition that increases susceptibility to SARS-CoV-2 complications or for which SARS-CoV-2 increases complications associated with the condition. Examples of conditions that increase susceptibility to SARS-CoV-2 complications or for which SARS-CoV-2 increases complications associated with the condition include conditions that affect the lung, such as cystic fibrosis, chronic obstructive pulmonary disease (COPD), emphysema, asthma, or bacterial infections (e.g., infections caused by Haemophilus influenzae, Streptococcus pneumoniae, Legionella pneumophila, and Chlamydia trachomatous); cardiovascular disease (e.g., congenital heart disease, congestive heart failure, and coronary artery disease); and endocrine disorders (e.g., diabetes).

In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) that resides in a group home, such as a nursing home. In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) that works in, or spends a significant amount of time in, a group home, e.g., a nursing home. In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) that is a health care worker (e.g., a doctor or nurse). In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered a subject (e.g., a human subject) that is a smoker.

In some embodiments, a recombinant NDV described herein, an immunogenic composition described herein, or a combination therapy described herein is administered to: (1) a subject (e.g., a human subject) who can transmit SARS-CoV-2 to those at high risk for complications, such as, e.g., members of households with high-risk subjects, including households that will include human infants (e.g., infants younger than 6 months), (2) a subject coming into contact with human infants (e.g., infants less than 6 months of age), (3) a subject who will come into contact with subjects who live in nursing homes or other long-term care facilities, (4) a subject who is or will come into contact with an elderly human, or (5) a subject who will come into contact with subjects with long-term disorders of the lungs, heart, or circulation; individuals with metabolic diseases (e.g., diabetes) or subjects with weakened immune systems (including immunosuppression caused by medications, malignancies such as cancer, organ transplant, or HIV infection).

5.5.2 Dosage and Frequency

The amount of a recombinant NDV or an immunogenic composition described herein, which will be effective in the prevention of COVID-19, or immunization against SARS-CoV-2 (e.g., SARS-CoV-2 Omicron variant) will depend on the route of administration, the general health of the subject, etc. Suitable dosage ranges of a recombinant NDV for administration are generally about 10⁴to about 10¹²EID50, and can be administered to a subject once, twice, three, four or more times with intervals as often as needed. In some embodiments, a recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 10⁴to about 10¹²EID50. In some embodiments, a dose of about 10⁴to about 10¹²EID50 of a composition comprising live recombinant NDV is administered to a subject (e.g., human). In a specific embodiment, a live recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 10⁷to 10⁹EID50. In another specific embodiment, a dose of 10⁷to 10⁹EID50 of a composition comprising a live recombinant NDV described herein is administered to a subject (e.g., a human). In a specific embodiment, a live recombinant NDV described herein is administered to a subject (e.g., human) at a dose of about 10⁸to about 10⁹EID50. In a specific embodiment, a live recombinant NDV described herein is administered to a subject (e.g., human) at a dose of about 10⁷to about 10⁸EID50.

In certain embodiments, a recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 1 to 15 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In some embodiments, a recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 1 to 10 micrograms of SARS-CoV-Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of a SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In a specific embodiment, a recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 1 microgram, 3 micrograms, or 10 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In another specific embodiment, a recombinant NDV described herein is administered to a subject (e.g., human) at a dose of 4 micrograms, 5 micrograms, 6 micrograms, 7 micrograms, 8 micrograms or 9 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein.

In certain embodiments, a composition described herein is administered to a subject (e.g., human) at a dose of 1 to 15 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In some embodiments, an immunogenic composition described herein is administered to a subject (e.g., human) at a dose of 1 to 10 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In a specific embodiment, an immunogenic composition NDV described herein is administered to a subject (e.g., human) at a dose of 1 microgram, 3 micrograms, or 10 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein. In another specific embodiment, an immunogenic composition described herein is administered to a subject (e.g., human) at a dose of 4 micrograms, 5 micrograms, 6 micrograms, 7 micrograms, 8 micrograms or 9 micrograms of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., the ectodomain of a SARS-CoV-2 Omicron variant spike protein), a derivative of SARS-CoV-2 Omicron variant spike protein or a portion thereof (e.g., a derivative of the ectodomain of a SARS-CoV-2 Omicron variant spike protein), or a chimeric F protein.

In some embodiments, an immunogenic composition described herein is administered to a subject (e.g., human) at a dose of 10 to 100 micrograms of inactivated recombinant NDV described herein. In some embodiments, an immunogenic composition described herein is administered to a subject (e.g., human) at a dose of 50 to 100 micrograms of inactivated recombinant NDV described herein. In specific embodiments, an immunogenic composition described herein is administered to a subject (e.g., human) at a dose of 10 micrograms, 25 micrograms, 30 micrograms, 50 micrograms, 75 micrograms, or 100 micrograms of inactivated recombinant NDV described herein.

In certain embodiments, dosages of a recombinant NDV described herein, or a composition described herein similar to those currently being used in clinical trials for NDV are administered to a subject.

In certain embodiments, a recombinant NDV or an immunogenic composition described herein is administered to a subject as a single dose followed by a second dose 1 to 6 weeks, 1 to 5 weeks, 1 to 4 weeks, 1 to 3 weeks, 1 to 2 weeks, 6 to 12 weeks, 3 to 6 months, 6 to 9 months, 6 to 12 months, or 6 to 9 months later. In some embodiments, a recombinant NDV or an immunogenic composition described herein is administered to a subject as a single dose followed by a second dose about 3 to about 6 months, about 6 to about 9 months, or about 6 to about 12 months later. In specific embodiments, a recombinant NDV or an immunogenic composition described herein is administered to a subject as a single dose followed by a second dose about 6 months, about 9 months, or about 12 months later. In accordance with these embodiments, booster inoculations may be administered to the subject at 3 to 6 month or 6 to 12 month intervals following the second inoculation. In accordance with these embodiments, booster inoculations may be administered to the subject at about 6 months following the second inoculation. In certain embodiments, a subject is administered one or more boosters. The recombinant NDV used for each booster may be the same or different. The two, three, four, or more recombinant NDVs described herein, or immunogenic compositions described herein administered to the subject may administered by the same or different routes. For example, one recombinant NDV or an immunogenic composition described herein may be administered to the subject intranasally and another recombinant NDV described herein or immunogenic composition described herein may be administered to the subject intramuscularly. In another example, one recombinant NDV herein or an immunogenic composition described herein may be administered to the subject intramuscularly and another recombinant NDV described herein or immunogenic composition described herein may be administered to the subject intranasally. In another example, one recombinant NDV described herein or an immunogenic composition described herein may be administered to the subject intranasally or intramuscularly and another recombinant NDV or immunogenic composition described herein may be administered to the subject by the same route of administration.

In certain embodiments, administration of the same recombinant NDV or immunogenic composition may be repeated and the administrations may be separated by at least 7 days, 10 days, 14 days, 15 days, 21 days, 28 days, 30 days, 45 days, 2 months, 75 days, 3 months, or at least 6 months. In other embodiments, administration of the same recombinant NDV or immunogenic composition may be repeated and the administrations may be separated by 1 to 14 days, 1 to 7 days, 7 to 14 days, 1 to 30 days, 15 to 30 days, 15 to 45 days, 15 to 75 days, 15 to 90 days, 1 to 3 months, 3 to 6 months, 3 to 12 months, or 6 to 12 months. In some embodiments, a first recombinant NDV or immunogenic composition is administered to a subject followed by the administration of a second recombinant NDV or a immunogenic composition. In some embodiments, the first and second recombinant NDV are different from each other. In certain embodiments, a first immunogenic composition is administered to a subject as a priming dose and after a certain period (e.g., 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 9 months, 12 months, 1-6 months, 6-9 months, or 9-12 months) a booster dose of a second immunogenic composition is administered.

In some embodiments, a regimen, such as described in Example 5, or similar to a regimen described in Example 5, is used to administer an immunogenic composition described herein.

In certain embodiments, a first dose of a recombinant NDV described herein or an immunogenic composition described herein may be administered to a subject (e.g., a human) and a second dose of the recombinant NDV or immunogenic composition may be administered to the subject 3 to 6 weeks later. In some embodiments, a first dose of a recombinant NDV described herein or an immunogenic composition described herein may be administered to a subject (e.g., a human) and a second dose of the recombinant NDV or immunogenic composition may be administered to the subject about 21 days later. In some embodiments, a first dose of a recombinant NDV described herein or immunogenic composition may be administered to a subject (e.g., a human) and a second dose of the recombinant NDV or an immunogenic composition described herein may be administered to the subject about 3-6 months later. In some embodiments, a first dose of a recombinant NDV described herein or an immunogenic composition described herein may be administered to a subject (e.g., a human) and a second dose of the recombinant NDV or immunogenic composition may be administered to the subject about 6-12 months later. In some embodiments, the subject is administered two or more boosters of the recombinant NDV.

In some embodiments, a recombinant NDV described herein or an immunogenic composition described is administered as a booster to a subject previously vaccinated with a COVID-19 vaccine. The COVID-9 vaccine may be an mRNA vaccine, a vector vaccine (e.g., a virus vector vaccine), or a protein subunit-based vaccine. The COVID-19 vaccine may be Pfizer's COVID-19 vaccine (BNT162b2), Pfizer-BioNTech bivalent COVID-19 vaccine, Moderna's COVID-19 vaccine (mRNA-1273), Moderna's bivalent COVID-19 vaccine, AstraZeneca's COVID-19 vaccine, Johnson & Johnson's COVID-19 (Ad26.COV2.S), SinoVac's COVID-19 vaccine, SinoPharm's COVID-19 vaccine, Bharat's COVID-19 vaccine, Novavax COVID-19 Vaccine, Adjuvanted, Cansino's COVID-19 vaccine, or another COVID-19 vaccine. In a specific embodiment, the subject was previously vaccinated with a COVID-19 other than an immunogenic composition described herein. In a specific embodiment, the subject was previously vaccinated with a COVID-19 other than a recombinant NDV-based COVID-19 vaccine.

In some embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered as a booster to a subject previously infected with SARS-CoV-2. In certain embodiments, a recombinant NDV described herein or an immunogenic composition described herein is administered as a booster to a subject previously diagnosed with a SARS-CoV-2 infection.

In certain embodiments, a recombinant NDV or an immunogenic composition described herein is administered to a subject in combination with one or more additional therapies, such as a therapy described in Section 5.5.3, infra. The dosage of the other one or more additional therapies will depend upon various factors including, e.g., the therapy, the route of administration, the general health of the subject, etc. and should be decided according to the judgment of a medical practitioner. In specific embodiments, the dose of the other therapy is the dose and/or frequency of administration of the therapy recommended for the therapy for use as a single agent is used in accordance with the methods disclosed herein. Recommended doses for approved therapies can be found in the Physician's Desk Reference.

In certain embodiments, a recombinant NDV or an immunogenic composition described herein is administered to a subject concurrently with the administration of one or more additional therapies. In some embodiments, an immunogenic composition comprising recombinant NDV and a pharmaceutical composition comprising one or more additional therapies may be administered concurrently, or before or after each other. In certain embodiments, the immunogenic composition and pharmaceutical composition are administered concurrently to the subject, or within 1 minute, 2 minutes, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 30 minutes, 45 minutes, 60 minutes, 1.5 hours, 2 hours, 3 hours, 4 hours, 5 hours, or 6 hours of each other. In certain embodiments, the first and second pharmaceutical compositions are administered to the subject within 7 days, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 8 weeks or 12 weeks of each other. In certain embodiments, the immunogenic composition and pharmaceutical compositions are administered to the subject within 3-6 months, 6-9 months, 6-12 months, or 3 months, 4 months, 6 months, 9 months, or 12 months of each other.

5.5.3 Additional Therapies

Additional therapies that can be used in a combination with a recombinant NDV described herein or a composition thereof include, but are not limited to, acetaminophen, ibuprofen, throat lozenges, cough suppressants, inhalers, antibiotics, monoclonal antibodies, and oxygen. In a specific embodiment, the additional therapy is a second recombinant NDV described herein. Additional therapies (e.g., acetaminophen, ibuprofen, throat lozenges, cough suppressants, inhalers, antibiotics, monoclonal antibodies, and oxygen) may also be used in combination with a composition described herein. In a specific embodiment, the additional therapy is a monoclonal antibody, such as sotrovimab. In another specific embodiment, the additional therapy(ies) may include remdesivir, sotrovimab, bamlanivimab plus etesevimab (AIIa), casirivimab plus imdevimab (AIIa), dexamethasone, tocilizumab, oxygen, or a combination thereof.

5.5.4 Other Uses of Recombinant NDV

In some embodiments, a recombinant NDV described herein, or an immunogenic composition described herein is administered to a non-human subject (e.g., a mouse, rat, etc.) and the antibodies generated in response to the polypeptide are isolated. In some embodiments, a polynucleotide described herein, a nucleotide sequence described herein, or a vector described herein is administered to a non-human subject (e.g., a mouse, rat, etc.) and the antibodies generated in response to the polypeptide are isolated. In some embodiments, a recombinant protein described herein is administered to a non-human subject (e.g., a mouse, rat, etc.) and the antibodies generated in response to the polypeptide are isolated. Hybridomas may be made and monoclonal antibodies produced as known to one of skill in the art. The antibodies may also be optimized. In some embodiments, the antibodies produced are humanized or chimerized. In certain embodiments, the non-human subject produces human antibodies. The antibodies produced using a recombinant NDV described herein, or immunogenic composition described herein may be optimized, using techniques known to one of skill in the art. In a specific embodiment, antibodies generated using a recombinant NDV described herein, or an immunogenic composition described herein may be used to prevent, treat or prevent and treat COVID-19.

In some embodiments, a recombinant NDV described herein is used in an immunoassay (e.g., an ELISA assay) known to one of skill in the art or described herein to detect antibody specific for SARS-CoV-2 Omicron variant spike protein. In one embodiment, method for detecting the presence of antibody specific to SARS-CoV-2 Omicron variant spike protein, comprising contacting a specimen with the recombinant NDV described herein in an immunoassay (e.g., an ELISA). In some embodiments, a recombinant protein described herein is used in an immunoassay (e.g., an ELISA assay) known to one of skill in the art or described herein to detect antibody specific for SARS-CoV-2 Omicron variant spike protein. In one embodiment, method for detecting the presence of antibody specific to SARS-CoV-2 Omicron variant spike protein, comprising contacting a specimen with a recombinant protein described herein in an immunoassay (e.g., an ELISA). In some embodiments, the specimen is a biological specimen. In a specific embodiment, the biological specimen is blood, plasma or sera from a subject (e.g., a human subject). In other embodiments, the specimen is an antibody or antisera.

5.6 BIOLOGICAL ASSAYS

In a specific embodiment, one, two or more of the assays described in Section 6 may be used to characterize a recombinant NDV described herein, a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., the ectodomain or receptor binding domain of the SARS-CoV-2 Omicron variant spike protein), a recombinant protein described herein, or a chimeric F protein. In another specific embodiment, assays known to one of skill in the art may be used to characterize immunoglobulin samples from a subject (e.g., a human subject) administered a recombinant NDV described herein or a composition described herein. For example, the IgG titer and microneutralization of IgG induced may be assessed as described herein or known to one of skill in the art. In some embodiments, a subject administered a recombinant NDV described herein or a composition described herein is assessed for anti-NDV antibodies as well as anti-SARS-CoV-2 Omicron variant spike protein antibodies. In some embodiments, a subject administered a recombinant NDV described herein or a composition described herein is assessed for anti-SARS-CoV-2 spike protein antibodies that cross-react with the spike protein of SARS-CoV-2 variants other than Omicron.

5.6.1 In Vitro Viral Assays

Viral assays include those that indirectly measure viral replication (as determined, e.g., by plaque formation) or the production of viral proteins (as determined, e.g., by western blot analysis) or viral RNAs (as determined, e.g., by RT-PCR or northern blot analysis) in cultured cells in vitro using methods which are well known in the art.

Growth of the recombinant NDVs described herein can be assessed by any method known in the art or described herein (e.g., in cell culture (e.g., cultures of BSTT7 or embryonated chicken cells) (see, e.g., Section 6). Viral titer may be determined by inoculating serial dilutions of a recombinant NDV described herein into cell cultures (e.g., BSTT7 or embryonated chicken cells), chick embryos (e.g., 9 to 11 day old embryonated eggs), or live non-human animals. After incubation of the virus for a specified time, the virus is isolated using standard methods. Physical quantitation of the virus titer can be performed using PCR applied to viral supernatants (Quinn & Trevor, 1997; Morgan et al., 1990), hemagglutination assays, tissue culture infectious doses (TCID50) or egg infectious doses (EID50).

Incorporation of nucleotide sequences encoding a heterologous peptide or protein (e.g., a transgene into the genome of a recombinant NDV described herein can be assessed by any method known in the art or described herein (e.g., in cell culture, an animal model or viral culture in embryonated eggs)). For example, viral particles from cell culture of the allantoic fluid of embryonated eggs can be purified by centrifugation through a sucrose cushion and subsequently analyzed for protein expression by Western blotting using methods well known in the art. In a specific embodiment, a method described in Section 6, infra, is used to assess the incorporation of a transgene into the genome of a recombinant NDV.

Immunofluorescence-based approaches may also be used to detect virus and assess viral growth. Such approaches are well known to those of skill in the art, e.g., fluorescence microscopy and flow cytometry. Methods for flow cytometry, including fluorescence activated cell sorting (FACS), are available (see, e.g., Owens, et al. (1994) Flow Cytometry Principles for Clinical Laboratory Practice, John Wiley and Sons, Hoboken, NJ; Givan (2001) Flow Cytometry, 2^nded.; Wiley-Liss, Hoboken, NJ; Shapiro (2003) Practical Flow Cytometry, John Wiley and Sons, Hoboken, NJ). Fluorescent reagents suitable for modifying nucleic acids, including nucleic acid primers and probes, polypeptides, and antibodies, for use, e.g., as diagnostic reagents, are available (Molecular Probesy (2003) Catalogue, Molecular Probes, Inc., Eugene, OR; Sigma-Aldrich (2003) Catalogue, St. Louis, MO).

Standard methods of histology of the immune system are described (see, e.g., Muller-Harmelink (ed.) (1986) Human Thymus: Histopathology and Pathology, Springer Verlag, New York, NY; Hiatt, et al. (2000) Color Atlas of Histology, Lippincott, Williams, and Wilkins, Phila, PA; Louis, et al. (2002) Basic Histology: Text and Atlas, McGraw-Hill, New York, NY).

5.6.2 Interferon Assays

IFN induction and release induced by a recombinant NDV described herein or a composition described herein may be determined using techniques known to one of skill in the art. For example, the amount of IFN induced in cells following infection with a recombinant NDV described herein may be determined using an immunoassay (e.g., an ELISA or Western blot assay) to measure IFN expression or to measure the expression of a protein whose expression is induced by IFN. Alternatively, the amount of IFN induced may be measured at the RNA level by assays, such as Northern blots and quantitative RT-PCR, known to one of skill in the art. In specific embodiments, the amount of IFN released may be measured using an ELISPOT assay. Further, the induction and release of cytokines and/or interferon-stimulated genes may be determined by, e.g., an immunoassay or ELISPOT assay at the protein level and/or quantitative RT-PCR or northern blots at the RNA level.

5.6.3 Toxicity Studies

In some embodiments, the recombinant NDVs described herein or compositions thereof, or combination therapies described herein are tested for cytotoxicity in mammalian, preferably human, cell lines. In certain embodiments, cytotoxicity is assessed in one or more of the following non-limiting examples of cell lines: U937, a human monocyte cell line; primary peripheral blood mononuclear cells (PBMC); Huh7, a human hepatoblastoma cell line; HL60 cells, HT1080, HEK 293T and 293H, MLPC cells, human embryonic kidney cell lines; human melanoma cell lines, such as SkMel2, SkMel-119 and SkMel-197; THP-1, monocytic cells; a HeLa cell line; and neuroblastoma cells lines, such as MC-IXC, SK-N-MC, SK-N-MC, SK-N-DZ, SH-SY5Y, and BE(2)-C. In some embodiments, the ToxLite assay is used to assess cytotoxicity. Many assays well-known in the art can be used to assess viability of cells or cell lines and, thus, determine the cytotoxicity.

Many assays well-known in the art can be used to assess viability of cells or cell lines following infection with a recombinant NDV described herein or a composition thereof, and, thus, determine the cytotoxicity of the recombinant NDV or composition thereof. For example, cell proliferation can be assayed by measuring Bromodeoxyuridine (BrdU) incorporation, (³H) thymidine incorporation, by direct cell count, or by detecting changes in transcription, translation or activity of known genes such as proto-oncogenes (e.g., fos, myc) or cell cycle markers (Rb, cdc2, cyclin A, D1, D2, D3, E, etc.). The levels of such protein and mRNA and activity can be determined by any method well known in the art. For example, protein can be quantitated by known immunodiagnostic methods such as ELISA, Western blotting or immunoprecipitation using antibodies, including commercially available antibodies. mRNA can be quantitated using methods that are well known and routine in the art, for example, using northern analysis, RNase protection, or polymerase chain reaction in connection with reverse transcription. Cell viability can be assessed by using trypan-blue staining or other cell death or viability markers known in the art. In a specific embodiment, the level of cellular ATP is measured to determined cell viability. In preferred embodiments, a recombinant NDV described herein or composition thereof does not kill healthy (i.e., non-cancerous) cells.

In specific embodiments, cell viability may be measured in three-day and seven-day periods using an assay standard in the art, such as the CellTiter-Glo Assay Kit (Promega) which measures levels of intracellular ATP. A reduction in cellular ATP is indicative of a cytotoxic effect. In another specific embodiment, cell viability can be measured in the neutral red uptake assay. In other embodiments, visual observation for morphological changes may include enlargement, granularity, cells with ragged edges, a filmy appearance, rounding, detachment from the surface of the well, or other changes.

The recombinant NDVs described herein or compositions described herein, or combination therapies can be tested for in vivo toxicity in animal models. For example, animals are administered a range of pfu of a recombinant NDV described herein, and subsequently, the animals are monitored over time for various parameters, such as one, two or more of the following: lethality, weight loss or failure to gain weight, and levels of serum markers that may be indicative of tissue damage (e.g., creatine phosphokinase level as an indicator of general tissue damage, level of glutamic oxalic acid transaminase or pyruvic acid transaminase as indicators for possible liver damage). These in vivo assays may also be adapted to test the toxicity of various administration mode and regimen in addition to dosages. See, e.g., the Examples, infra, for assays that may be used to assess toxicity.

The toxicity, efficacy or both of a recombinant NDV described herein or a composition thereof, or a combination therapy described herein can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Therapies that exhibit large therapeutic indices are preferred.

The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage of the therapies for use in subjects.

5.6.4 Biological Activity Assays

The recombinant NDVs described herein or compositions described herein, or combination therapies described herein can be tested for biological activity using animal models for inhibiting COVID-19, antibody response to the recombinant NDVs, etc. Such animal model systems include, but are not limited to, rats, mice, hamsters, cotton rats, chicken, cows, monkeys (e.g., African green monkey), pigs, dogs, rabbits, etc.

In a specific embodiment, the recombinant NDVs described herein, compositions described herein, or combination therapies described herein may be tested using animal models for the ability to induce a certain geometric mean titer of antibody (ies) that binds to the SARS-CoV-2 spike protein. An immunoassay, such as an ELISA, or known to one of skill in the art may be used to measure antibody titer. In another specific embodiment, the recombinant NDVs described herein, compositions described herein, or combination therapies described herein may be tested using animal models for the ability to induce antibodies that have neutralizing activity against SARS-CoV-2 spike protein (e.g., SARS-CoV-2 Omicron variant spike protein) in a microneutralization assay. In some embodiments, the recombinant NDVs described herein, compositions described herein, or combination therapies described herein may be tested using animal models for the ability to induce antibodies that neutralize SARS-CoV-2 (e.g., SARS-CoV-2 Omicron virus) in a microneutralization assay. In some embodiments, the recombinant NDVs described herein, compositions described herein, or combination therapies described herein may be tested using animal models for the ability to induce a certain geometric mean titer of antibody (ies) that binds to the SARS-CoV-2 spike protein (e.g., SARS-CoV-2 Omicron variant spike) and neutralizes SARS-CoV-2 (e.g., SARS-CoV-2 Omicron variant) in a microneutralization assay. In some embodiments, the recombinant NDVs described herein or compositions thereof, or combination therapies described herein may be tested using animal models for the ability to induce a certain geometric mean titer of antibody (ies) that binds to the SARS-CoV-2 spike protein (e.g., SARS-CoV-2 Omicron variant spike protein) and neutralizes SARS-CoV-2 (e.g., SARS-CoV-2 Omicron variant) in a microneutralization assay such as described herein. In certain embodiments, the recombinant NDVs described herein, or compositions described herein, or combination therapies described herein may be tested using animal models for the ability to induce a protective immune response. In some embodiments, the recombinant NDVs described herein, or compositions described herein, or combination therapies described herein may be tested using animal models, such as described in Example 5.

In a specific embodiment, a recombinant NDV described herein, a composition described herein, or a combination therapy described herein may be tested in a clinical trial study. In certain embodiments, a recombinant NDV described herein, a composition described herein, or a combination therapy described herein is administered to a human subject. In some embodiments, a human subject administered a recombinant NDV described herein, a composition described herein, or a combination therapy described herein may be assessed for one, two or more, or all of the following may be assessed following administration of a recombinant NDV described herein, or a composition described herein, or a combination therapy described herein: GMT, anti-SARS-CoV-2 spike protein Ig (e.g., IgG, IgA, IgM, etc.), T cell response, NT50 seropositive response, NT80 seropositive response, T cell response, anti-NDV HN antibody, and anti-NDV F antibody.

5.6.5 Expression of Transgene

Assays for testing the expression of SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein in cells infected with a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or chimeric F protein, respectively may be conducted using any assay known in the art, such as, e.g., western blot, immunofluorescence, and ELISA, or any assay described herein. Immunoassays, such as e.g., western blot, immunofluorescence, and ELISA, or another known to one of skill in the art may be used to assess expression of a protein described herein.

In a specific aspect, ELISA is utilized to detect expression of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein in cells infected with a recombinant NDV comprising a packaged genome comprising a transgene that comprises a nucleotide sequence encoding of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein.

In one embodiment, a SARS-CoV-Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein encoded by a packaged genome of a recombinant NDV described herein is assayed for proper folding by testing its ability to bind specifically to an anti-SARS-CoV-2 Omicron variant spike protein using any assay for antibody-antigen interaction known in the art. In another embodiment, a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein encoded by a packaged genome of a recombinant NDV described herein is assayed for proper folding by determination of the structure or conformation of the SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or chimeric F protein, respectively using any method known in the art such as, e.g., NMR, X-ray crystallographic methods, or secondary structure prediction methods, e.g., circular dichroism. Additional assays assessing the conformation and antigenicity of SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), a derivative of a SARS-CoV-2 Omicron variant spike protein or portion thereof (e.g., SARS-CoV-2 Omicron variant spike protein ectodomain or receptor binding domain), or a chimeric F protein may include, e.g., immunofluorescence microscopy, flow cytometry, western blot, and ELISA may be used. Assays such as, e.g., NMR, X-ray crystallographic methods, secondary structure prediction methods, e.g., circular dichroism, or other assays/techniques known to one of skill in the art may be used to assess the structure or conformation of a protein described herein.

5.7 Kits

In one aspect, provided herein is a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of a composition (e.g., an immunogenic compositions) described herein. In a specific embodiment, provided herein is a pharmaceutical pack or kit comprising a container, wherein the container comprises a recombinant NDV described herein. In a specific embodiment, provided herein is a pharmaceutical pack or kit comprising a container, wherein the container comprises an immunogenic composition described herein. The immunogenic composition may be monovalent or multivalent. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

In another embodiment, provided herein is a kit comprising in one or more containers filled with one or more recombinant NDVs described herein. In another embodiment, provided herein is a kit comprising in one or more containers one or more transgenes described herein. In another embodiment, provided herein is a kit comprising in one or more containers one or more nucleotide sequences comprising the genome of NDV and a transgene described herein. In another embodiment, provided herein is a kit comprising, in a container, a vector comprising a transgene described herein.

In another embodiment, provided herein is a kit comprising in one or more containers filled with one or more recombinant proteins described herein or nucleic acid sequence described herein. In another embodiment, provided herein is a kit comprising in one or more containers filled with one or more polynucleotides described herein or nucleic acid sequence described herein. In another embodiment, provided herein is a kit comprising, in a container, a vector comprising a polynucleotide described herein, a nucleotide sequence described herein, or a nucleic acid sequence described herein.

In a specific embodiment, provided herein is a kit comprising, in a container, a nucleotide sequence comprising a transgene described herein and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit. In some embodiments, the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain.

In a specific embodiment, provided herein is a kit comprising, in a container, a vector comprising a nucleotide sequence, wherein the nucleotide sequence comprises a transgene described herein and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit. In some embodiments, the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain.

5.8 Sequences

TABLE 1

cDNA of genome of NDV Strains

SEQ ID

Description
Sequence
NO:

cDNA of
accaaacagagaatccgtgagttacgataaaaggcgaaggagcaattgaagtcgcacggg
SEQ ID

genomic
tagaaggtgtgaatctcgagtgcgagcccgaagcacaaactcgagaaagccttctgccaac
NO: 1

sequence of
atgtcttccgtatttgatgagtacgaacagctcctcgcggctcagactcgccccaatggagct

NDV strain
catggagggggagaaaaagggagtaccttaaaagtagacgtcccggtattcactcttaaca

LaSota
gtgatgacccagaagatagatggagctttgtggtattctgcctccggattgctgttagcgaag

atgccaacaaaccactcaggcaaggtgctctcatatctcttttatgctcccactcacaggtaat

gaggaaccatgttgccCttgcagggaaacagaatgaagccacattggccgtgcttgagatt

gatggctttgccaacggcacgccccagttcaacaataggagtggagtgtctgaagagagag

cacagagatttgcgatgatagcaggatctctccctcgggcatgcagcaacggaaccccgttc

gtcacagccggggcCgaagatgatgcaccagaagacatcaccgataccctggagaggat

cctctctatccaggctcaagtatgggtcacagtagcaaaagccatgactgcgtatgagactg

cagatgagtcggaaacaaggcgaatcaataagtatatgcagcaaggcagggtccaaaaga

aatacatcctctaccccgtatgcaggagcacaatccaactcacgatcagacagtctcttgcag

tccgcatctttttggttagcgagctcaagagaggccgcaacacggcaggtggtacctctactt

attataacctggtaggggacgtagactcatacatcaggaataccgggcttactgcattcttctt

gacactcaagtacggaatcaacaccaagacatcagcccttgcacttagtagcctctcaggcg

acatccagaagatgaagcagctcatgcgtttgtatcggatgaaaggagataatgcgccgtac

atgacattacttggtgatagtgaccagatgagctttgcgcctgccgagtatgcacaactttact

cctttgccatgggtatggcatcagtcctagataaaggtactgggaaataccaatttgccaggg

actttatgagcacatcattctggagacttggagtagagtacgctcaggctcagggaagtagc

attaacgaggatatggctgccgagctaaagctaaccccagcagcaaGgaGgggcctggc

agctgctgcccaacgggtctccgaGgaGaccagcagcataGacatgcctactcaacaag

tcggagtcctcactgggcttagcgagggggggtcccaagctctacaaggcggatcgaata

gatcgcaagggcaaccagaagccggggatggggagacccaattcctggatctgatgaga

gcggtagcaaatagcatgagggaggcgccaaactctgcacagggcactccccaatcggg

gcctcccccaactcctgggccatoccaagataacgacaccgactgggggtattgatggaca

aaacccagcctgcttccacaaaaacatcccaatgccctcacccgtagtcgacccctcgatttg

cggctctatatgaccacaccctcaaacaaacatccccctotttcctccctccccctgctgtaca

actAcgTacgccctagataccacaggcacaatgcggctcactaacaatcaaaacagagc

cgagggaattagaaaaaagtacgggtagaagagggatattcagagatcagggcaagtctc

ccgagtctctgctctctcctctacctgatagaccaggacaaacatggccacctttacagatgc

agagatcgacgagctatttgagacaagtggaactgtcattgacaacataattacagcccagg

gtaaaccagcagagactgttggaaggagtgcaatcccacaaggcaagaccaaggtgctga

gcgcagcatgggagaagcatgggagcatccagccaccggccagtcaagacaaccccgat

cgacaggacagatctgacaaacaaccatccacacccgagcaaacgaccccgcatgacag

cccgccggccacatccgccgaccagccccccacccaggccacagacgaagccgtcgac

acacagCtcaggaccggagcaagcaactctctgctgttgatgcttgacaagctcagcaata

aatcgtccaatgctaaaaagggcccatggtcgagcccccaagaggggaatcaccaacgtc

cgactcaacagcaggggagtcaacccagtcgcggaaacagtcaggaaagaccgcagaa

ccaagtcaaggccgcccctggaaaccagggcacagacgtgaacacagcatatcatggac

aatgggaggagtcacaactatcagctggtgcaacccctcatgctctccgatcaaggcagag

ccaagacaatacccttgtatctgcggatcatgtccagccacctgtagactttgtgcaagcgat

gatgtctatgatggaggcgatatcacagagagtaagtaaggttgactatcagctagatcttgtc

ttgaaacagacatcctccatccctatgatgoggtccgaaatccaacagctgaaaacatctgtt

gcagtcatggaagccaacttgggaatgatgaagattctggatcccggttgtgccaacatttca

tctctgagtgatctacgggcagttgcccgatctcacccggttttagtttcaggccctggagacc

cctctccctatgtgacacaaggaggcgaaatggcacttaataaactttcgcaaccagtgcca

catccatctgaattgattaaacccgccactgcatgcgggcctgatataggagtggaaaagga

cactgtccgtgcattgatcatgtcacgcccaatgcacccgagttcttcagccaagctcctaag

caagttagatgcagccgggtcgatcgaggaaatcaggaaaatcaagcgccttgctctaaat

ggctaattactactgccacacgtagcgggtccctgtccactcggcatcacacggaatctgca

ccgagttcccccccgcGgacccaaggtccaactctccaagcggcaatcctctctcgcttcct

cagccccactgaatgAtcgcgtaaccgtaattaatctagctacatttaagattaagaaaaaat

acgggtagaattggagtgccccaattgtgccaagatggactcatctaggacaattgggctgt

actttgattctgcccattcttctagcaacctgttagcatttccgatcgtcctacaagAcacagga

gatgggaagaagcaaatcgccccgcaatataggatccagcgccttgacttgtggactgata

gtaaggaggactcagtattcatcaccacctatggattcatctttcaagttgggaatgaagaagc

cacCgtcggcatgatcgatgataaacccaagcgcgagttactttccgctgcgatgctctgcc

taggaagcgtcccaaataccggagaccttattgagctggcaagggcctgtctcactatgata

gtcacatgcaagaagagtgcaactaatactgagagaatggttttctcagtagtgcaggcacc

ccaagtgctgcaaagctgtagggttgtggcaaacaaatactcatcagtgaatgcagtcaagc

acgtgaaagcgccagagaagattcccgggagtggaaccctagaatacaaggtgaactttgt

ctccttgactgtggtaccgaagaGggatgtctacaagatcccagctgcagtattgaaggtttc

tggctcgagtctgtacaatcttgcgctcaatgtcactattaatgtggaggtagacccgaggagt

cctttggttaaatctCtgtctaagtctgacagcggatactatgctaacctcttcttgcatattgga

cttatgaccacTgtagataggaaggggaagaaagtgacatttgacaagctggaaaagaaa

ataaggagccttgatctatctgtcgggctcagtgatgtgctcgggccttccgtgttggtaaaag

caagaggtgcacggactaagcttttggcacctttcttctctagcagtgggacagcctgctatc

ccatagcaaatgcttctcctcaggtggccaagatactctggagtcaaaccgcgtgcctgcgg

agcgttaaaatcattatccaagcaggtacccaacgcgctgtcgcagtgaccgccgaccacg

aggttacctctactaagctggagaaggggcacacccttgccaaatacaatccttttaagaaat

aagctgcgtctctgagattgcgctccgcccactcacccagatcatcatgacacaaaaaacta

atctgtcttgattatttacagttagtttacctgtctatcaagttagaaaaaacacgggtagaagatt

ctggatcccggttggcgccctccaggtgcaagatgggctccagaccttctaccaagaaccc

agcacctatgatgctgactatccgggttgcgctggtactgagttgcatctgtccggcaaactc

cattgatggcaggcctcttgcagctgcaggaattgtggttacaggagacaaagccgtcaaca

tatacacctcatcccagacaggatcaatcatagttaagctcctcccgaatctgcccaaggata

aggaggcatgtgcgaaagcccccttggatgcatacaacaggacattgaccactttgctcacc

ccccttggtgactctatccgtaggatacaagagtctgtgactacatctggaggggggagaca

ggggcgccttataggcgccattattggcggtgtggctcttggggttgcaactgccgcacaaa

taacagcggccgcagctctgatacaagccaaacaaaatgctgccaacatcctccgacttaaa

gagagcattgccgcaaccaatgaggctgtgcatgaggtcactgacggattatcgcaactag

cagtggcagttgggaagatgcagcagtttgttaatgaccaatttaataaaacagctcaggaat

tagactgcatcaaaattgcacagcaagttggtgtagagctcaacctgtacctaaccgaattga

ctacagtattcggaccacaaatcacttcacctgctttaaacaagctgactattcaggcactttac

aatctagctggtggaaatatggattacttattgactaagttaggtgtagggaacaatcaactca

gctcattaatcggtagcggcttaatcaccggtaaccctattctatacgactcacagactcaact

cttgggtatacaggtaactctaccttcagtcgggaacctaaataatatgcgtgccacctacttg

gaaaccttatccgtaagcacaaccaggggatttgcctcggcacttgtcccAaaagtggtga

cacaggtcggttctgtgatagaagaacttgacacctcatactgtatagaaactgacttagattta

tattgtacaagaatagtaacgttccctatgtcccctggtatttattcctgcttgagcggcaatacg

tcggcctgtatgtactcaaagaccgaaggcgcacttactacaccatacatgactatcaaaggt

tcagtcatcgccaactgcaagatgacaacatgtagatgtgtaaaccccccgggtatcatatcg

caaaactatggagaagccgtgtctctaatagataaacaatcatgcaatgttttatccttaggcg

ggataactttaaggctcagtggggaattcgatgtaacttatcagaagaatatctcaatacaaga

ttctcaagtaataataacaggcaatcttgatatctcaactgagcttgggaatgtcaacaactcg

atcagtaatgctttgaataagttagaggaaagcaacagaaaactagacaaagtcaatgtcaa

actgactagcacatctgctctcattacctatatcgttttgactatcatatctcttgtttttggtata

cttagcctgattctagcatgctacctaatgtacaagcaaaaggcgcaacaaaagaccttattatgg

cttgggaataatactctagatcagatgagagccactacaaaaatgtgaacacagatgaggaa

cgaaggtttccctaatagtaatttgtgtgaaagttctggtagtctgtcagttcagagagttaaga

aaaaactaccggttgtagatgaccaaaggacgatatacgggtagaacggtaagagaggcc

gcccctcaattgcgagccaggcttcacaacctccgttctaccgcttcaccgacaacagtcctc

aatcatggaccgcgccgttagccaagttgcgttagagaatgatgaaagagaggcaaaaaat

acatggcgcttgatattccggattgcaatcttattcttaacagtagtgaccttggctatatctgta

gcctcccttttatatagcatgggggctagcacacctagcgatcttgtaggcataccgactagg

atttccagggcagaagaaaagattacatctacacttggttccaatcaagatgtagtagatagg

atatataagcaagtggcccttgagtctccgttggcattgttaaatactgagaccacaattatgaa

cgcaataacatctctctcttatcagattaatggagctgcaaacaacagtgggggggggcac

ctatccatgacccagattatataggggggataggcaaagaactcattgtagatgatgctagtg

atgtcacatcattctatccctctgcatttcaagaacatctgaattttatcccggcgcctactacag

gatcaggttgcactcgaataccctcatttgacatgagtgctacccattactgctacacccataat

gtaatattgtctggatgcagagatcactcacattcatatcagtatttagcacttggtgtgctccg

gacatctgcaacagggagggtattcttttctactctgcgttccatcaacctggacgacaccca

aaatcggaagtcttgcagtgtgagtgcaactcccctgggttgtgatatgctgtgctcgaaagt

cacggagacagaggaagaagattataactcagctgtccctacgcggatggtacatgggag

gttagggttcgacggccagtaccacgaaaaggacctagatgtcacaacattattcggggact

gggtggccaactacccaggagtagggggtggatcttttattgacagccgcgtatggttctca

gtctacggagggttaaaacccaattcacccagtgacactgtacaggaagggaaatatgtgat

atacaagcgatacaatgacacatgcccagatgagcaagactaccagattcgaatggccaag

tcttcgtataagcctggacggtttggtgggaaacgcatacagcaggctatcttatctatcaagg

tgtcaacatccttaggcgaagacccggtactgactgtaccgcccaacacagtcacactcatg

ggggccgaaggcagaattctcacagtagggacatctcatttcttgtatcaacgagggtcatca

tacttctctcccgcgttattatatcctatgacagtcagcaacaaaacagccactcttcatagtcct

tatacattcaatgccttcactcggccaggtagtatcccttgccaggcttcagcaagatgcccca

actcgtgtgttactggagtctatacagatccatatcccctaatcttctatagaaaccacaccttg

cgaggggtattcgggacaatgcttgatggtgtacaagcaagacttaaccctgcgtctgcagt

attcgatagcacatcccgcagtcgcattactcgagtgagttcaagcagtaccaaagcagcat

acacaacatcaacttgttttaaagtggtcaagactaataagacctattgtctcagcattgctgaa

atatctaatactctcttcggagaattcagaatcgtcccgttactagttgagatcctcaaagatga

cggggttagagaagccaggtctggctagttgagtcaattataaaggagttggaaagatggca

ttgtatcacctatcttctgcgacatcaagaatcaaaccgaatgccggcgcgtgctcgaattcca

tgttgccagttgaccacaatcagccagtgctcatgcgatcagattaagccttgtcaAtaGtct

cttgattaagaaaaaatgtaagtggcaatgagatacaaggcaaaacagctcatggtTaaCa

atacgggtaggacatggcgagctccggtcctgaaagggcagagcatcagattatcctacca

gagTcacacctgtcttcaccattggtcaagcacaaactactctattactggaaattaactggg

ctaccgcttcctgatgaatgtgacttcgaccacctcattctcagccgacaatggaaaaaaata

cttgaatcggcctctcctgatactgagagaatgataaaactcggaagggcagtacaccaaac

tcttaaccacaattccagaataaccggagtgctccaccccaggtgtttagaaGaactggcta

atattgaggtcccagattcaaccaacaaatttcggaagattgagaagaagatccaaattcaca

acacgagatatggagaactgttcacaaggctgtgtacgcatatagagaagaaactgctggg

gtcatcttggtctaacaatgtcccccggtcagaggagttcagcagcattcgtacggatccggc

attctggtttcactcaaaatggtccacagccaagtttgcatggctccatataaaacagatccag

aggcatctgatggtggcagctaGgacaaggtctgcggccaacaaattggtgatgctaaccc

ataaggtaggccaagtctttgtcactcctgaacttgtcgttgtgacgcatacgaatgagaacaa

gttcacatgtcttacccaggaacttgtattgatgtatgcagatatgatggagggcagagatatg

gtcaacataatatcaaccacggcggtgcatctcagaagcttatcagagaaaattgatgacattt

tgcggttaatagacgctctggcaaaagacttgggtaatcaagtctacgatgttgtatcactaat

ggagggatttgcatacggagctgtccagctactcgagccgtcaggtacatttgcaggagattt

cttcgcattcaacctgcaggagcttaaagacattctaattggcctcctccccaatgatatagca

gaatccgtgactcatgcaatcgctactgtattctctggtttagaacagaatcaagcagctgaga

tgttgtgtctgttgcgtctgtggggtcacccactgcttgagtcccgtattgcagcaaaggcagt

caggagccaaatgtgcgcaccgaaaatggtagactttgatatgatccttcaggtactgtctttc

ttcaagggaacaatcatcaacgggtacagaaagaagaatgcaggtgtgtggccgcgagtc

aaagtggatacaatatatgggaaggtcattgggcaactacatgcagattcagcagagatttca

cacgatatcatgttgagagagtataagagtttatctgcacttgaatttgagccatgtatagaatat

gaccctgtcaccaacctgagcatgttcctaaaagacaaggcaatcgcacaccccaacgata

attggcttgcctcgtttaggcggaaccttctctccgaagaccagaagaaacatgtaaaagaa

gcaacttcgactaatcgcctcttgatagagtttttagagtcaaatgattttgatccatataaagag

atggaatatctgacgacccttgagtaccttagagatgacaatgtggcagtatcatactcgctca

aggagaaggaagtgaaagttaatggacggatcttcgctaagctgacaaagaagttaaggaa

ctgtcaggtgatggcggaagggatcctagccgatcagattgcacctttctttcagggaaatgg

agtcattcaggatagcatatccttgaccaagagtatgctagcgatgagtcaactgtcttttaaca

gcaataagaaacgtatcactgactgtaaagaaagagtatcttcaaaccgcaatcatgatccga

aaagcaagaaccgtcggagagttgcaaccttcataacaactgacctgcaaaagtactgtctt

aattggagatatcagacaatcaaattgttcgctcatgccatcaatcagttgatgggcctacctc

acttcttcgaatggattcacctaagactgatggacactacgatgttcgtaggagaccctttcaat

cctccaagtgaccctactgactgtgacctctcaagagtccctaatgatgacatatatattgtca

gtgccagagggggtatcgaaggattatgccagaagctatggacaatgatctcaattgctgca

atccaacttgctgcagctagatcgcattgtcgtgttgcctgtatggtacagggtgataatcaag

taatagcagtaacgagagaggtaagatcagacgactctccggagatggtgttgacacagttg

catcaagccagtgataatttcttcaaggaattaattcatgtcaatcatttgattggccataatttga

aggatcgtgaaaccatcaggtcagacacattcttcatatacagcaaacgaatcttcaaagatg

gagcaatcctcagtcaagtcctcaaaaattcatctaaattagtgctagtgtcaggtgatctcagt

gaaaacaccgtaatgtcctgtgccaacattgcctctactgtagcacggctatgcgagaacgg

gcttcccaaagacttctgttactatttaaactatataatgagttgtgtgcagacatactttgactct

gagttctccatcaccaacaattcgcaccccgatcttaatcagtcgtggattgaggacatctcttt

tgtgcactcatatgttctgactcctgcccaattagggggactgagtaaccttcaatactcaagg

ctctacactagaaatatcggtgacccggggactactgcttttgcagagatcaagcgactaga

agcagtgggattactgagtcctaacattatgactaatatcttaactaggccgcctgggaatgg

agattgggccagtctgtgcaacgacccatactctttcaattttgagactgttgcaagcccaaat

attgttcttaagaaacatacgcaaagagtcctatttgaaacttgttcaaatcccttattgtctgga

gtgcacacagaggataatgaggcagaagagaaggcattggctgaattcttgcttaatcaaga

ggtgattcatccccgcgttgcgcatgccatcatggaggcaagctctgtaggtaggagaaag

caaattcaagggcttgttgacacaacaaacaccgtaattaagattgcgcttactaggaggcca

ttaggcatcaagaggctgatgcggatagtcaattattctagcatgcatgcaatgctgtttagag

acgatgttttttcctccagtagatccaaccaccccttagtctcttctaatatgtgttctctgacact

ggcagactatgcacggaatagaagctggtcacctttgacgggaggcaggaaaatactgggt

gtatctaatcctgatacgatagaactcgtagagggtgagattcttagtgtaagcggagggtgt

acaagatgtgacagcggagatgaacaatttacttggttccatcttccaagcaatatagaattga

ccgatgacaccagcaagaatcctccgatgagggtaccatatctcgggtcaaagacacagga

gaggagagctgcctcacttgcaaaaatagctcatatgtcgccacatgtaaaggctgccctaa

gggcatcatccgtgttgatctgggcttatggggataatgaagtaaattggactgctgctcttac

gattgcaaaatctcggtgtaatgtaaacttagagtatcttcggttactgtcccctttacccacgg

ctgggaatcttcaacatagactagatgatggtataactcagatgacattcacccctgcatctct

ctacaggGtgtcaccttacattcacatatccaatgattctcaaaggctgttcactgaagaagg

agtcaaagaggggaatgtggtttaccaacagatcatgctcttgggtttatctctaatcgaatcg

atctttccaatgacaacaaccaggacatatgatgagatcacactgcacctacatagtaaattta

gttgctgtatcagagaagcacctgttgcggttcctttcgagctacttggggtggtaccggaact

gaggacagtgacctcaaataagtttatgtatgatcctagccctgtatcggagggagactttgc

gagacttgacttagctatcttcaagagttatgagcttaatctggagtcatatcccacgatagag

ctaatgaacattctttcaatatccagcgggaagttgattggccagtctgtggtttcttatgatgaa

gatacctccataaagaatgacgccataatagtgtatgacaatacccgaaattggatcagtgaa

gctcagaattcagatgtggtccgcctatttgaatatgcagcacttgaagtgctcctcgactgttc

ttaccaactctattacctgagagtaagaggcctGgacaatattgtcttatatatgggtgatttata

caagaatatgccaggaattctactttccaacattgcagctacaatatctcatcccgtcattcattc

aaggttacatgcagtgggcctggtcaaccatgacggatcacaccaacttgcagatacggatt

ttatcgaaatgtctgcaaaactattagtatcttgcacccgacgtgtgatctccggcttatattcag

gaaataagtatgatctgctgttcccatctgtcttagatgataacctgaatgagaagatgcttcag

ctgatatcccggttatgctgtctgtacacggtactctttgctacaacaagagaaatcccgaaaa

taagaggcttaactgcagaagagaaatgttcaatactcactgagtatttactgtcggatgctgt

gaaaccattacttagccccgatcaagtgagctctatcatgtctcctaacataattacattcccag

ctaatctgtactacatgtctcggaagagcctcaatttgatcagggaaagggaggacagggat

actatcctggcgttgttgttcccccaagagccattattagagttcccttctgtgcaagatattggt

gctcgagtgaaagatccattcacccgacaacctgcggcatttttgcaagagttagatttgagt

gctccagcaaggtatgacgcattcacacttagtcagattcatcctgaactcacatctccaaatc

cggaggaagactacttagtacgatacttgttcagagggatagggactgcatcttcctcttggta

taaggcatctcatctcctttctgtacccgaggtaagatgtgcaagacacgggaactccttatac

ttagctgaagggagcggagccatcatgagtcttctcgaactgcatgtaccacatgaaactatc

tattacaatacgctcttttcaaatgagatgaaccccccgcaacgacatttcgggcegacccca

actcagtttttgaattcggttgtttataggaatctacaggcggaggtaacatgcaaagatggatt

tgtccaagagttccgtccattatggagagaaaatacagaggaaagCgacctgacctcagat

aaagTagtggggtatattacatctgcagtgccctacagatctgtatcattgctgcattgtgaca

ttgaaattcctccagggtccaatcaaagcttactagatcaactagctatcaatttatctctgattg

ccatgcattctgtaagggagggcggggtagtaatcatcaaagtgttgtatgcaatgggatact

actttcatctactcatgaacttgtttgctccgtgttccacaaaaggatatattctctctaatggttat

gcatgtcgaggagatatggagtgttacctggtatttgtcatgggttacctgggcgggcctaca

tttgtacatgaggtggtgaggatggcGaaaactctggtgcagcggcacggtacgctTttgt

ctaaatcagatgagatcacactgaccaggttattcacctcacagcggcagcgtgtgacagac

atcctatccagtcctttaccaagattaataaagtacttgaggaagaatattgacactgcgctgat

tgaagccgggggacagcccgtccgtccattctgtgcggagagtctggtgagcacgctagc

gaacataactcagataacccagatCatcgctagtcacattgacacagttatccggtctgtgat

atatatggaagctgagggtgatctcgctgacacagtatttctatttaccccttacaatctctctac

tgacgggaaaaagaggacatcacttaAacagtgcacgagacagatcctagaggttacaat

actaggtcttagagtcgaaaatctcaataaaataggcgatataatcagcctagtgcttaaagg

catgatctccatggaggaccttatcccactaaggacatacttgaagcatagtacctgccctaa

atatttgaaggctgtcctaggtattaccaaactcaaagaaatgtttacagacacttctgtaCtgt

acttgactcgtgctcaacaaaaattctacatgaaaactataggcaatgcagtcaaaggatatta

cagtaactgtgactcttaacgaaaatcacatattaataggctccttttttggccaattgtattcttgt

tgatttaatcatattatgttagaaaaaagttgaaccctgactccttaggactcgaattcgaactca

aataaatgtcttaaaaaaaggttgcgcacaattattcttgagtgtagtctcgtcattcaccaaatc

tttgtttggt

cDNA of
ACCAAACAGAGAATCCGTAAGTTACGATAAAAGGCGA
SEQ ID

genomic
AGGAGCAATTGAAGTCGCACGGGTAGAAGGTGTGAATC
NO: 2

sequence of
TCGAGTGCGAGCCCGAAGCACAAACTCGAGGAAGCCTT

NDV strain
CTGCCAACATGTCTTCCGTATTCGACGAGTACGAACAG

Hitchner B1
CTCCTCGCGGCTCAGACTCGCCCCAATGGAGCTCATGG

AGGGGGGGAGAAAGGGAGTACCTTAAAAGTAGACGTC

CCGGTATTCACTCTTAACAGTGATGACCCAGAAGATAG

GTGGAGCTTTGTGGTATTCTGCCTCCGGATTGCTGTTAG

CGAAGATGCCAACAAACCACTCAGGCAAGGTGCTCTCA

TATCTCTTTTATGCTCCCACTCACAGGTAATGAGGAACC

ATGTTGCCCTTGCAGGGAAACAGAATGAAGCCACATTG

GCCGTGCTTGAGATTGATGGCTTTGCCAACGGCACGCC

CCAGTTCAACAATAGGAGTGGAGTGTCTGAAGAGAGAG

CACAGAGATTTGCGATGATAGCAGGATCTCTCCCTCGG

GCATGCAGCAACGGCACCCCGTTCGTCACAGCCGGGGC

TGAAGATGATGCACCAGAAGACATCACCGATACCCTGG

AGAGGATCCTCTCTATCCAGGCTCAAGTATGGGTCACA

GTAGCAAAAGCCATGACTGCGTATGAGACTGCAGATGA

GTCGGAAACAAGGCGAATCAATAAGTATATGCAGCAAG

GCAGGGTCCAAAAGAAATACATCCTCTACCCCGTATGC

AGGAGCACAATCCAACTCACGATCAGACAGTCTCTTGC

AGTCCGCATCTTTTTGGTTAGCGAGCTCAAGAGAGGCC

GCAACACGGCAGGTGGTACCTCTACTTATTATAACCTA

GTAGGGGACGTAGACTCATATATCAGGAATACCGGGCT

TACTGCATTCTTCTTGACACTCAAGTACGGAATCAACAC

CAAGACATCAGCCCTTGCACTTAGTAGCCTCTCAGGCG

ACATCCAGAAGATGAAGCAGCTCATGCGTTTGTATCGG

ATGAAAGGAGATAATGCGCCGTACATGACATTACTTGG

TGATAGTGACCAGATGAGCTTTGCGCCTGCCGAGTATG

CACAACTTTACTCCTTTGCCATGGGTATGGCATCAGTCC

TAGATAAAGGTACTGGGAAATACCAATTTGCCAGGGAC

TTTATGAGCACATCATTCTGGAGACTTGGAGTAGAGTA

CGCTCAGGCTCAGGGAAGTAGCATTAACGAGGATATGG

CTGCCGAGCTAAAGCTAACCCCGGCAGCAAGGAGGGGC

CTGGCAGCTGCTGCCCAACGAGTCTCCGAGGTGACCAG

CAGCATAGACATGCCTACTCAACAAGTCGGAGTCCTCA

CTGGGCTTAGCGAGGGGGGATCCCAAGCCCTACAAGGC

GGATCGAATAGATCGCAAGGGCAACCAGAAGCCGGGG

ATGGGGAGACCCAATTCCTGGATCTGATGAGAGCGGTA

GCAAATAGCATGAGGGAGGCGCCAAACTCTGCACAGG

GCACTCCCCAATCGGGGCCTCCCCCAACTCCTGGGCCAT

CCCAAGATAACGACACCGACTGGGGGTATTGATTGACA

AAACCCAGCCTGCTTCTACAAGAACATCCCAATGCTCTC

ACCCGTAGTCGACCCCTCGATTTGCGGCTCTATATGACC

ACACCCTCAAACAAACATCCCCCTCTTTCCTCCCTCCCC

CTGCTGTACAACTCCGCACGCCCTAGATACCACAGGCA

CACCGCGGCTCACTAACAATCAAAACAGAGCCGAGGGA

ATTAGAAAAAAGTACGGGTAGAAGAGGGATATTCAGA

GATCAGGGCAAGTCTCCCGAGTCTCTGCTCTCTCCTCTA

CCTGATAGACCAGGACAAACATGGCCACCTTTACAGAT

GCAGAGATCGACGAGCTATTTGAGACAAGTGGAACTGT

CATTGACAACATAATTACAGCCCAGGGTAAACCAGCAG

AGACTGTTGGAAGGAGTGCAATCCCACAGGGCAAGACC

AAGGTGCTGAGCGCAGCATGGGAGAAGCATGGGAGCA

TCCAGCCACCGGCCAGTCAAGACAACCTCGATCGACAG

GACAGATCTGACAAACAACCATCCACACCCGAGCAAAC

GACCCCGCACGACAGCCCGCCGGCCACATCCGCTGACC

AGCCCCCCACCCAGGCCACAGACGAAGCCGTCGACACA

CAGCTCAGGACCGGAGCAAGCAACTCTCTGCTGTTGAT

GCTTGACAAGCTCAGCAATAAATCGTCCAATGCTAAAA

AGGGCCCATGGTCGAGCCCCCAAGAGGGGAATCACCAA

CGTCCGACTCAACAGCAGGGGAGTCAACCCAGTCGCGG

AAACAGCCAGGAAAGACTGCAGAACCAAGTCAAGGCC

GCCCCTGGAAACCAGGGCACAGACGTGAACACAGCATA

TCATGGACAATGGGAGGAGTCACAACTATCAGCTGGTG

CAACCCCTCATGCTCTCCGATCAAGGCAGAGCCAAGAC

AATACCCTTGTATCTGCGGATCATGTCCAGCCACCTGTA

GACTTTGTGCAAGCGATGATGTCTATGATGGGGGCGAT

ATCACAGAGAGTAAGTAAGGTTGACTATCAGCTAGATC

TTGTCTTGAAACAGACATCCTCCATCCCTATGATGCGGT

CCGAAATCCAACAGCTGAAAACATCTGTTGCAGTCATG

GAAGCCAACTTGGGAATGATGAAGATTCTGGATCCCGG

TTGTGCCAACATTTCATCTCTGAGTGATCTACGGGCAGT

TGCCCGATCTCACCCGGTTTTAGTTTCAGGCCCTGGAGA

CCCATCTCCCTATGTGATACAAGGAGGCGAAATGGCAC

TTAATAAACTTTCGCAACCAGTGCCACATCCATCTGAAT

TGATTAAACCCGCCACTGCATGCGGGCCTGATATAGGA

GTGGAGAGGGACACTGTCCGTGCATTGATCATGTCACG

CCCAATGCACCCGAGTTCTTCAGCCAAGCTCCTAAGCA

AGTTAGATGCAGCCGGGTCGATCGAGGAAATCAGGAAA

ATCAAGCGCCTTGCTCTAAATGGCTAATTACTACTGCCA

CACGTAGCGGGTCCCTGTCCACTCGGCATCACACGGAA

TCTGCACCGAGTTCCCCCCCGCAGACCCAAGGTCCAAC

TCTAGAAGCGGCAATCCTCTCTCGCTTCCTCAGCCCCAC

TGAATGATCGCGTAACCGTAATTAATCTAGCTACATTAA

GGATTAAGAAAAAATACGGGTAGAATTGGAGTGCCCCA

ATTGTGCCAAGATGGACTCATCTAGGACAATTGGGCTG

TACTTTGATTCTGCCCATTCTTCTAGCAACCTGTTAGCA

TTTCCGATCGTCCTACAAGACACAGGAGATGGGAAGAA

GCAAATCGCCCCGCAATATAGGATCCAGCGCCTTGACT

CGTGGACTGATAGTAAGGAAGACTCAGTATTCATCACC

ACCTATGGATTCATCTTTCAAGTTGGGAATGAGGAAGC

CACTGTCGGCATGATCGATGATAAACCCAAGCGCGAGT

TACTTTCCGCTGCGATGCTCTGCCTAGGAAGCGTCCCAA

ATACCGGAGACCTTGTTGAGCTGGCAAGGGCCTGTCTC

ACTATGATGGTCACATGCAAGAAGAGTGCAACTAATAC

TGAGAGAATGGTTTTCTCAGTAGTGCAGGCACCCCAAG

TGCTGCAAAGCTGTAGGGTTGTGGCAAATAAATACTCA

TCAGTGAATGCAGTCAAGCACGTGAAAGCGCCAGAGAA

GATCCCCGGGAGTGGAACCCTAGAATACAAGGTGAACT

TTGTCTCCTTGACTGTGGTACCGAAGAAGGATGTCTACA

AGATCCCAGCTGCAGTATTGAAGATTTCTGGCTCGAGTC

TGTACAATCTTGCGCTCAATGTCACTATTAATGTGGAGG

TAGACCCGAGGAGTCCTTTGGTTAAATCTCTGTCTAAGT

CTGACAGCGGATACTATGCTAACCTCTTCTTGCATATTG

GACTTATGACCACCGTAGATAGGAAGGGGAAGAAAGT

GACATTTGACAAGCTGGAAAAGAAAATAAGGAGCCTTG

ATCTATCTGTCGGGCTCAGTGATGTGCTCGGGCCTTCCG

TGTTGGTAAAAGCAAGAGGTGCACGGACTAAGCTTTTG

GCACCTTTCTTCTCTAGCAGTGGGACAGCCTGCTATCCC

ATAGCAAATGCTTCTCCTCAGGTGGCCAAGATACTCTG

GAGTCAAACCGCGTGCCTGCGGAGCGTTAAAATCATTA

TCCAAGCAGGTACCCAACGCGCTGTCGCAGTGACCGCT

GACCACGAGGTTACCTCTACTAAGCTGGAGAAGGGGCA

CACCCTTGCCAAATACAATCCTTTTAAGAAATAAGCTGC

GTCTCTGAGATTGCGCTCCGCCCACTCACCCAGATCATC

ATGACACAAAAAACTAATCTGTCTTGATTATTTACAGTT

AGTTTACCTGTCCATCAAGTTAGAAAAAACACGGGTAG

AAGATTCTGGATCCCGGTTGGCGCCCTCCAGGTGCAGG

ATGGGCTCCAGACCTTCTACCAAGAACCCAGCACCTAT

GATGCTGACTATCCGGGTCGCGCTGGTACTGAGTTGCAT

CTGCCCGGCAAACTCCATTGATGGCAGGCCTCTTGCAG

CTGCAGGAATTGTGGTTACAGGAGACAAAGCAGTCAAC

ATATACACCTCATCCCAGACAGGATCAATCATAGTTAA

GCTCCTCCCGAATCTGCCCAAGGATAAGGAGGCATGTG

CGAAAGCCCCCTTGGATGCATACAACAGGACATTGACC

ACTTTGCTCACCCCCCTTGGTGACTCTATCCGTAGGATA

CAAGAGTCTGTGACTACATCTGGAGGGGGGAGACAGGG

GCGCCTTATAGGCGCCATTATTGGCGGTGTGGCTCTTGG

GGTTGCAACTGCCGCACAAATAACAGCGGCCGCAGCTC

TGATACAAGCCAAACAAAATGCTGCCAACATCCTCCGA

CTTAAAGAGAGCATTGCCGCAACCAATGAGGCTGTGCA

TGAGGTCACTGACGGATTATCGCAACTAGCAGTGGCAG

TTGGGAAGATGCAGCAGTTTGTTAATGACCAATTTAAT

AAAACAGCTCAGGAATTAGACTGCATCAAAATTGCACA

GCAAGTTGGTGTAGAGCTCAACCTGTACCTAACCGAAT

TGACTACAGTATTCGGACCACAAATCACTTCACCTGCCT

TAAACAAGCTGACTATTCAGGCACTTTACAATCTAGCTG

GTGGGAATATGGATTACTTATTGACTAAGTTAGGTATA

GGGAACAATCAACTCAGCTCATTAATCGGTAGCGGCTT

AATCACCGGTAACCCTATTCTATACGACTCACAGACTCA

ACTCTTGGGTATACAGGTAACTCTACCTTCAGTCGGGAA

CCTAAATAATATGCGTGCCACCTACTTGGAAACCTTATC

CGTAAGCACAACCAGGGGATTTGCCTCGGCACTTGTCC

CAAAAGTGGTGACACAGGTCGGTTCTGTGATAGAAGAA

CTTGACACCTCATACTGTATAGAAACTGACTTAGATTTA

TATTGTACAAGAATAGTAACGTTCCCTATGTCCCCTGGT

ATTTACTCCTGCTTGAGCGGCAATACATCGGCCTGTATG

TACTCAAAGACCGAAGGCGCACTTACTACACCATATAT

GACTATCAAAGGCTCAGTCATCGCTAACTGCAAGATGA

CAACATGTAGATGTGTAAACCCCCCGGGTATCATATCG

CAAAACTATGGAGAAGCCGTGTCTCTAATAGATAAACA

ATCATGCAATGTTTTATCCTTAGGCGGGATAACTTTAAG

GCTCAGTGGGGAATTCGATGTAACTTATCAGAAGAATA

TCTCAATACAAGATTCTCAAGTAATAATAACAGGCAAT

CTTGATATCTCAACTGAGCTTGGGAATGTCAACAACTCG

ATCAGTAATGCTTTGAATAAGTTAGAGGAAAGCAACAG

AAAACTAGACAAAGTCAATGTCAAACTGACCAGCACAT

CTGCTCTCATTACCTATATCGTTTTGACTATCATATCTCT

TGTTTTTGGTATACTTAGCCTGATTCTAGCATGCTACCT

AATGTACAAGCAAAAGGCGCAACAAAAGACCTTATTAT

GGCTTGGGAATAATACCCTAGATCAGATGAGAGCCACT

ACAAAAATGTGAACACAGATGAGGAACGAAGGTTTCCC

TAATAGTAATTTGTGTGAAAGTTCTGGTAGTCTGTCAGT

TCGGAGAGTTAAGAAAAAACTACCGGTTGTAGATGACC

AAAGGACGATATACGGGTAGAACGGTAAGAGAGGCCG

CCCCTCAATTGCGAGCCAGACTTCACAACCTCCGTTCTA

CCGCTTCACCGACAACAGTCCTCAATCATGGACCGCGC

CGTTAGCCAAGTTGCGTTAGAGAATGATGAAAGAGAGG

CAAAAAATACATGGCGCTTGATATTCCGGATTGCAATC

TTATTCTTAACAGTAGTGACCTTGGCTATATCTGTAGCC

TCCCTTTTATATAGCATGGGGGCTAGCACACCTAGCGAT

CTTGTAGGCATACCGACTAGGATTTCCAGGGCAGAAGA

AAAGATTACATCTACACTTGGTTCCAATCAAGATGTAGT

AGATAGGATATATAAGCAAGTGGCCCTTGAGTCTCCAT

TGGCATTGTTAAATACTGAGACCACAATTATGAACGCA

ATAACATCTCTCTCTTATCAGATTAATGGAGCTGCAAAC

AACAGCGGGTGGGGGGCACCTATTCATGACCCAGATTA

TATAGGGGGGATAGGCAAAGAACTCATTGTAGATGATG

CTAGTGATGTCACATCATTCTATCCCTCTGCATTTCAAG

AACATCTGAATTTTATCCCGGCGCCTACTACAGGATCAG

GTTGCACTCGAATACCCTCATTTGACATGAGTGCTACCC

ATTACTGCTACACCCATAATGTAATATTGTCTGGATGCA

GAGATCACTCACACTCACATCAGTATTTAGCACTTGGTG

TGCTCCGGACATCTGCAACAGGGAGGGTATTCTTTTCTA

CTCTGCGTTCCATCAACCTGGACGACACCCAAAATCGG

AAGTCTTGCAGTGTGAGTGCAACTCCCCTGGGTTGTGAT

ATGCTGTGCTCGAAAGCCACGGAGACAGAGGAAGAAG

ATTATAACTCAGCTGTCCCTACGCGGATGGTACATGGG

AGGTTAGGGTTCGACGGCCAATATCACGAAAAGGACCT

AGATGTCACAACATTATTCGGGGACTGGGTGGCCAACT

ACCCAGGAGTAGGGGGTGGATCTTTTATTGACAGCCGC

GTATGGTTCTCAGTCTACGGAGGGTTAAAACCCAATAC

ACCCAGTGACACTGTACAGGAAGGGAAATATGTGATAT

ACAAGCGATACAATGACACATGCCCAGATGAGCAAGAC

TACCAGATTCGAATGGCCAAGTCTTCGTATAAGCCTGG

ACGGTTTGGTGGGAAACGCATACAGCAGGCTATCTTAT

CTATCAAAGTGTCAACATCCTTAGGCGAAGACCCGGTA

CTGACTGTACCGCCCAACACAGTCACACTCATGGGGGC

CGAAGGCAGAATTCTCACAGTAGGGACATCCCATTTCT

TGTATCAGCGAGGGTCATCATACTTCTCTCCCGCGTTAT

TATATCCTATGACAGTCAGCGACAAAACAGCCACTCTT

CATAGTCCTTATACATTCAATGCCTTCACTCGGCCAGGT

AGTATCCCTTGCCAGGCTTCAGCAAGATGCCCCAACTC

GTGTGTTACTGGAGTCTATACAGATCCATATCCCCTAAT

CTTCTATAGAAACCACACCTTGCGAGGGGTATTCGGGA

CAATGCTTGATGGTGAACAAGCAAGACTTAACCCTGCG

TCTGCAGTATTCGATAGCACATCCCGCAGTCGCATAACT

CGAGTGAGTTCAAGCAGCATCAAAGCAGCATACACAAC

ATCAACTTGTTTTAAAGTGGTCAAGACCAATAAGACCT

ATTGTCTCAGCATTGCTGAAATATCTAATACTCTCTTCG

GAGAATTCAGAATCGTCCCGTTACTAGTTGAGATCCTCA

AAGATGACGGGGTTAGAGAAGCCAGGTCTGGCTAGTTG

AGTCAACTATGAAAGAGTTGGAAAGATGGCATTGTATC

ACCTATCTTCTGCGACATCAAGAATCAAACCGAATGCC

GGCGCGTGCTCGAATTCCATGTCGCCAGTTGACCACAA

TCAGCCAGTGCTCATGCGATCAGATTAAGCCTTGTCAAT

AGTCTCTTGATTAAGAAAAAATGTAAGTGGCAATGAGA

TACAAGGCAAAACAGCTCACGGTAAATAATACGGGTAG

GACATGGCGAGCTCCGGTCCTGAAAGGGCAGAGCATCA

GATTATCCTACCAGAGTCACACCTGTCTTCACCATTGGT

CAAGCACAAACTACTCTATTATTGGAAATTAACTGGGC

TACCGCTTCCTGATGAATGTGACTTCGACCACCTCATTC

TCAGCCGACAATGGAAAAAAATACTTGAATCGGCCTCT

CCTGATACTGAGAGAATGATAAAACTCGGAAGGGCAGT

ACACCAAACTCTTAACCACAATTCCAGAATAACCGGAG

TACTCCACCCCAGGTGTTTAGAAGAACTGGCTAATATTG

AGGTCCCTGATTCAACCAACAAATTTCGGAAGATTGAG

AAGAAGATCCAAATTCACAACACGAGATATGGAGAACT

GTTCACAAGGCTGTGTACGCATATAGAGAAGAAACTGC

TGGGGTCATCTTGGTCTAACAATGTCCCCCGGTCAGAG

GAGTTCAGCAGCATTCGTACGGATCCGGCATTCTGGTTT

CACTCAAAATGGTCCACAGCCAAGTTTGCATGGCTCCA

TATAAAACAGATCCAGAGGCATCTGATTGTGGCAGCTA

GGACAAGGTCTGCGGCCAACAAATTGGTGATGCTAACC

CATAAGGTAGGCCAAGTCTTTGTCACTCCTGAACTTGTT

GTTGTGACGCATACGAATGAGAACAAGTTCACATGTCT

TACCCAGGAACTTGTATTGATGTATGCAGATATGATGG

AGGGCAGAGATATGGTCAACATAATATCAACCACGGCG

GTGCATCTCAGAAGCTTATCAGAGAAAATTGATGACAT

TTTGCGGTTAATAGACGCTCTGGCAAAAGACTTGGGTA

ATCAAGTCTACGATGTTGTATCACTAATGGAGGGATTTG

CATACGGAGCTGTCCAGCTACTCGAGCCGTCAGGTACA

TTTGCGGGAGATTTCTTCGCATTCAACCTGCAGGAGCTT

AAAGACATTCTAATTGGCCTCCTCCCCAATGATATAGCA

GAATCCGTGACTCATGCAATCGCTACTGTATTCTCTGGT

TTAGAACAGAATCAAGCAGCTGAGATGTTGTGCCTGTT

GCGTCTGTGGGGTCACCCACTGCTTGAGTCCCGTATTGC

AGCAAAGGCAGTCAGGAGCCAAATGTGCGCACCGAAA

ATGGTAGACTTTGATATGATCCTTCAGGTACTGTCTTTC

TTCAAGGGAACAATCATCAACGGATACAGAAAGAAGA

ATGCAGGTGTGTGGCCGCGAGTCAAAGTGGATACAATA

TATGGGAAGGTCATTGGGCAACTACATGCAGATTCAGC

AGAGATTTCACACGATATCATGTTGAGAGAGTATAAGA

GTTTATCTGCACTTGAATTTGAGCCATGTATAGAATACG

ACCCTGTCACTAACCTGAGCATGTTCCTAAAAGACAAG

GCAATCGCACACCCCAACGATAATTGGCTTGCCTCGTTT

AGGCGGAACCTTCTCTCCGAAGACCAGAAGAAACATGT

AAAGGAAGCGACTTCGACTAACCGCCTCTTGATAGAGT

TTTTAGAGTCAAATGATTTTGATCCATATAAAGAGATGG

AATATCTGACGACCCTTGAGTACCTTAGAGATGACAAT

GTGGCAGTATCATACTCGCTCAAAGAGAAGGAAGTGAA

AGTTAATGGACGGATCTTCGCTAAGCTGACAAAGAAGT

TAAGGAACTGTCAGGTGATGGCGGAAGGGATCCTAGCC

GATCAGATTGCACCTTTCTTTCAGGGAAATGGAGTCATT

CAGGATAGCATATCCTTGACCAAGAGTATGCTAGCGAT

GAGTCAACTGTCTTTTAACAGCAATAAGAAACGTATCA

CTGACTGTAAAGAAAGAGTATGTTCAAACCGCAATCAT

GATCCGAAAAGCAAGAACCGTCGGAGAGTTGCAACCTT

CATAACAACTGACCTGCAAAAGTACTGTCTTAATTGGA

GATATCAGACGATCAAATTGTTCGCTCATGCCATCAATC

AGTTGATGGGCCTACCTCATTTCTTCGAGTGGATTCACC

TAAGACTGATGGACACTACGATGTTCGTAGGAGACCCT

TTCAATCCTCCAAGTGACCCTACTGACTGTGACCTCTCA

AGAGTCCCTAATGATGACATATATATTGTCAGTGCCAG

AGGGGGTATCGAAGGATTATGCCAGAAGCTATGGACAA

TGATCTCAATTGCTGCAATCCAACTTGCTGCAGCTAGAT

CGCATTGTCGTGTTGCCTGTATGGTACAGGGTGATAATC

AAGTAATAGCAGTAACGAGAGAGGTAAGATCAGATGA

CTCTCCGGAGATGGTGTTGACACAGTTGCATCAAGCCA

GTGATAATTTCTTCAAGGAATTAATCCATGTCAATCATT

TGATTGGCCATAATTTGAAGGATCGTGAAACCATCAGG

TCAGACACATTCTTCATATACAGCAAACGAATCTTCAA

AGATGGAGCAATCCTCAGTCAAGTCCTCAAAAATTCAT

CTAAATTAGTGCTAGTGTCAGGTGATCTCAGTGAAAAC

ACCGTAATGTCCTGTGCCAACATTGCCTCTACTGTAGCA

CGGCTATGCGAGAACGGGCTTCCCAAAGACTTCTGTTA

CTATTTAAACTATATAATGAGTTGTGTGCAGACATACTT

TGACTCTGAGTTCTCCATCACCAACAATTCGCACCCCGA

TCTTAATCAGTCGTGGATTGAGGACATCTCTTTTGTGCA

CTCATATGTTCTGACTCCTGCCCAATTAGGGGGACTGAG

TAACCTTCAATACTCAAGGCTCTACACTAGAAATATCG

GTGACCCGGGGACTACTGCTTTTGCAGAGATCAAGCGA

CTAGAAGCAGTGGGACTACTGAGTCCTAACATTAGGAC

TAATATCTTAACTAGGCCGCCTGGGAATGGAGATTGGG

CCAGTCTGTGCAACGACCCATACTCTTTCAATTTTGAGA

CTGTTGCAAGCCCAAACATTGTTCTTAAGAAACATACG

CAAAGAGTCCTATTTGAAACTTGTTCAAATCCCTTATTG

TCTGGAGTGCACACAGAGGATAATGAGGCAGAAGAGA

AGGCATTGGCTGAATTCTTGCTTAATCAAGAGGTGATTC

ATCCCCGCGTTGCGCATGCCATCATGGAGGCAAGCTCT

GTAGGTAGGAGAAAGCAAATTCAAGGGCTTGTTGACAC

AACAAACACTGTAATTAAGATTGCGCTTACTAGGAGGC

CATTAGGCATCAAGAGGCTGATGCGGATAGTCAATTAT

TCTAGCATGCATGCAATGCTGTTTAGAGACGATGTTTTT

TCCTCTAGTAGATCCAACCACCCCTTAGTCTCTTCTAAT

ATGTGTTCTCTGACACTGGCAGACTATGCACGGAATAG

AAGCTGGTCACCTTTGACGGGAGGCAGGAAAATACTGG

GTGTATCTAATCCTGATACGATAGAACTCGTAGAGGGT

GAGATTCTTAGTGTAAGCGGAGGGTGTACAAGATGTGA

CAGCGGAGATGAACAATTTACTTGGTTCCATCTTCCAAG

CAATATAGAATTGACCGATGACACCAGCAAGAATCCTC

CGATGAGGGTACCATATCTCGGGTCAAAGACACAGGAG

AGGAGAGCTGCCTCACTTGCGAAAATAGCTCATATGTC

GCCACATGTGAAGGCTGCCCTAAGGGCATCATCCGTGT

TGATCTGGGCTTATGGGGATAATGAAGTAAATTGGACT

GCTGCTCTTACGATTGCAAAATCTCGGTGTAATGTAAAC

TTAGAGTATCTTCGGTTACTGTCCCCTTTACCCACGGCT

GGGAATCTTCAACATAGACTAGATGATGGTATAACTCA

GATGACATTCACCCCTGCATCTCTCTACAGGGTGTCACC

TTACATTCACATATCCAATGATTCTCAAAGGCTGTTCAC

TGAAGAAGGAGTCAAAGAGGGGAATGTGGTTTACCAAC

AGATCATGCTCTTGGGTTTATCTCTAATCGAATCGATCT

TTCCAATGACAACAACCAGAACATATGATGAGATCACA

CTGCACCTACATAGTAAATTTAGTTGCTGTATCAGGGAA

GCACCTGTTGCGGTTCCTTTCGAGCTACTTGGGGTGGCA

CCGGAACTGAGGACAGTGACCTCAAATAAGTTTATGTA

TGATCCTAGCCCTGTATCGGAGGGAGACTTTGCGAGAC

TTGACTTAGCTATCTTCAAGAGTTATGAGCTTAATCTGG

AGTCATATCCCACGATAGAGCTAATGAACATTCTTTCAA

TATCCAGCGGGAAGTTGATTGGCCAGTCTGTGGTTTCTT

ATGATGAAGATACCTCCATAAAGAATGATGCCATAATA

GTGTATGACAATACCCGAAATTGGATCAGTGAAGCTCA

GAATTCAGATGTGGTCCGCCTATTTGAATATGCAGCACT

TGAAGTGCTCCTCGACTGTTCTTACCAACTCTATTACCT

GAGAGTAAGAGACCTAGACAATATTGTCTTATATATGG

GTGATTTATACAAGAATATGCCAGGAATTCTACTTTCCA

ACATTGCAGCTACAATATCTCATCCTGTCATTCATTCAA

GGTTACATGCAGTGGGCCTGGTCAACCATGACGGATCA

CACCAACTTGCAGATACGGATTTTATCGAAATGTCTGCA

AAACTGTTAGTATCTTGCACCCGACGTGTGATCTCCGGC

TTATATTCAGGAAATAAGTATGATCTGCTGTTCCCATCT

GTCTTAGATGATAACCTGAATGAGAAGATGCTTCAGCT

GATATCCCGGTTATGCTGTCTGTACACGGTACTCTTTGC

TACAACAAGAGAAATCCCGAAAATAAGAGGCTTAACTG

CAGAAGAGAAATGTTCAATACTCACTGAGTATTTACTG

TCGGATGCTGTGAAACCATTACTTAGCCCCGATCAAGT

GAGCTCTATCATGTCTCCTAACATAATTACATTCCCAGC

TAATCTGTACTACATGTCTCGGAAGAGCCTCAATTTGAT

CAGGGAAAGGGAGGACAGGGATACTATCCTGGCGTTGT

TGTTCCCCCAAGAGCCATTATTAGAGTTCCCTTCTGTGC

AAGATATTGGTGCTCGAGTGAAAGATCCATTCACCCGA

CAACCTGCGGCATTTTTGCAAGAGTTAGATTTGAGTGCT

CCAGCAAGGTATGACGCATTCACACTTAGTCAGATTCA

TCCTGAACTCACATCTCCAAATCCGGAGGAAGACTACT

TAGTACGATACTTGTTCAGAGGGATAGGGACTGCATCT

TCCTCTTGGTATAAGGCATCCCATCTCCTTTCTGTACCC

GAGGTAAGATGTGCAAGACACGGGAACTCCTTATACTT

GGCTGAAGGAAGCGGAGCCATCATGAGTCTTCTTGAAC

TGCATGTACCACATGAAACTATCTATTACAATACGCTCT

TTTCAAATGAGATGAACCCCCCGCAACGACATTTCGGG

CCGACCCCAACTCAGTTTTTGAATTCGGTTGTTTATAGG

AATCTACAGGCGGAGGTAACATGCAAGGATGGATTTGT

CCAAGAGTTCCGTCCATTATGGAGAGAAAATACAGAGG

AAAGTGACCTGACCTCAGATAAAGCAGTGGGGTATATT

ACATCTGCAGTACCCTACAGATCTGTATCATTGCTGCAT

TGTGACATTGAAATTCCTCCAGGGTCCAATCAAAGCTTA

CTAGATCAACTAGCTATCAATTTATCTCTGATTGCCATG

CATTCTGTAAGGGAGGGCGGGGTAGTAATCATCAAAGT

GTTGTATGCAATGGGATACTACTTTCATCTACTCATGAA

CTTGTTTGCTCCGTGTTCCACAAAAGGATATATTCTCTC

TAATGGTTATGCATGTCGAGGGGATATGGAGTGTTACC

TGGTATTTGTCATGGGTTACCTGGGCGGGCCTACATTTG

TACATGAGGTGGTGAGGATGGCAAAAACTCTGGTGCAG

CGGCACGGTACGCTTTTGTCTAAATCAGATGAGATCAC

ACTGACCAGGTTATTCACCTCACAGCGGCAGCGTGTGA

CAGACATCCTATCCAGTCCTTTACCAAGATTAATAAAGT

ACTTGAGGAAGAATATTGACACTGCGCTGATTGAAGCC

GGGGGACAGCCCGTCCGTCCATTCTGTGCGGAGAGTCT

GGTGAGCACGCTAGCGAACATAACTCAGATAACCCAGA

TCATCGCTAGTCACATTGACACAGTCATCCGGTCTGTGA

TATATATGGAAGCTGAGGGTGATCTCGCTGACACAGTA

TTTCTATTTACCCCTTACAATCTCTCTACTGACGGGAAA

AAGAGGACATCACTTAAACAGTGCACGAGACAGATCCT

AGAGGTTACAATACTAGGTCTTAGAGTCGAAAATCTCA

ATAAAATAGGCGATATAATCAGCCTAGTGCTTAAAGGC

ATGATCTCCATGGAGGACCTTATCCCACTAAGGACATA

CTTGAAGCATAGTACCTGCCCTAAATATTTGAAGGCTGT

CCTAGGTATTACCAAACTCAAAGAAATGTTTACAGACA

CTTCTGTACTGTACTTGACTCGTGCTCAACAAAAATTCT

ACATGAAAACTATAGGCAATGCAGTCAAAGGATATTAC

AGTAACTGTGACTCCTAACGAAAATCACATATTAATAG

GCTCCTTTTTTGGCCAATTGTATTCTTGTTGATTTAATTA

TATTATGTTAGAAAAAAGTTGAACTCTGACTCCTTAGGA

CTCGAATTCGAACTCAAATAAATGTCTTTAAAAAAGGT

TGCGCACAATTATTCTTGAGTGTAGTCTCGTCATTCACC

AAATCTTTGTTTGGT

cDNA of
accaaacagagaatccgtgagttacgataaaaggcgaaggagcaattgaagtcgcacggg
SEQ ID

genomic
tagaaggtgtgaatctcgagtgcgagcccgaagcacaaactegagaaagccttctgccaac
NO: 3

sequence of
atgtcttccgtatttgatgagtacgaacagctcctcgcggctcagactcgccccaatggagct

NDV strain
catggagggggagaaaaagggagtaccttaaaagtagacgtcccggtattcactcttaaca

LaSota
gtgatgacccagaagatagatggagctttgtggtattctgcctccggattgctgttagcgaag

(L289A
atgccaacaaaccactcaggcaaggtgctctcatatctcttttatgctcccactcacaggtaat

mutation)
gaggaaccatgttgcccttgcagggaaacagaatgaagccacattggccgtgcttgagattg

atggctttgccaacggcacgccccagttcaacaataggagtggagtgtctgaagagagagc

acagagatttgcgatgatagcaggatctctccctcgggcatgcagcaacggaaccccgttc

gtcacagccggggccgaagatgatgcaccagaagacatcaccgataccctggagaggat

cctctctatccaggctcaagtatgggtcacagtagcaaaagccatgactgcgtatgagactg

cagatgagtcggaaacaaggcgaatcaataagtatatgcagcaaggcagggtccaaaaga

aatacatcctctaccccgtatgcaggagcacaatccaactcacgatcagacagtctcttgcag

tccgcatctttttggttagcgagctcaagagaggccgcaacacggcaggtggtacctctactt

attataacctggtaggggacgtagactcatacatcaggaataccgggcttactgcattcttctt

gacactcaagtacggaatcaacaccaagacatcagcccttgcacttagtagcctctcaggcg

acatccagaagatgaagcagctcatgcgtttgtatcggatgaaaggagataatgcgccgtac

atgacattacttggtgatagtgaccagatgagctttgcgcctgccgagtatgcacaactttact

cctttgccatgggtatggcatcagtcctagataaaggtactgggaaataccaatttgccaggg

actttatgagcacatcattctggagacttggagtagagtacgctcaggctcagggaagtagc

attaacgaggatatggctgccgagctaaagctaaccccagcagcaaggaggggcctggca

gctgctgcccaacgggtctccgaggagaccagcagcatagacatgcctactcaacaagtc

ggagtcctcactgggcttagcgagggggggtcccaagctctacaaggcggatcgaataga

tcgcaagggcaaccagaagccggggatggggagacccaattcctggatctgatgagagc

ggtagcaaatagcatgagggaggcgccaaactctgcacagggcactccccaatcggggc

ctcccccaactcctgggccatcccaagataacgacaccgactgggggtattgatggacaaa

acccagcctgcttccacaaaaacatcccaatgccctcacccgtagtcgacccctcgatttgc

ggctctatatgaccacaccctcaaacaaacatccccctctttcctccctccccctgctgtacaa

ctacgtacgccctagataccacaggcacaatgcggctcactaacaatcaaaacagagccga

gggaattagaaaaaagtacgggtagaagagggatattcagagatcagggcaagtctcccg

agtctctgctctctcctctacctgatagaccaggacaaacatggccacctttacagatgcaga

gatcgacgagctatttgagacaagtggaactgtcattgacaacataattacagcccagggta

aaccagcagagactgttggaaggagtgcaatcccacaaggcaagaccaaggtgctgagc

gcagcatgggagaagcatgggagcatccagccaccggccagtcaagacaaccccgatcg

acaggacagatctgacaaacaaccatccacacccgagcaaacgaccccgcatgacagcc

cgccggccacatccgccgaccagccccccacccaggccacagacgaagccgtcgacac

acagctcaggaccggagcaagcaactctctgctgttgatgcttgacaagctcagcaataaat

cgtccaatgctaaaaagggcccatggtcgagcccccaagaggggaatcaccaacgtccga

ctcaacagcaggggagtcaacccagtcgcggaaacagtcaggaaagaccgcagaaccaa

gtcaaggccgcccctggaaaccagggcacagacgtgaacacagcatatcatggacaatgg

gaggagtcacaactatcagctggtgcaacccctcatgctctccgatcaaggcagagccaag

acaatacccttgtatctgcggatcatgtccagccacctgtagactttgtgcaagcgatgatgtc

tatgatggaggcgatatcacagagagtaagtaaggttgactatcagctagatcttgtcttgaaa

cagacatcctccatccctatgatgcggtccgaaatccaacagctgaaaacatctgttgcagtc

atggaagccaacttgggaatgatgaagattctggatcccggttgtgccaacatttcatctctga

gtgatctacgggcagttgcccgatctcacccggttttagtttcaggccctggagacccctctc

cctatgtgacacaaggaggcgaaatggcacttaataaactttcgcaaccagtgccacatcca

tctgaattgattaaacccgccactgcatgcgggcctgatataggagtggaaaaggacactgt

ccgtgcattgatcatgtcacgcccaatgcacccgagttcttcagccaagctcctaagcaagtt

agatgcagccgggtcgatcgaggaaatcaggaaaatcaagcgccttgctctaaatggctaa

ttactactgccacacgtagcgggtccctgtccactcggcatcacacggaatctgcaccgagtt

cccccccgcggacccaaggtccaactctccaagcggcaatcctctctcgcttcctcagcccc

actgaatgatcgcgtaaccgtaattaatctagctacatttaagattaagaaaaaatacgggtag

aattggagtgccccaattgtgccaagatggactcatctaggacaattgggctgtactttgattct

gcccattcttctagcaacctgttagcatttccgatcgtcctacaagacacaggagatgggaag

aagcaaatcgccccgcaatataggatccagcgccttgacttgtggactgatagtaaggagg

actcagtattcatcaccacctatggattcatctttcaagttgggaatgaagaagccaccgtcgg

catgatcgatgataaacccaagcgcgagttactttccgctgcgatgctctgcctaggaagcgt

cccaaataccggagaccttattgagctggcaagggcctgtctcactatgatagtcacatgcaa

gaagagtgcaactaatactgagagaatggttttctcagtagtgcaggcaccccaagtgctgc

aaagctgtagggttgtggcaaacaaatactcatcagtgaatgcagtcaagcacgtgaaagc

gccagagaagattcccgggagtggaaccctagaatacaaggtgaactttgtctccttgactgt

ggtaccgaagagggatgtctacaagatcccagctgcagtattgaaggtttctggctcgagtct

gtacaatcttgcgctcaatgtcactattaatgtggaggtagacccgaggagtcctttggttaaat

ctctgtctaagtctgacagcggatactatgctaacctcttcttgcatattggacttatgaccactg

tagataggaaggggaagaaagtgacatttgacaagctggaaaagaaaataaggagccttg

atctatctgtcgggctcagtgatgtgctcgggccttccgtgttggtaaaagcaagaggtgcac

ggactaagcttttggcacctttcttctctagcagtgggacagcctgctatcccatagcaaatgc

ttctcctcaggtggccaagatactctggagtcaaaccgcgtgcctgcggagcgttaaaatcat

tatccaagcaggtacccaacgcgctgtcgcagtgaccgccgaccacgaggttacctctact

aagctggagaaggggcacacccttgccaaatacaatccttttaagaaataagctgcgtctctg

agattgcgctccgcccactcacccagatcatcatgacacaaaaaactaatctgtcttgattattt

acagttagtttacctgtctatcaagttagaaaaaacacgggtagaagattctggatcccggttg

gcgccctccaggtgcaagatgggctccagaccttctaccaagaacccagcacctatgatgc

tgactatccgggttgcgctggtactgagttgcatctgtccggcaaactccattgatggcaggc

ctcttgcagctgcaggaattgtggttacaggagacaaagccgtcaacatatacacctcatccc

agacaggatcaatcatagttaagctcctcccgaatctgcccaaggataaggaggcatgtgcg

aaagcccccttggatgcatacaacaggacattgaccactttgctcaccccccttggtgactct

atccgtaggatacaagagtctgtgactacatctggaggggggagacaggggcgccttatag

gcgccattattggcggtgtggctcttggggttgcaactgccgcacaaataacagcggccgc

agctctgatacaagccaaacaaaatgctgccaacatcctccgacttaaagagagcattgccg

caaccaatgaggctgtgcatgaggtcactgacggattatcgcaactagcagtggcagttgg

gaagatgcagcagtttgttaatgaccaatttaataaaacagctcaggaattagactgcatcaaa

attgcacagcaagttggtgtagagctcaacctgtacctaaccgaattgactacagtattcgga

ccacaaatcacttcacctgctttaaacaagctgactattcaggcactttacaatctagctggtgg

aaatatggattacttattgactaagttaggtgtagggaacaatcaactcagctcattaatcggta

gcggcttaatcaccggtaaccctattctatacgactcacagactcaactcttgggtatacaggt

aactgccccttcagtcgggaacctaaataatatgcgtgccacctacttggaaaccttatccgta

agcacaaccaggggatttgcctcggcacttgtcccaaaagtggtgacacaggtcggttctgt

gatagaagaacttgacacctcatactgtatagaaactgacttagatttatattgtacaagaatag

taacgttccctatgtcccctggtatttattcctgcttgagcggcaatacgtcggcctgtatgtact

caaagaccgaaggcgcacttactacaccatacatgactatcaaaggttcagtcatcgccaac

tgcaagatgacaacatgtagatgtgtaaaccccccgggtatcatatcgcaaaactatggaga

agccgtgtctctaatagataaacaatcatgcaatgttttatccttaggcgggataactttaaggc

tcagtggggaattcgatgtaacttatcagaagaatatctcaatacaagattctcaagtaataata

acaggcaatcttgatatctcaactgagcttgggaatgtcaacaactcgatcagtaatgctttga

ataagttagaggaaagcaacagaaaactagacaaagtcaatgtcaaactgactagcacatct

gctctcattacctatatcgttttgactatcatatctcttgtttttggtatacttagcctgattctag

catgctacctaatgtacaagcaaaaggcgcaacaaaagaccttattatggcttgggaataatactc

tagatcagatgagagccactacaaaaatgtgaacacagatgaggaacgaaggtttccctaat

agtaatttgtgtgaaagttctggtagtctgtcagttcagagagttaagaaaaaactaccggttgt

agatgaccaaaggacgatatacgggtagaacggtaagagaggccgcccctcaattgcgag

ccaggcttcacaacctccgttctaccgcttcaccgacaacagtcctcaatcatggaccgcgc

cgttagccaagttgcgttagagaatgatgaaagagaggcaaaaaatacatggcgcttgatatt

ccggattgcaatcttattcttaacagtagtgaccttggctatatctgtagcctcccttttatatagc

atgggggctagcacacctagcgatcttgtaggcataccgactaggatttccagggcagaag

aaaagattacatctacacttggttccaatcaagatgtagtagataggatatataagcaagtggc

ccttgagtctccgttggcattgttaaatactgagaccacaattatgaacgcaataacatctctct

cttatcagattaatggagctgcaaacaacagtgggggggggcacctatccatgacccagat

tatataggggggataggcaaagaactcattgtagatgatgctagtgatgtcacatcattctatc

cctctgcatttcaagaacatctgaattttatcccggcgcctactacaggatcaggttgcactcg

aataccctcatttgacatgagtgctacccattactgctacacccataatgtaatattgtctggatg

cagagatcactcacattcatatcagtatttagcacttggtgtgctccggacatctgcaacaggg

agggtattcttttctactctgcgttccatcaacctggacgacacccaaaatcggaagtcttgca

gtgtgagtgcaactcccctgggttgtgatatgctgtgctcgaaagtcacggagacagaggaa

gaagattataactcagctgtccctacgcggatggtacatgggaggttagggttcgacggcca

gtaccacgaaaaggacctagatgtcacaacattattcggggactgggtggccaactaccca

ggagtagggggtggatcttttattgacagccgcgtatggttctcagtctacggagggttaaaa

cccaattcacccagtgacactgtacaggaagggaaatatgtgatatacaagcgatacaatga

cacatgcccagatgagcaagactaccagattcgaatggccaagtcttcgtataagcctggac

ggtttggtgggaaacgcatacagcaggctatcttatctatcaaggtgtcaacatccttaggcg

aagacccggtactgactgtaccgcccaacacagtcacactcatgggggccgaaggcagaa

ttctcacagtagggacatctcatttcttgtatcaacgagggtcatcatacttctctcccgcgttatt

atatcctatgacagtcagcaacaaaacagccactcttcatagtccttatacattcaatgccttca

ctcggccaggtagtatcccttgccaggcttcagcaagatgccccaactcgtgtgttactggag

tctatacagatccatatcccctaatcttctatagaaaccacaccttgcgaggggtattcgggac

aatgcttgatggtgtacaagcaagacttaaccctgcgtctgcagtattcgatagcacatcccg

cagtcgcattactcgagtgagttcaagcagtaccaaagcagcatacacaacatcaacttgtttt

aaagtggtcaagactaataagacctattgtctcagcattgctgaaatatctaatactctcttcgg

agaattcagaatcgtcccgttactagttgagatcctcaaagatgacggggttagagaagcca

ggtctggctagttgagtcaattataaaggagttggaaagatggcattgtatcacctatcttctgc

gacatcaagaatcaaaccgaatgccggcgcgtgctcgaattccatgttgccagttgaccaca

atcagccagtgctcatgcgatcagattaagccttgtcaatagtctcttgattaagaaaaaatgta

agtggcaatgagatacaaggcaaaacagctcatggttaacaatacgggtaggacatggcga

gctccggtcctgaaagggcagagcatcagattatcctaccagagtcacacctgtcttcaccat

tggtcaagcacaaactactctattactggaaattaactgggctaccgcttcctgatgaatgtga

cttcgaccacctcattctcagccgacaatggaaaaaaatacttgaatcggcctctcctgatact

gagagaatgataaaactcggaagggcagtacaccaaactcttaaccacaattccagaataa

ccggagtgctccaccccaggtgtttagaagaactggctaatattgaggtcccagattcaacc

aacaaatttcggaagattgagaagaagatccaaattcacaacacgagatatggagaactgtt

cacaaggctgtgtacgcatatagagaagaaactgctggggtcatcttggtctaacaatgtccc

ccggtcagaggagttcagcagcattcgtacggatccggcattctggtttcactcaaaatggtc

cacagccaagtttgcatggctccatataaaacagatccagaggcatctgatggtggcagcta

ggacaaggtctgcggccaacaaattggtgatgctaacccataaggtaggccaagtctttgtc

actcctgaacttgtcgttgtgacgcatacgaatgagaacaagttcacatgtcttacccaggaa

cttgtattgatgtatgcagatatgatggagggcagagatatggtcaacataatatcaaccacg

gcggtgcatctcagaagcttatcagagaaaattgatgacattttgcggttaatagacgctctgg

caaaagacttgggtaatcaagtctacgatgttgtatcactaatggagggatttgcatacggag

ctgtccagctactcgagccgtcaggtacatttgcaggagatttcttcgcattcaacctgcagga

gcttaaagacattctaattggcctcctccccaatgatatagcagaatccgtgactcatgcaatc

gctactgtattctctggtttagaacagaatcaagcagctgagatgttgtgtctgttgcgtctgtg

gggtcacccactgcttgagtcccgtattgcagcaaaggcagtcaggagccaaatgtgcgca

ccgaaaatggtagactttgatatgatccttcaggtactgtctttcttcaagggaacaatcatcaa

cgggtacagaaagaagaatgcaggtgtgtggccgcgagtcaaagtggatacaatatatgg

gaaggtcattgggcaactacatgcagattcagcagagatttcacacgatatcatgttgagaga

gtataagagtttatctgcacttgaatttgagccatgtatagaatatgaccctgtcaccaacctga

gcatgttcctaaaagacaaggcaatcgcacaccccaacgataattggcttgcctcgtttaggc

ggaaccttctctccgaagaccagaagaaacatgtaaaagaagcaacttcgactaatcgcctc

ttgatagagtttttagagtcaaatgattttgatccatataaagagatggaatatctgacgaccctt

gagtaccttagagatgacaatgtggcagtatcatactcgctcaaggagaaggaagtgaaagt

taatggacggatcttcgctaagctgacaaagaagttaaggaactgtcaggtgatggcggaa

gggatcctagccgatcagattgcacctttctttcagggaaatggagtcattcaggatagcatat

ccttgaccaagagtatgctagcgatgagtcaactgtcttttaacagcaataagaaacgtatcac

tgactgtaaagaaagagtatcttcaaaccgcaatcatgatccgaaaagcaagaaccgtcgga

gagttgcaaccttcataacaactgacctgcaaaagtactgtcttaattggagatatcagacaat

caaattgttcgctcatgccatcaatcagttgatgggcctacctcacttcttcgaatggattcacct

aagactgatggacactacgatgttcgtaggagaccctttcaatcctccaagtgaccctactga

ctgtgacctctcaagagtccctaatgatgacatatatattgtcagtgccagagggggtatcga

aggattatgccagaagctatggacaatgatctcaattgctgcaatccaacttgctgcagctag

atcgcattgtcgtgttgcctgtatggtacagggtgataatcaagtaatagcagtaacgagaga

ggtaagatcagacgactctccggagatggtgttgacacagttgcatcaagccagtgataattt

cttcaaggaattaattcatgtcaatcatttgattggccataatttgaaggatcgtgaaaccatca

ggtcagacacattcttcatatacagcaaacgaatcttcaaagatggagcaatcctcagtcaag

tcctcaaaaattcatctaaattagtgctagtgtcaggtgatctcagtgaaaacaccgtaatgtcc

tgtgccaacattgcctctactgtagcacggctatgcgagaacgggcttcccaaagacttctgtt

actatttaaactatataatgagttgtgtgcagacatactttgactctgagttctccatcaccaaca

attcgcaccccgatcttaatcagtcgtggattgaggacatctcttttgtgcactcatatgttctga

ctcctgcccaattagggggactgagtaaccttcaatactcaaggctctacactagaaatatcg

gtgacccggggactactgcttttgcagagatcaagcgactagaagcagtgggattactgagt

cctaacattatgactaatatcttaactaggccgcctgggaatggagattgggccagtctgtgc

aacgacccatactctttcaattttgagactgttgcaagcccaaatattgttcttaagaaacatac

gcaaagagtcctatttgaaacttgttcaaatcccttattgtctggagtgcacacagaggataat

gaggcagaagagaaggcattggctgaattcttgcttaatcaagaggtgattcatccccgcgtt

gogcatgccatcatggaggcaagctctgtaggtaggagaaagcaaattcaagggcttgttg

acacaacaaacaccgtaattaagattgcgcttactaggaggccattaggcatcaagaggctg

atgcggatagtcaattattctagcatgcatgcaatgctgtttagagacgatgttttttcctccagt

agatccaaccaccccttagtctcttctaatatgtgttctctgacactggcagactatgcacgga

atagaagctggtcacctttgacgggaggcaggaaaatactgggtgtatctaatcctgatacg

atagaactcgtagagggtgagattcttagtgtaagcggagggtgtacaagatgtgacagcg

gagatgaacaatttacttggttccatcttccaagcaatatagaattgaccgatgacaccagcaa

gaatcctccgatgagggtaccatatctcgggtcaaagacacaggagaggagagctgcctca

cttgcaaaaatagctcatatgtcgccacatgtaaaggctgccctaagggcatcatccgtgttg

atctgggcttatggggataatgaagtaaattggactgctgctcttacgattgcaaaatctcggt

gtaatgtaaacttagagtatcttcggttactgtcccctttacccacggctgggaatcttcaacat

agactagatgatggtataactcagatgacattcacccctgcatctctctacagggtgtcacctt

acattcacatatccaatgattctcaaaggctgttcactgaagaaggagtcaaagaggggaat

gtggtttaccaacagatcatgctcttgggtttatctctaatcgaatcgatctttccaatgacaaca

accaggacatatgatgagatcacactgcacctacatagtaaatttagttgctgtatcagagaa

gcacctgttgcggttcctttcgagctacttggggggtaccggaactgaggacagtgacctca

aataagtttatgtatgatcctagccctgtatcggagggagactttgcgagacttgacttagctat

cttcaagagttatgagcttaatctggagtcatatcccacgatagagctaatgaacattctttcaat

atccagcgggaagttgattggccagtctgtggtttcttatgatgaagatacctccataaagaat

gacgccataatagtgtatgacaatacccgaaattggatcagtgaagctcagaattcagatgtg

gtccgcctatttgaatatgcagcacttgaagtgctcctcgactgttcttaccaactctattacctg

agagtaagaggcctggacaatattgtcttatatatgggtgatttatacaagaatatgccaggaa

ttctactttccaacattgcagctacaatatctcatcccgtcattcattcaaggttacatgcagtgg

gcctggtcaaccatgacggatcacaccaacttgcagatacggattttatcgaaatgtctgcaa

aactattagtatcttgcacccgacgtgtgatctccggcttatattcaggaaataagtatgatctg

ctgttcccatctgtcttagatgataacctgaatgagaagatgcttcagctgatatcccggttatg

ctgtctgtacacggtactctttgctacaacaagagaaatcccgaaaataagaggcttaactgc

agaagagaaatgttcaatactcactgagtatttactgtcggatgctgtgaaaccattacttagcc

ccgatcaagtgagctctatcatgtctcctaacataattacattcccagctaatctgtactacatgt

ctcggaagagcctcaatttgatcagggaaagggaggacagggatactatcctggcgttgttg

ttcccccaagagccattattagagttcccttctgtgcaagatattggtgctcgagtgaaagatc

cattcacccgacaacctgcggcatttttgcaagagttagatttgagtgctccagcaaggtatga

cgcattcacacttagtcagattcatcctgaactcacatctccaaatccggaggaagactactta

gtacgatacttgttcagagggatagggactgcatcttcctcttggtataaggcatctcatctcct

ttctgtacccgaggtaagatgtgcaagacacgggaactccttatacttagctgaagggagcg

gagccatcatgagtcttctcgaactgcatgtaccacatgaaactatctattacaatacgctctttt

caaatgagatgaaccccccgcaacgacatttcgggccgaccccaactcagtttttgaattcg

gttgtttataggaatctacaggcggaggtaacatgcaaagatggatttgtccaagagttccgtc

cattatggagagaaaatacagaggaaagcgacctgacctcagataaagtagtggggtatatt

acatctgcagtgccctacagatctgtatcattgctgcattgtgacattgaaattcctccagggtc

caatcaaagcttactagatcaactagctatcaatttatctctgattgccatgcattctgtaaggga

gggcggggtagtaatcatcaaagtgttgtatgcaatgggatactactttcatctactcatgaact

tgtttgctccgtgttccacaaaaggatatattctctctaatggttatgcatgtcgaggagatatgg

agtgttacctggtatttgtcatgggttacctgggcgggcctacatttgtacatgaggtggtgag

gatggcgaaaactctggtgcagcggcacggtacgcttttgtctaaatcagatgagatcacact

gaccaggttattcacctcacagcggcagcgtgtgacagacatcctatccagtcctttaccaag

attaataaagtacttgaggaagaatattgacactgcgctgattgaagccgggggacagcccg

tccgtccattctgtgcggagagtctggtgagcacgctagcgaacataactcagataacccag

atcatcgctagtcacattgacacagttatccggtctgtgatatatatggaagctgagggtgatct

cgctgacacagtatttctatttaccccttacaatctctctactgacgggaaaaagaggacatca

cttaaacagtgcacgagacagatcctagaggttacaatactaggtcttagagtcgaaaatctc

aataaaataggcgatataatcagcctagtgcttaaaggcatgatctccatggaggaccttatc

ccactaaggacatacttgaagcatagtacctgccctaaatatttgaaggctgtcctaggtatta

ccaaactcaaagaaatgtttacagacacttctgtactgtacttgactcgtgctcaacaaaaattc

tacatgaaaactataggcaatgcagtcaaaggatattacagtaactgtgactcttaacgaaaat

cacatattaataggctccttttttggccaattgtattcttgttgatttaatcatattatgttagaaa

aaagttgaaccctgactccttaggactcgaattcgaactcaaataaatgtcttaaaaaaaggttgc

gcacaattattcttgagtgtagtctcgtcattcaccaaatctttgtttggt

TABLE 2

NDV LaSota F protein

SEQ ID

Description
Sequence
NO:

Amino acid
MGSRPSTKNPAPMTLTIRVALVLSCICPANSIDGRPLAAAG
SEQ ID

sequence of F
IVVTGDKAVNIYTSSQTGSIIVKLLPNLPKDKEACAKAPLD
NO: 4

protein of NDV
AYNRTLTTLLTPLGDSIRRIQESVTTSGGGRQGRLIGAIIGG

strain LaSota
VALGVATAAQITAAAALIQAKQNAANILRLKESIAATNEA

(transmembrane
VHEVTDGLSQLAVAVGKMQQFVNDQFNKTAQELDCIKIA

domain is
QQVGVELNLYLTELTTVFGPQITSPALNKLTIQALYNLAG

underlined and
GNMDYLLTKLGVGNNQLSSLIGSGLITGNPILYDSQTQLLG

cytoplasmic
IQVTLPSVGNLNNMRATYLETLSVSTTRGFASALVPKVVT

domain is in
QVGSVIEELDTSYCIETDLDLYCTRIVTFPMSPGIYSCLSGN

bold)
TSACMYSKTEGALTTPYMTIKGSVIANCKMTTCRCVNPPG

IISQNYGEAVSLIDKQSCNVLSLGGITLRLSGEFDVTYQKNI

SIQDSQVIITGNLDISTELGNVNNSISNALNKLEESNRKLDK

VNVKLTSTSALITYIVLTIISLVFGILSLILACYLMYKQKAQ

QKTLLWLGNNTLDQMRATTKM

Amino acid
LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNN
SEQ ID

sequence of
TLDQMRATTKM
NO:5

transmembrane

and cytoplasmic

domains of F

protein of NDV

strain LaSota

TABLE 3

SARS-CoV-2 Omicron Spike Nucleotide and Protein Sequences

Nucleotide sequence of Omicron BA.1: SEQ ID NO: 6 (signal peptide in bold; HXP-S

ectodomain; GS linker sequence in bold and underlined; transmembrane and

cytoplasmic domains of NDV F protein double underlined)

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGA

CCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAGT

GCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAGC

CCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACG

GCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacGG

CGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCC

CTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCG

TGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACAA

GAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCC

GTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCG

GAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGT

ACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGAC

ACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGG

CTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCG

GCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCC

AGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCC

TACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAG

AGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTG

CGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACC

CAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAA

GAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGG

CGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGC

cctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCA

GTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCT

GGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATC

GGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTC

AACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGG

GAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAA

GCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAGCAG

ACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGC

AGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAG

CCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAA

GAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCC

CCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATT

TCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAG

GCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGA

GCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTG

ATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCT

TCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACC

TGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCG

ACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAG

AACTGGGGAAGTACGAGCAGTACATCAAGTGGCCCggcggaggtgggtcgCTCATAACA

TACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGC

ATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCGGT

AACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTGA

Nucleotide sequence of Omicron BA.1: SEQ ID NO: 7 (HXP-S ectodomain; GS linker

sequence in bold and underlined; transmembrane and cytoplasmic domains of NDV F

protein double underlined)

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagc

TTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAG

CcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCG

AGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACC

GATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGC

GGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCC

TACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAG

CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGC

AGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGC

ACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGC

TGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACT

GATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAG

AGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGT

GTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATG

AGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGC

CCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAG

CCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGAC

CCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCT

GGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGC

AGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACA

CAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGA

ACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAG

AGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

ggcggaggtgggtcg
CTCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGT

ATTTTGTCTTTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGA

AGACTCTCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAA

AGATGTGA

Amino acid sequence of Omicron BA.1: SEQ ID NO: 8 (signal peptide in bold; HXP-S

ectodomain; GS linker sequence in bold and underlined; transmembrane and

cytoplasmic domains of NDV F protein double underlined)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGG

GS

LITYIVLTIISLVEGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Amino acid sequence of Omicron BA.1: SEQ ID NO: 9 (HXP-S ectodomain; GS linker

sequence in bold and underlined; transmembrane and cytoplasmic domains of NDV F

protein double underlined)

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGGGSLITYIVLTIISLVFGI

LSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Nucleotide sequence of Omicron BA.1 (H655_deCSV6871): SEQ ID NO: 10 (signal

peptide in bold; HXP-S ectodomain; GS linker sequence bold and underlined;

transmembrane and cytoplasmic domains of NDV F protein double underlined)

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGA

CCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAGT

GCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAGC

CCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACG

GCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacGG

CGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCC

CTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCG

TGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACAA

GAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCC

GTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCG

GAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGT

ACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGAC

ACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGG

CTGTCTGATCGGAGCCGAGcacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAatcGCCAGCCAGAGCATCA

TTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAACAACTC

TATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGCCTGTG

TCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTCCACCG

AGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGaagAGAGCC

CTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCGCCCAA

GTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGCGGCTTCAATTTCAG

CCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCcctATCGAGGACCTG

CTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATGGCGATT

GTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTaagGGACTG

ACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACATCTGCCC

TGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCAG

ATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGACCCAGAA

TGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATCGG

CAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGGAC

GTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCaag

TTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAGCAGACTGGACccccctGAAG

CCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGCAGTCCCTGCAGACCT

ACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGG

CCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTT

GCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGT

GTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCA

GCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCA

ACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCAC

CACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAAC

AATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTG

GATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACCTGGGCGATATCAGC

GGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGGCTGAACGAG

GTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGTAC

GAGCAGTACATCAAGTGGCCCggcggaggtgggtcgCTCATAACATACATCGTCCTGAC

TATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGCATGCTATTTGATGTA

TAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCGGTAACAACACACTCGA

CCAGATGAGAGCAACTACAAAGATGTGA

Nucleotide sequence of Omicron BA.1 (H655_deCSV687I): SEQ ID NO: 11 (HXP-S

ectodomain; GS linker sequence bold and underlined; transmembrane and cytoplasmic

domains of NDV F protein double underlined)

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagc

TTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGcacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAatcGCC

AGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCC

TACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAG

AGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTG

CGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACC

CAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAA

GAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGG

CGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGC

cctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCA

GTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCT

GGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATC

GGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTC

AACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGG

GAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAA

GCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAGCAG

ACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGC

AGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAG

CCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAA

GAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCC

CCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATT

TCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAG

GCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGA

GCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTG

ATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCT

TCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACC

TGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCG

ACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAG

AACTGGGGAAGTACGAGCAGTACATCAAGTGGCCCggcggaggtgggtcgCTCATAACA

TACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGC

ATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCGGT

AACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTGA

Amino acid sequence of Omicron BA.1 (H655_deCSV6871): SEQ ID NO: 12 (signal

peptide in bold; HXP-S ectodomain; GS linker sequence bold and underlined;

transmembrane and cytoplasmic domains of NDV F protein double underlined)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTIASQSIIAYTMSLGAE

NSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCT

QLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIED

LLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALL

AGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQ

DSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQI

DRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHL

MSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVT

QRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPD

VDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGGGSLIT

YIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Amino acid sequence of Omicron BA.1 (H655_deCSV6871): SEQ ID NO: 13 (HXP-S

ectodomain; GS linker sequence bold and underlined; transmembrane and cytoplasmic

domains of NDV F protein double underlined)

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEHVNNSYECDIPIGAGICASYQTQTIASQSIIAYTMSLGAENSVAYSNNSIAIPTN

FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQD

KNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFI

KQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAG

PALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQ

DVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTY

VTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFL

HVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT

FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVN

IQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGGGSLITYIVLTIISLVFGILSLIL

ACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Nucleotide sequence of Omicron BA.1 (Q493Q498): SEQ ID NO: 14 (signal peptide in

bold; HXP-S ectodomain; GS linker sequence bold and underlined; transmembrane

and cytoplasmic domains of NDV F protein double underlined)

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGA

CCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAGT

GCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAGC

CCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACG

GCGTGgccGGCTTCAACTGCTACTTCCCACTGcagTCCTACagcTTTcagCCCACAtacGG

CGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCC

CTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCG

TGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACAA

GAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCC

GTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCG

GAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGT

ACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGAC

ACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGG

CTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCG

GCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCC

AGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCC

TACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAG

AGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTG

CGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACC

CAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAA

GAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGG

CGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGC

cctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCA

GTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCT

GGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATC

GGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTC

AACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGG

GAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAA

GCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAGCAG

ACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGC

AGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAG

CCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAA

GAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCC

CCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATT

TCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAG

GCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGA

GCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTG

ATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCT

TCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACC

TGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCG

ACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAG

AACTGGGGAAGTACGAGCAGTACATCAAGTGGCCCggcggaggtgggtcgCTCATAACA

TACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGC

ATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCGGT

AACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTGA

Nucleotide sequence of Omicron BA.1 (Q493Q498): SEQ ID NO: 15 (HXP-S

ectodomain; GS linker sequence bold and underlined; transmembrane and cytoplasmic

domains of NDV F protein double underlined)

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcagTCCTACagc

TTTcagCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAG

CcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCG

AGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACC

GATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGC

GGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCC

TACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAG

CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGC

AGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGC

ACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGC

TGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACT

GATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAG

AGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGT

GTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATG

AGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGC

CCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAG

CCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGAC

CCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCT

GGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGC

AGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACA

CAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGA

ACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAG

AGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

ggcggaggtgggtcg

CTCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGT

ATTTTGTCTTTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGA

AGACTCTCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAA

AGATGTGA

Amino acid sequence of Omicron BA.1 (Q493Q498): SEQ ID NO: 16 (signal peptide in

bold; HXP-S ectodomain; GS linker sequence bold and underlined; transmembrane

and cytoplasmic domains of NDV F protein double underlined)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLQSYSFQPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Amino acid sequence of Omicron BA.1 (Q493Q498): SEQ ID NO: 17 (HXP-S

ectodomain; GS linker sequence bold and underlined; transmembrane and cytoplasmic

domains of NDV F protein double underlined)

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLQSYSFQPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPGGGGSLITYIVLTIISLVFGI

LSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM*

Nucleotide sequence of Omicron BA.1 Spike Protein Ectodomain: SEQ ID NO: 18

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagc

TTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAG

CcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCG

AGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACC

GATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGC

GGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCC

TACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAG

CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGC

AGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGC

ACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGC

TGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACT

GATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAG

AGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGT

GTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATG

AGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGC

CCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAG

CCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGAC

CCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCT

GGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGC

AGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACA

CAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGA

ACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAG

AGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino acid sequence of Omicron BA.1 Spike Protein Ectodomain: SEQ ID NO: 19

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide sequence of Omicron BA.1 (H655_deCSV6871) Spike Protein Ectodomain:

SEQ ID NO: 20

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagc

TTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGcacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAatcGCC

AGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCC

TACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAG

AGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTG

CGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACC

CAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAA

GAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGG

CGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGC

cctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCA

GTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCT

GGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATC

GGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTC

AACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGG

GAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAA

GCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAGCAG

ACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGC

AGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAG

CCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAA

GAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCC

CCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATT

TCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAG

GCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGA

GCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTG

ATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCT

TCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACC

TGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCG

ACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAG

AACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino acid sequence of Omicron BA.1 (H655_deCSV6871) Spike Protein Ectodomain:

SEQ ID NO: 21

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEHVNNSYECDIPIGAGICASYQTQTIASQSIIAYTMSLGAENSVAYSNNSIAIPTN

FTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQD

KNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFI

KQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAG

PALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQ

DVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTY

VTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFL

HVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNT

FVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVN

IQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide sequence of Omicron BA.1 (Q493Q498) Spike Protein Ectodomain:

SEQ ID NO: 22

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACctgGCCcctTTCttcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcagTCCTACagc

TTTcagCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAG

CcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCG

AGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACC

GATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGC

GGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCC

TACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAG

CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGC

AGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGC

ACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGC

TGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACT

GATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAG

AGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGT

GTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATG

AGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGC

CCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAG

CCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGAC

CCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCT

GGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGC

AGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACA

CAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGA

ACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAG

AGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino acid sequence of Omicron BA.1 (Q493Q498) Spike Protein Ectodomain:

SEQ ID NO: 23

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLQSYSFQPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.1 S371 S373 S375 (Signal peptide in bold; GS linker is

in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID NO: 30

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACtccGCCagcTTCagcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACG

ACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAG

TGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacG

GCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCC

CCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGC

GTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACA

AGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGC

CGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGC

GGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTG

TACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGA

CACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCG

GCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGC

CAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGC

CTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACA

GAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCT

GCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCAC

CCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCA

AGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCG

GCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGA

GCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATC

AAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCC

AGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCC

CAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGA

GCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGC

ATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAG

TTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCC

TGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGT

CAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

A

Amino Acid Sequence of BA.1 S371 S373 S375 (Signal peptide in bold; GS linker is

in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID NO: 31

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.1 S371 S373 S375 (Signal peptide in bold; Spike

ectodomain is underlined; S371 S373 S375 is in bold, underlined and italics):

SEQ ID NO: 32

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACtccGCCagcTTCagcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACG

ACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAG

TGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacG

GCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCC

CCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGC

GTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACA

AGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGC

CGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGC

GGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTG

TACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGA

CACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCG

GCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGC

CAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGC

CTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACA

GAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCT

GCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCAC

CCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCA

AGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCG

GCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGA

GCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATC

AAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCC

AGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCC

CAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGA

GCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGC

ATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAG

TTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCC

TGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGT

CAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.1 S371 S373 S375 (Signal peptide in bold; Spike

ectodomain is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ

ID NO: 33

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.1 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 34

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACtccGCCagcTTCagcACCTTCAAGTGCTACGGCGTGTCCCC

TACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATC

CGGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACT

ACAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCA

ACaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGA

AGTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCG

GCaacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACa

gcTTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTC

GAACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCG

TGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCT

GACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGC

CGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCAC

CCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAAT

CAGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTC

ACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTT

TCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAG

TGCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagA

GCcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCC

GAGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCA

TCAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACT

GCACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTA

CGGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAG

GACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCT

CCTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAA

GCCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCC

GACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGG

GATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGAC

CGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAG

CGGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGC

CTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAA

GCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAG

CAGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGG

CACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTG

CTGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGAC

TGATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCA

GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGT

GTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGA

TGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGT

GCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAA

AGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTG

ACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGT

CTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCT

GCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCA

CACAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGT

GAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACG

AGAGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGC

CC

Amino Acid Sequence of BA.1 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 35

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 36

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAAC

GACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAG

TGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAta

cGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATG

CCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAAT

GCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCA

ACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAG

ACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTT

CGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGT

GCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAG

CTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGA

GCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCC

CCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGC

GTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGA

CCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT

ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTT

CTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAAC

ACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGt

acTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAG

CGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTT

CATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGC

GCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGA

TCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATT

TGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAA

CGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAA

CCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGC

GCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCC

TGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATC

CTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGG

AAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGA

GATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGC

CAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCT

CAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAG

AGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCC

TAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAA

CTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGC

GACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGC

TGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCG

ACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGA

AAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCG

ACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTC

TTTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACT

CTCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAG

ATGTGA

Amino Acid Sequence of BA.2 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 37

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GG

GGS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.2 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 38

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAAC

GACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAG

TGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAta

cGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATG

CCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAAT

GCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCA

ACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAG

ACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTT

CGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGT

GCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAG

CTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGA

GCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCC

CCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGC

GTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGA

CCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT

ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTT

CTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAAC

ACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGt

acTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAG

CGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTT

CATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGC

GCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGA

TCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATT

TGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAA

CGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAA

CCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGC

GCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCC

TGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATC

CTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGG

AAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGA

GATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGC

CAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCT

CAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAG

AGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCC

TAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAA

CTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGC

GACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGC

TGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCG

ACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGA

AAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCG

ACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.2 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 39

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKENGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2 (Spike ectodomain without signal peptide): SEQ

ID NO: 40

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGG

CACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGT

GTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACC

ACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTG

GTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTA

TCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGC

CAACAACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGC

AAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGC

TACTTCAAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCA

GGGCTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACC

CGGTTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGC

AGCAGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCT

AGAACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGAT

TGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGG

AgAAGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGT

GCGGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCA

GATTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCG

ACTACTCCGTGCTGTACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCC

TACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATC

CGGGGAaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTAC

AACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACa

agCTGGACTCCAAAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGeggTCCTACGG

CTTTcggCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTC

GAACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCG

TGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGC

TGACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCG

CCGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCA

CCCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAA

TCAGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATT

CACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTG

TTTCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACG

AGTGCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaa

gAGCcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCG

CCGAGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCAC

CATCAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGA

CTGCACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAG

TACGGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAAC

AGGACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCC

CTCCTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCA

AGCCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGC

CGACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAG

GGATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTG

ACCGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACA

AGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATG

GCCTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAG

AAGCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTG

AGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCA

GGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTG

TGCTGAACGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGAC

AGACTGATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTG

ATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCT

GAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCAC

CTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACAT

ACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACG

GCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTT

CGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTC

GTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACC

CTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGA

ACCACACAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCG

TCGTGAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGA

ACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGT

GGCCC

Amino Acid Sequence of BA.2 (Spike ectodomain without signal peptide): SEQ ID

NO: 41

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN

GTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEF

QFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKN

LREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY

LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKS

FTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA

DYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIAD

YNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGN

KPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNL

VKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCS

FGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRA

GCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYS

NNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRAL

TGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKV

TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITS

GWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTP

SALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGR

LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAP

HGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ

IITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGI

NASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics

and underlined): SEQ ID NO: 42

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAA

CGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAA

GTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAA

GCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAA

CGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAt

acGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCAT

GCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAA

TGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGC

AACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACA

GACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCT

TCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAG

TGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCA

GCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAG

AGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATC

CCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGC

GTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGA

CCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT

ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTT

CTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAAC

ACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGt

acTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAG

CGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTT

CATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGC

GCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGA

TCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATT

TGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAA

CGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAA

CCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGC

GCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCC

TGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATC

CTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGG

AAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGA

GATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGC

CAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCT

CAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAG

AGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCC

TAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAA

CTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGC

GACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGC

TGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCG

ACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGA

AAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCG

ACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTC

TTTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACT

CTCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAG

ATGTGA

Amino Acid Sequence of BA.2 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics and

underlined): SEQ ID NO: 43

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GG

GGS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.2 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics

and underlined): SEQ ID NO: 44

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAA

CGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAA

GTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAA

GCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAA

CGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAt

acGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCAT

GCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAA

TGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGC

AACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACA

GACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCT

TCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAG

TGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCA

GCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAG

AGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATC

CCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGC

GTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGA

CCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT

ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTT

CTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAAC

ACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGt

acTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAG

CGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTT

CATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGC

GCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGA

TCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATT

TGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAA

CGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAA

CCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGC

GCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCC

TGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATC

CTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGG

AAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGA

GATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGC

CAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCT

CAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAG

AGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCC

TAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAA

CTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGC

GACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGC

TGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCG

ACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGA

AAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCG

ACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.2 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics

and underlined): SEQ ID NO: 45

MFVFLVLLPLVSS
QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, italics and underlined): SEQ ID

NO: 46

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGG

CACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGT

GTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACC

ACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTG

GTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTA

TCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGC

CAACAACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGC

AAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGC

TACTTCAAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCA

GGGCTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACC

CGGTTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGC

AGCAGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCT

AGAACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGAT

TGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGG

AgAAGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGT

GCGGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCA

GATTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCG

ACTACTCCGTGCTGTACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCC

CCTACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGA

TCCGGGGAaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACT

ACAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCA

ACaagCTGGACTCCAAAGTCGGCGGCAACTACAATTACCTGTACCGGCTGTTCCGG

AAGTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCC

GGCaacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTA

CGGCTTTcggCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGC

TTCGAACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATC

TCGTGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCG

TGCTGACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATA

TCGCCGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACA

TCACCCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAG

CAATCAGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCC

ATTCACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAAT

GTGTTTCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTA

CGAGTGCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGAC

AaagAGCcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGG

CGCCGAGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTC

ACCATCAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTG

GACTGCACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGC

AGTACGGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGA

ACAGGACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGAC

CCCTCCTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAG

CAAGCCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTG

GCCGACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCA

GGGATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCT

GACCGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCAC

AAGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGAT

GGCCTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCA

GAAGCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCT

GAGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCC

AGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCT

GTGCTGAACGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGA

CAGACTGATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCT

GATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTC

TGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCA

CCTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACA

TACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACG

GCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTT

CGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTC

GTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACC

CTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGA

ACCACACAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCG

TCGTGAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGA

ACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGT

GGCCC

Amino Acid Sequence of BA.2 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, italics and underlined): SEQ

ID NO: 47

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN

GTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEF

QFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKN

LREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY

LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKS

FTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA

DYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIAD

YNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGN

KPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNL

VKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCS

FGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRA

GCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYS

NNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRAL

TGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKV

TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITS

GWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTP

SALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGR

LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAP

HGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ

IITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGI

NASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2.12.1 (Signal peptide is in bold and underlined; Spike

protein ectodomain underlined; GS linker is in italics; TM and CT From F in bold

and double underlined): SEQ ID NO: 48

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAAC

GACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAG

TGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAta

cGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATG

CCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAAT

GCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCA

ACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAG

ACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTT

CGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGT

GCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAG

CTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGA

GCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCC

CCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACctgGT

GGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACC

ACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTAC

ATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCT

GCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACA

CCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtac

TTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGC

GGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTC

ATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCG

CCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGAT

CGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTT

GGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAAC

GGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAAC

CAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCG

CCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCT

GGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCC

TGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGA

AGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAG

ATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCC

AGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTC

AGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGA

GAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCT

AGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAAC

TTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCG

ACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCT

GGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGA

CGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAA

AGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGA

CCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

C

TCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCT

TTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTC

TCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGA

TGTGA

Amino Acid Sequence of BA.2.12.1 (Signal peptide is in bold and underlined; Spike

protein ectodomain underlined; GS linker is in italics; TM and CT From F in bold

and double underlined): SEQ ID NO: 49

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQE

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GG

GGS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.2.12.1 (Signal peptide is in bold and underlined; Spike

protein ectodomain underlined): SEQ ID NO: 50

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAAC

GACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAG

TGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTG

CCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAA

AGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAta

cGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATG

CCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAAT

GCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCA

ACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAG

ACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTT

CGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGT

GCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAG

CTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGA

GCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCC

CCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACctgGT

GGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACC

ACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTAC

ATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCT

GCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACA

CCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtac

TTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGC

GGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTC

ATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCG

CCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGAT

CGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTT

GGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAAC

GGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAAC

CAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCG

CCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCT

GGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCC

TGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGA

AGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAG

ATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCC

AGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTC

AGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGA

GAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCT

AGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAAC

TTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCG

ACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCT

GGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGA

CGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAA

AGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGA

CCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.2.12.1 (Signal peptide is in bold and underlined; Spike

protein ectodomain underlined): SEQ ID NO: 51

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2.12.1 (Spike protein ectodomain without signal

peptide): SEQ ID NO: 52

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGG

CACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGT

GTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACC

ACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTG

GTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTA

TCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGC

CAACAACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGC

AAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGC

TACTTCAAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCA

GGGCTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACC

CGGTTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGC

AGCAGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCT

AGAACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGAT

TGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGG

AgAAGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGT

GCGGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCA

GATTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCG

ACTACTCCGTGCTGTACAACttcGCCcctTTCttegccTTCAAGTGCTACGGCGTGTCCCC

TACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATC

CGGGGAaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTAC

AACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACa

agCTGGACTCCAAAGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGGAAG

TCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCa

acaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGC

TTTcggCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCT

GACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGC

CGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCAC

CCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAAT

CAGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTC

ACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTT

TCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAG

TGCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagA

GCcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCC

GAGAACctgGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGAC

CGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAG

CGGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGC

CTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAA

GCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAG

CAGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGG

CACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTG

CTGAACGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAG

ACTGATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATC

AGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAG

TGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTG

ATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACG

TGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCA

AAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGT

GACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGT

GTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCT

CTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAAC

CACACAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTC

GTGAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAAC

GAGAGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGG

CCC

Amino Acid Sequence of BA.2.12.1 (Spike protein ectodomain without signal

peptide): SEQ ID NO: 53

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN

GTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEF

QFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKN

LREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY

LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKS

FTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA

DYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIAD

YNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAG

NKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTN

LVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPC

SFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRA

GCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENLVAYS

NNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRAL

TGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKV

TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITS

GWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTP

SALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGR

LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAP

HGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ

IITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGI

NASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2.12.1 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 54

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAA

CGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAA

GTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGGAAGTCCAATCTGAA

GCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAA

CGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAt

acGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCAT

GCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAA

TGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGC

AACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACA

GACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCT

TCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAG

TGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCA

GCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAG

AGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATC

CCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACctgGT

GGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACC

ACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTAC

ATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCT

GCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACA

CCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtac

TTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGC

GGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTC

ATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCG

CCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGAT

CGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTT

GGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAAC

GGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAAC

CAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCG

CCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCT

GGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCC

TGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGA

AGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAG

ATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCC

AGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTC

AGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGA

GAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCT

AGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAAC

TTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCG

ACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCT

GGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGA

CGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAA

AGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGA

CCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

C

TCATAACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCT

TTGATTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTC

TCCTGTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGA

TGTGA

Amino Acid Sequence of BA.2.12.1 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 55

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTELLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GG

GGS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.2.12.1 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 56

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCA

CCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCA

AGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGT

GCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAAC

AAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACC

TTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACT

TCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTA

CAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTC

TGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACT

GCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGAC

AGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTG

AAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCT

CTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTAC

CAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATA

TCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTG

TACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTG

TACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAA

CGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAA

GTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGGAAGTCCAATCTGAA

GCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAA

CGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTACGGCTTTcggCCCACAt

acGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCAT

GCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAA

TGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGC

AACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACA

GACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCT

TCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAG

TGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCA

GCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAG

AGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATC

CCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACctgGT

GGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACC

ACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTAC

ATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCT

GCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACA

CCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtac

TTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGC

GGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTC

ATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCG

CCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGAT

CGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTT

GGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAAC

GGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAAC

CAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCG

CCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCT

GGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCC

TGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGA

AGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAG

ATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCC

AGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTC

AGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGA

GAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCT

AGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAAC

TTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCG

ACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCT

GGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGA

CGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAA

AGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGA

CCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.2.12.1 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 57

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPF

LMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGIN

ITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNE

VSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLK

PFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLH

APATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDA

VRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTW

RVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAY

TMSLGAENLVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLL

QYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKP

SKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMI

AQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQF

NSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLD

PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC

GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNG

THWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFK

NHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.2.12.1 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 58

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGG

CACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGT

GTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACC

ACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTG

GTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTA

TCACAAGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGC

CAACAACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGC

AAGCAGGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGC

TACTTCAAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCA

GGGCTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACC

CGGTTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGC

AGCAGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCT

AGAACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGAT

TGTGCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGG

AgAAGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGT

GCGGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCA

GATTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCG

ACTACTCCGTGCTGTACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCC

CCTACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGA

TCCGGGGAaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACT

ACAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCA

ACaagCTGGACTCCAAAGTCGGCGGCAACTACAATTACcagTACCGGCTGTTCCGG

AAGTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCC

GGCaacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGcggTCCTA

CGGCTTTcggCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGC

TTCGAACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATC

TCGTGAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCG

TGCTGACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATA

TCGCCGATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACA

TCACCCCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAG

CAATCAGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCC

ATTCACGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAAT

GTGTTTCAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTA

CGAGTGCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGAC

AaagAGCcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGG

CGCCGAGAACctgGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCA

CCATCAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGG

ACTGCACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCA

GTACGGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAA

CAGGACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACC

CCTCCTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGC

AAGCCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGG

CCGACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAG

GGATCTGATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTG

ACCGATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACA

AGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATG

GCCTACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAG

AAGCTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTG

AGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCA

GGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTG

TGCTGAACGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGAC

AGACTGATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTG

ATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCT

GAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCAC

CTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACAT

ACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACG

GCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTT

CGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTC

GTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACC

CTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGA

ACCACACAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCG

TCGTGAACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGA

ACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGT

GGCCC

Amino Acid Sequence of BA.2.12.1 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 59

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN

GTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEF

QFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKN

LREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSY

LTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKS

FTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVA

DYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIAD

YNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYQYRLFRKSNLKPFERDISTEIYQAG

NKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTN

LVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPC

SFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRA

GCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENLVAYS

NNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRAL

TGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKV

TLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITS

GWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTP

SALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGR

LQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAP

HGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQ

IITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGI

NASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.4/5 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 60

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACC

TGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcC

AGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGA

CGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTCg

gcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

A

Amino Acid Sequence of BA.4/5 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 61

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.4/5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 62

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACC

TGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcC

AGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGA

CGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTCg

gcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.4/5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 63

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.4/5 (Spike ectodomain without signal peptide): SEQ ID

NO: 64

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAA

TGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTT

GCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTG

GACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATC

AAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTT

CTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTT

CAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGC

CTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCC

GTGCTGTACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAG

CTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAa

acGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACA

AGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGA

CTCCAAAGTCggcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCT

GAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTG

TAACGGCGTGgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCA

CAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGC

ATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACA

AATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGA

GCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCAC

AGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAG

CTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGC

AGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGAT

CAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCA

GAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACAT

CCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCT

CTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACA

GCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGT

GACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCAT

GTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGC

TTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGA

ACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCA

AGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGC

AAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCG

GCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGAT

TTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAG

ATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGG

ACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGG

TTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATC

GCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACA

cccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAA

CACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACG

ATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATC

ACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCC

GCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGC

TGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCT

TCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGC

TCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCA

CTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAG

CGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCA

ACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCC

CGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAG

CCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACAT

CCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCC

TGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.4/5 (Spike ectodomain without signal peptide): SEQ ID

NO: 65

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGT

KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF

CNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR

EFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.4/5 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 66

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGAC

CTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagc

CAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCG

ACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTC

ggcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

A

Amino Acid Sequence of BA.4/5 S371 S373 S375 (Signal peptide is in bold and

underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 67

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.4/5 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 68

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGAC

CTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagc

CAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCG

ACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTC

ggcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.4/5 S371 S373 S375 (Signal peptide is in bold and

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, underlined

and italics): SEQ ID NO: 69

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.4/5 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 70

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAA

TGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTT

GCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTG

GACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATC

AAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTT

CTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTT

CAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGC

CTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCC

GTGCTGTACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAA

GCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGG

AaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTA

CAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTG

GACTCCAAAGTCggcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAA

TCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCC

TTGTAACGGCGTGgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggC

CCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGC

TGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAA

CAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGA

GAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATAC

CACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTG

CAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGT

GGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCC

GATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGA

CCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGA

CATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacG

CCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAA

CAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGC

GTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACC

ATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCA

GCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAA

GAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTAT

CAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCA

GCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGC

CGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTG

ATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATG

AGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCT

GGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACC

GGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGA

TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCA

CAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTG

AACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAA

CGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGA

TCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAG

CCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGT

GCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAG

CTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCC

GCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCC

CACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCC

AGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGG

CAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAG

CCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACA

AGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAAC

ATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAG

CCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.4/5 S371 S373 S375 (Spike ectodomain without signal

peptide is underlined; S371 S373 S375 is in bold, underlined and italics): SEQ ID

NO: 71

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGT

KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF

CNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR

EFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNERVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.5 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 74

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACC

TGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcC

AGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGA

CGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTCa

gcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

ATAA

Amino Acid Sequence of BA.5 (Signal peptide is in bold and underlined; GS linker

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain

is underlined): SEQ ID NO: 75

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYRYRLFRKSNLKPFE

RDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPA

TVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP

QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS

TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSL

GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGS

FCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSP

IEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKENGLTVLPPLLTDEMIAQYTS

ALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIG

KIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAE

VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGY

HLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWF

VTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTS

PDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGGGS

L

ITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM
*

Nucleotide Sequence of BA.5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 76

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACC

TGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcC

AGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGA

CGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTCa

gcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 77

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYRYRLFRKSNLKPFE

RDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPA

TVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP

QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS

TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSL

GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGS

FCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSP

IEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTS

ALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIG

KIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAE

VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGY

HLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWF

VTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTS

PDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.5 (Spike ectodomain without signal peptide is

underlined): SEQ ID NO: 78

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAA

TGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTT

GCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTG

GACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATC

AAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTT

CTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTT

CAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGC

CTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCC

GTGCTGTACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAG

CTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAa

acGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACA

AGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGA

CTCCAAAGTCagcGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCAATCT

GAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTG

TAACGGCGTGgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCA

CAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGC

ATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACA

AATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGA

GCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCAC

AGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAG

CTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGC

AGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGAT

CAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCA

GAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACAT

CCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCT

CTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACA

GCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGT

GACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCAT

GTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGC

TTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGA

ACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCA

AGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGC

AAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCG

GCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGAT

TTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAG

ATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGG

ACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGG

TTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATC

GCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACA

cccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAA

CACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACG

ATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATC

ACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCC

GCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGC

TGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCT

TCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGC

TCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCA

CTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAG

CGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCA

ACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCC

CGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAG

CCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACAT

CCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCC

TGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.5 (Spike ectodomain without signal peptide is underlined):

SEQ ID NO: 79

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGT

KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF

CNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR

EFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNERVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKENGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Signal peptide is

in bold and underlined; GS linker is in italics; TM and CT From F is in bold and

double underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics

and underlined): SEQ ID NO: 80

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGAC

CTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagc

CAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCG

ACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTC

agcGGCAACTACAATTACctgTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

A

Amino Acid Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Signal peptide is

in bold and underlined; GS linker is in italics; TM and CT From F is in bold and double

underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold, italics and

underlined): SEQ ID NO: 81

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFE

RDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPA

TVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP

QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS

TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSL

GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGS

FCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSP

IEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTS

ALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIG

KIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAE

VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGY

HLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWF

VTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTS

PDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGGGS

L

ITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTKM
*

Nucleotide Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Signal peptide is

in bold and underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold,

italics and underlined): SEQ ID NO: 82

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTACG

CCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACA

ACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGAC

CTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagc

CAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCG

ACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAGTC

agcGGCAACTACAATTACctgTACCGGCTGTTCCGGAAGTCCAATCTGAAGCCCTTC

GAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGT

GgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGT

GGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTG

CCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGA

ACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGA

AGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGT

TAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGG

AGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTAC

CAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACAC

CTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCT

GTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGG

CGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCA

GCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCT

ACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGA

GATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGC

GGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCC

AGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAG

AGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGC

GGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCc

ctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAA

GCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAG

AAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCC

AGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAG

CTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCA

TCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGT

TCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCT

GGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTC

AAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Signal peptide is

in bold and underlined; Spike ectodomain is underlined; S371 S373 S375 is in bold,

italics and underlined): SEQ ID NO: 83

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVY

AWNRKRISNCVADYSVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFE

RDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPA

TVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDP

QTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYS

TGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSL

GAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGS

FCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSP

IEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKENGLTVLPPLLTDEMIAQYTS

ALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIG

KIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAE

VQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGY

HLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWF

VTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTS

PDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Spike ectodomain

without signal peptide is underlined; S371 S373 S375 is in bold, italics and

underlined): SEQ ID NO: 84

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAA

TGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTT

GCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTG

GACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATC

AAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTT

CTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTT

CAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGC

CTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCC

GTGCTGTACAACtccGCCagcTTCagcgccTTCAAGTGCTACGGCGTGTCCCCTACCAA

GCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGG

AaacGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTA

CAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTG

GACTCCAAAGTCagcGGCAACTACAATTACctgTACCGGCTGTTCCGGAAGTCCAAT

CTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCT

TGTAACGGCGTGgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCC

CACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCT

GCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAA

CAAATGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGA

GAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATAC

CACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTG

CAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGT

GGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCC

GATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGA

CCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGA

CATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacG

CCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAA

CAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGC

GTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACC

ATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCA

GCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAA

GAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTAT

CAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCA

GCAAGCGGAGCcctATCGAGGACCTGTGTTCAACAAAGTGACACTGGCCGACGC

CGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTG

ATTTGCGCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATG

AGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCT

GGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACC

GGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGA

TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCA

CAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTG

AACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAA

CGATATCCTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGA

TCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAG

CCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGT

GCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAG

CTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCC

GCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCC

CACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCC

AGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGG

CAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAG

CCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACA

AGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAAC

ATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAG

CCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.5 S371 S373 S375 L452 (BA.5 SSS L452) (Spike

ectodomain without signal peptide is underlined; S371 S373 S375 is in bold, italics

and underlined): SEQ ID NO: 85

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGT

KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF

CNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR

EFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNERVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNSASFSAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BQ.1.1 (Signal peptide is in bold and underlined; GS linker is

in italics; TM and CT From F is in bold and double underlined; Spike ectodomain is

underlined): SEQ ID NO: 86

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCaccTTCGCCTCTGTGTACGCC

TGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACAACt

tcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGT

GCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcCAG

ATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGACG

ACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCaccGTCggcGG

CAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCaagCTGAAGCCCTTCGAGCG

GGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGTGgccGG

CgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGTGGGCca

cCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTGCCACA

GTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTC

AACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGTTC

CTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAG

ATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGGAGTGTC

TGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGggc

GTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACAT

GGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCTGTCTGAT

CGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGC

ATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCAGCCAGAG

CATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAAC

AACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGC

CTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTC

CACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGaagA

GAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCG

CCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGCGGCTTCAAT

TTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCcctATCGAGG

ACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATG

GCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAA

CGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACA

TCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCTGGCcctGC

TCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGA

CCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCG

CCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGGGAAAGCT

GCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTG

TCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGACTGGA

CccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGCAGTCCC

TGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTG

CCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAG

TGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCA

CGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATTTCACC

ACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTG

TTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCC

AGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTGATCGG

CATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAA

GAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACCTGGGC

GATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGG

CTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAGAACTG

GGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCATAACATACA

TCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGCA

TGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCG

GTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTGATAA

Amino Acid Sequence of BQ.1.1 (Signal peptide is in bold and underlined; GS linker is

in italics; TM and CT From F is in bold and double underlined; Spike ectodomain is

underlined): SEQ ID NO: 87

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATTFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSTVGGNYNYRYRLFRKSKLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BQ.1.1 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 88

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAATGGCACCAAGAG

ATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAG

AAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAAGACC

CAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAG

TTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAA

GAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGC

AAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGA

ACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTG

GCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAGCT

GGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGT

ACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGA

GCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGA

CCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCAC

CAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCaccTTCGCCTCTGTGTACGCC

TGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTACAACt

tcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGT

GCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcCAG

ATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGACG

ACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCaccGTCggcGG

CAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCaagCTGAAGCCCTTCGAGCG

GGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGTGgccGG

CgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGTGGGCca

CCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTGCCACA

GTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTC

AACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGTTC

CTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAG

ATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGGAGTGTC

TGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGggc

GTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACAT

GGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCTGTCTGAT

CGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGC

ATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCAGCCAGAG

CATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAAC

AACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGC

CTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTC

CACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGaagA

GAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCG

CCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGCGGCTTCAAT

TTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCcctATCGAGG

ACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATG

GCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAA

CGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACA

TCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCTGGCcctGC

TCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGA

CCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCG

CCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGGGAAAGCT

GCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTG

TCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGACTGGA

CccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGCAGTCCC

TGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTG

CCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAG

TGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCA

CGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATTTCACC

ACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTG

TTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCC

AGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTGATCGG

CATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAA

GAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACCTGGGC

GATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGG

CTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAGAACTG

GGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BQ.1.1 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 89

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVN

NATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINIT

RFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCA

LDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATTFASVY

AWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVS

QIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSTVGGNYNYRYRLFRKSKLKPF

ERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BQ.1.1 (Spike ectodomain without signal peptide is underlined):

SEQ ID NO: 90

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCTCCGGCACCAA

TGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTT

GCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTG

GACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATC

AAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTACTATCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCAACCTCggcCGGGATCTGCCTCAGGGCTT

CTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTT

CAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCaccTTCGCC

TCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCC

GTGCTGTACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAG

CTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAa

acGAAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACA

AGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGA

CTCCaccGTCggGGCAACTACAATTACcggTACCGGCTGTTCCGGAAGTCCaagCTGA

AGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTA

ACGGCGTGgccGGCgtgAACTGCTACTTCCCACTGcagTCCTACGGCTTTcggCCCACAt

acGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCAT

GCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAA

TGCGTGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGC

AACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACA

GACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCT

TCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAG

TGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCA

GCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAG

AGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATC

CCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCT

GTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGC

GTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGA

CCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGT

ACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTT

CTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAAC

ACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGt

acTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAG

CGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTT

CATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGC

GCCCAGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGA

TCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATT

TGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAA

CGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAA

CCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGC

GCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCC

TGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATC

CTGAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGG

AAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGA

GATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGC

CAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCT

CAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAG

AGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCC

TAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAA

CTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGC

GACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGC

TGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCG

ACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGA

AAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCG

ACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BQ.1.1 (Spike ectodomain without signal peptide is

underlined): SEQ ID NO: 91

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGT

KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF

CNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLR

EFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATTFASVYAWNRKRISNCVADY

SVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSTVGGNYNYRYRLFRKSKLKPFERDISTEIYQAGNKP

CNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of XBB.1.5 (Signal peptide is in bold and underlined; GS linker is

in italics; TM and CT From F is in bold and double underlined; Spike ectodomain is

underlined): SEQ ID NO: 92

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCgctCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCAC

CGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAA

GACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTG

CGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTATcagAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGgagGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCAACCTCgagCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGAA

CCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTGG

CCCTGCACAGAAGCTACCTGACACCTgtcGATAGCAGCAGCGGATGGACAGCTGG

TGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGTAC

AACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGAGC

GAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGACC

AGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCACCA

ATCTGTGCCCCTTCcacGAGGTGTTCAATGCCACCaccTTCGCCTCTGTGTACGCCTG

GAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGatcTACAACttcGC

CcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGTGCT

TCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcCAGATT

GCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGACGACT

TCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAcccagcGGCA

ACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCaagCTGAAGCCCTTCGAGCGG

GACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGTGgccGGCc

ctAACTGCTACtctCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGTGGGCcacCAG

CCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTGCCACAGTGT

GCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTCAACT

TCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGTTCCTGC

CATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAGATCC

CCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGGAGTGTCTGTG

ATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGggcGTGA

ACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACATGGCG

GGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCTGTCTGATCGGA

GCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGCATCTG

TGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCAGCCAGAGCATCA

TTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAACAACTC

TATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGCCTGTG

TCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTCCACCG

AGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGaagAGAGCC

CTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCGCCCAA

GTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGCGGCTTCAATTTCAG

CCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCcctATCGAGGACCTG

CTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATGGCGATT

GTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAACGGACT

GACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACATCTGCC

CTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCA

GATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGACCCAGA

ATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATCG

GCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGG

ACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCC

aagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGACTGGACccccctG

AAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGCAGTCCCTGCAGA

CCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCT

GGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTT

TTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTG

GTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTC

CAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTC

CAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATC

ACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGA

ACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAAC

TGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACCTGGGCGATATCA

GCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGGCTGAACG

AGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGT

ACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCATAACATACATCGTCCT

GACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGATTCTTGCATGCTATT

TGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCTGTGGCTCGGTAACA

ACACACTCGACCAGATGAGAGCAACTACAAAGATGTGATAA

Amino Acid Sequence of XBB.1.5 (Signal peptide is in bold and underlined; GS linker=

is in italics; TM and CT From F is in bold and double underlined; Spike ectodomain is

underlined): SEQ ID NO: 93

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFL

MDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASV

YAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEV

SQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPF

ERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of XBB.1.5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 94

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCG

ACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTT

CTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACCAATGGCACC

AAGAGATTCGACAACCCCgctCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCAC

CGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAGCAA

GACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTG

CGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTATcagAAGAACAACAAGAG

CTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGA

GTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGgagGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCAACCTCgagCGGGATCTGCCTCAGGGCTTCTCTGCTCTGGAA

CCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGCTGG

CCCTGCACAGAAGCTACCTGACACCTgtcGATAGCAGCAGCGGATGGACAGCTGG

TGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAAGTAC

AACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTGAGC

GAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAGACC

AGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCACCA

ATCTGTGCCCCTTCcacGAGGTGTTCAATGCCACCaccTTCGCCTCTGTGTACGCCTG

GAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGatcTACAACttcGC

CcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACGACCTGTGCT

TCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacGAAGTGagcCAGATT

GCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCTGCCCGACGACT

TCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCAAAcccagcGGCA

ACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCaagCTGAAGCCCTTCGAGCGG

GACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAACGGCGTGgccGGCc

ctAACTGCTACtctCCACTGcagTCCTACGGCTTTcggCCCACAtacGGCGTGGGCcacCAG

CCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCCCTGCCACAGTGT

GCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCGTGAACTTCAACT

TCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACAAGAAGTTCCTGC

CATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGCCGTTAGAGATCC

CCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGCGGAGTGTCTGTG

ATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTGTACCAGggcGTGA

ACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGACACCTACATGGCG

GGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCGGCTGTCTGATCGGA

GCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATCGGCGCTGGCATCTG

TGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGCCAGCCAGAGCATCA

TTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGCCTACTCCAACAACTC

TATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACAGAGATCCTGCCTGTG

TCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCTGCGGCGATTCCACCG

AGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCACCCAGCTGaagAGAGCC

CTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCAAGAGGTGTTCGCCCAA

GTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCGGCGGCTTCAATTTCAG

CCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGAGCcctATCGAGGACCTG

CTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATCAAGCAGTATGGCGATT

GTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCCAGAAGTTTAACGGACT

GACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCCCAGTACACATCTGCC

CTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGAGCTGGCcctGCTCTGCA

GATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGCATCGGAGTGACCCAGA

ATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAGTTCAACAGCGCCATCG

GCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCCTGGGAAAGCTGCAGG

ACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCC

aagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGACTGGACccccctG

AAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGCTGCAGTCCCTGCAGA

CCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTAGAGCCTCTGCCAATCT

GGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTT

TTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTCTGCCCCTCACGGCGTG

GTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAGAATTTCACCACCGCTC

CAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAGAAGGCGTGTTCGTGTC

CAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTACGAGCCCCAGATCATC

ACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTCGTGATCGGCATTGTGA

ACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGACAGCTTCAAAGAGGAAC

TGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTGGACCTGGGCGATATCA

GCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAGATCGACCGGCTGAACG

AGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTGCAAGAACTGGGGAAGT

ACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of XBB.1.5 (Signal peptide is in bold and underlined; Spike

ectodomain is underlined): SEQ ID NO: 95

MFVFLVLLPLVSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN

VTWFHAIHVSGTNGTKRFDNPALPENDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLI

VNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFL

MDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFHEVFNATTFASV

YAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEV

SQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPF

ERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of XBB.1.5 (Spike ectodomain without signal peptide is

underlined): SEQ ID NO: 96

CAGTGTGTGAACCTGatcACAAGAACCCAGagcTACACCAACAGCTTTACCAGAGG

CGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGAC

CTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGG

CACCAATGGCACCAAGAGATTCGACAACCCCgctCTGCCCTTCAACGACGGGGTGT

ACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCA

CACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGG

TCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacGTCTATcagA

AGAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAAC

AACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGg

agGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTT

CAAGATCTACAGCAAGCACACCCCTATCAACCTCgagCGGGATCTGCCTCAGGGC

TTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGT

TTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTgtcGATAGCAGCAGC

GGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCT

TTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCT

GGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGG

CATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTC

CCCAATATCACCAATCTGTGCCCCTTCcacGAGGTGTTCAATGCCACCaccTTCGCCT

CTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCG

TGatcTACAACttcGCCcctTTCttcgccTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTG

AACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAaacG

AAGTGagcCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAG

CTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTC

CAAAcccagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCaagCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCcctAACTGCTACtctCCACTGcagTCCTACGGCTTTcggCCCACAtacGG

CGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCCC

CTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGCG

TGAACTTCAACTTCAACGGCCTGACCGGCACCGGCGTGCTGACAGAGAGCAACA

AGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGC

CGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGC

GGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTG

TACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGA

CACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCG

GCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGC

CAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGC

CTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACA

GAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCT

GCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCAC

CCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCA

AGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCG

GCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGA

GCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATC

AAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCC

AGAAGTTTAACGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGC

CCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGG

AGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGG

CATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCA

GTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCC

CTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGG

TCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTG

AGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAG

GCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATT

AGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAG

AGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAG

TCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGA

AGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAG

AGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTC

TACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACG

TCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGA

CAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGT

GGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGA

GATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCT

GCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of XBB.1.5 (Spike ectodomain without signal peptide is

underlined): SEQ ID NO: 97

QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTN

GTKRFDNPALPENDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEF

QFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLR

EFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PVDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNERVQPTESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADY

SVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNY

KLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPC

NGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKN

KCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGG

VSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLI

GAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNNSI

AIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIA

VEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLAD

AGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTF

GAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALG

KLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSL

QTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGV

VFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITT

DNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINAS

VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.1 S371 S375 (Signal peptide is in bold and underlined; GS

linker is in italics; transmembrane and cytoplasmic domains of NDV F protein are in

bold and double underlined; HXP-S ectodomain is underlined; S371 S375 is in bold,

italics and underlined): SEQ ID NO: 98

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACtccGCCcctTTCagcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACG

ACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAG

TGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacG

GCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCC

CCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGC

GTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACA

AGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGC

CGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGC

GGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTG

TACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGA

CACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCG

GCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGC

CAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGC

CTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACA

GAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCT

GCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCAC

CCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCA

AGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCG

GCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGA

GCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATC

AAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCC

AGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCC

CAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGA

GCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGC

ATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAG

TTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCC

TGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGT

CAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC
ggcggaggtgggtcg

CTCAT

AACATACATCGTCCTGACTATAATCAGCTTGGTATTTGGTATTTTGTCTTTGA

TTCTTGCATGCTATTTGATGTATAAACAGAAAGCTCAGCAGAAGACTCTCCT

GTGGCTCGGTAACAACACACTCGACCAGATGAGAGCAACTACAAAGATGTG

Amino Acid Sequence of BA.1 S371 S375 (Signal peptide is in bold and underlined; GS

linker is in italics; transmembrane and cytoplasmic domains of NDV F protein are in

bold and double underlined; HXP-S ectodomain is underlined; S371 S375 is in bold,

italics and underlined): SEQ ID NO: 99

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSAPFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP
GGG

GS

LITYIVLTIISLVFGILSLILACYLMYKQKAQQKTLLWLGNNTLDQMRATTK

M
*

Nucleotide Sequence of BA.1 S371 S375 (Signal peptide are in bold and underlined;

HXP-S ectodomain is underlined; S371 S375 is in bold, italics and underlined): SEQ ID

NO: 100

ATGTTCGTGTTTCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCT

GACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGT

GTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACTCTACCCAGGACCTG

TTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCTCCGGCACCAATGGC

ACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCA

GCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGCACCACACTGGACAG

CAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGT

GTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAAGAACAACAAGAGC

TGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACAACTGCACCTTCGAG

TACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCAGGGCAACTTCAAG

AACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTCAAGATCTACAGCA

AGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGGCTTCTCTGCTCTG

GAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGGTTTCAGACACTGC

TGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGCAGCGGATGGACAG

CTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGAACCTTTCTGCTGAA

GTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGTGCTCTGGATCCTCTG

AGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgAAGGGCATCTACCAG

ACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGCGGTTCCCCAATATCA

CCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGATTCGCCTCTGTGTAC

GCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACTACTCCGTGCTGTAC

AACtccGCCcctTTCagcACCTTCAAGTGCTACGGCGTGTCCCCTACCAAGCTGAACG

ACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCCGGGGAGATGAAG

TGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTACAACTACAAGCT

GCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAACaagCTGGACTCCA

AAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAAGTCCAATCTGAAG

CCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGCaacaagCCTTGTAAC

GGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagcTTTagaCCCACAtacG

GCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCGAACTGCTGCATGCC

CCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGTGAAGAACAAATGC

GTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTGACAGAGAGCAACA

AGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCCGATACCACAGACGC

CGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACCCCTTGCAGCTTCGGC

GGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATCAGGTGGCAGTGCTG

TACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCACGCCGATCAGCTGA

CACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTTCAGACCAGAGCCG

GCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGTGCGACATCCCCATC

GGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAGCcacGCCTCTGTGGC

CAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCGAGAACAGCGTGGC

CTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCATCAGCGTGACCACA

GAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTGCACCATGTACATCT

GCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTACGGCAGCTTCTGCAC

CCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGGACAAGAACACCCA

AGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTCCTATCAAGtacTTCG

GCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAGCCCAGCAAGCGGA

GCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCGACGCCGGCTTCATC

AAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGGATCTGATTTGCGCCC

AGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACCGATGAGATGATCGCC

CAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGCGGCTGGACATTTGGA

GCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCCTACCGGTTCAACGGC

ATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAGCTGATCGCCAACCAG

TTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAcccAGCGCCC

TGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGCACTGAACACCCTGGT

CAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGCTGAACGATATCttcAG

CAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACTGATCACCGGAAGGC

TGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAGAGCCGCCGAGATTA

GAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGA

GCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACCTGATGAGCTTCCCTCAGTC

TGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGCCCGCTCAAGAGAAG

AATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAGCCCACTTTCCTAGAG

AAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGACCCAGCGGAACTTCTA

CGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCTGGCAACTGCGACGTC

GTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGCAGCCCGAGCTGGAC

AGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACACAAGCCCCGACGTG

GACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGAACATCCAGAAAGAG

ATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAGAGCCTGATCGACCTG

CAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.1 S371 S375 (Signal peptide is in bold and underlined;

HXP-S ectodomain is underlined; S371 S375 is in bold, italics and underlined): SEQ ID

NO: 101

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLL

IVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLM

DLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI

TRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDC

ALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASV

YAWNRKRISNCVADYSVLYNSAPFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV

RQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPF

ERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAP

ATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVR

DPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRV

YSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYT

MSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQ

YGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPS

KRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIA

QYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFN

SAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPP

EAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCG

KGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGT

HWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKN

HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Nucleotide Sequence of BA.1 S371 S375 (HXP-S ectodomain without signal peptide is

underlined; S371 S375 is in bold, italics and underlined): SEQ ID NO: 102

CAGTGTGTGAACCTGACCACAAGAACCCAGCTGCCTCCAGCCTACACCAACAGC

TTTACCAGAGGCGTGTACTACCCCGACAAGGTGTTCAGATCCAGCGTGCTGCACT

CTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACgtgATCT

CCGGCACCAATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACG

GGGTGTACTTTGCCAGCatcGAGAAGTCCAACATCATCAGAGGCTGGATCTTCGGC

ACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAAC

GTGGTCATCAAAGTGTGCGAGTTCCAGTTCTGCAACGACCCCTTCCTGgacCACAA

GAACAACAAGAGCTGGATGGAAAGCGAGTTCCGGGTGTACAGCAGCGCCAACA

ACTGCACCTTCGAGTACGTGTCCCAGCCTTTCCTGATGGACCTGGAAGGCAAGCA

GGGCAACTTCAAGAACCTGCGCGAGTTCGTGTTCAAGAACATCGACGGCTACTTC

AAGATCTACAGCAAGCACACCCCTATCatcGTGCGGgaacccgaaGATCTGCCTCAGGG

CTTCTCTGCTCTGGAACCCCTGGTGGATCTGCCCATCGGCATCAACATCACCCGG

TTTCAGACACTGCTGGCCCTGCACAGAAGCTACCTGACACCTGGCGATAGCAGC

AGCGGATGGACAGCTGGTGCCGCCGCTTACTATGTGGGCTACCTGCAGCCTAGA

ACCTTTCTGCTGAAGTACAACGAGAACGGCACCATCACCGACGCCGTGGATTGT

GCTCTGGATCCTCTGAGCGAGACAAAGTGCACCCTGAAGTCCTTCACCGTGGAgA

AGGGCATCTACCAGACCAGCAACTTCCGGGTGCAGCCCACCGAATCCATCGTGC

GGTTCCCCAATATCACCAATCTGTGCCCCTTCgacGAGGTGTTCAATGCCACCAGA

TTCGCCTCTGTGTACGCCTGGAACCGGAAGCGGATCAGCAATTGCGTGGCCGACT

ACTCCGTGCTGTACAACtccGCCcctTTCagcACCTTCAAGTGCTACGGCGTGTCCCCT

ACCAAGCTGAACGACCTGTGCTTCACAAACGTGTACGCCGACAGCTTCGTGATCC

GGGGAGATGAAGTGCGGCAGATTGCCCCTGGACAGACAGGCaacATCGCCGACTA

CAACTACAAGCTGCCCGACGACTTCACCGGCTGTGTGATTGCCTGGAACAGCAA

CaagCTGGACTCCAAAGTCagcGGCAACTACAATTACCTGTACCGGCTGTTCCGGAA

GTCCAATCTGAAGCCCTTCGAGCGGGACATCTCCACCGAGATCTATCAGGCCGGC

aacaagCCTTGTAACGGCGTGgccGGCTTCAACTGCTACTTCCCACTGagaTCCTACagc

TTTagaCCCACAtacGGCGTGGGCcacCAGCCCTACAGAGTGGTGGTGCTGAGCTTCG

AACTGCTGCATGCCCCTGCCACAGTGTGCGGCCCTAAGAAgAGCACCAATCTCGT

GAAGAACAAATGCGTGAACTTCAACTTCAACGGCCTGaagGGCACCGGCGTGCTG

ACAGAGAGCAACAAGAAGTTCCTGCCATTCCAGCAGTTTGGCCGGGATATCGCC

GATACCACAGACGCCGTTAGAGATCCCCAGACACTGGAAATCCTGGACATCACC

CCTTGCAGCTTCGGCGGAGTGTCTGTGATCACCCCTGGCACCAACACCAGCAATC

AGGTGGCAGTGCTGTACCAGggcGTGAACTGTACCGAAGTGCCCGTGGCCATTCA

CGCCGATCAGCTGACACCTACATGGCGGGTGTACTCCACCGGCAGCAATGTGTTT

CAGACCAGAGCCGGCTGTCTGATCGGAGCCGAGtacGTGAACAATAGCTACGAGT

GCGACATCCCCATCGGCGCTGGCATCTGTGCCAGCTACCAGACACAGACAaagAG

CcacGCCTCTGTGGCCAGCCAGAGCATCATTGCCTACACAATGTCTCTGGGCGCCG

AGAACAGCGTGGCCTACTCCAACAACTCTATCGCTATCCCCACCAACTTCACCAT

CAGCGTGACCACAGAGATCCTGCCTGTGTCCATGACCAAGACCAGCGTGGACTG

CACCATGTACATCTGCGGCGATTCCACCGAGTGCTCCAACCTGCTGCTGCAGTAC

GGCAGCTTCTGCACCCAGCTGaagAGAGCCCTGACAGGGATCGCCGTGGAACAGG

ACAAGAACACCCAAGAGGTGTTCGCCCAAGTGAAGCAGATCTACAAGACCCCTC

CTATCAAGtacTTCGGCGGCTTCAATTTCAGCCAGATTCTGCCCGATCCTAGCAAG

CCCAGCAAGCGGAGCcctATCGAGGACCTGCTGTTCAACAAAGTGACACTGGCCG

ACGCCGGCTTCATCAAGCAGTATGGCGATTGTCTGGGCGACATTGCCGCCAGGG

ATCTGATTTGCGCCCAGAAGTTTaagGGACTGACAGTGCTGCCTCCTCTGCTGACC

GATGAGATGATCGCCCAGTACACATCTGCCCTGCTGGCCGGCACAATCACAAGC

GGCTGGACATTTGGAGCTGGCcctGCTCTGCAGATCCCCTTTccaATGCAGATGGCC

TACCGGTTCAACGGCATCGGAGTGACCCAGAATGTGCTGTACGAGAACCAGAAG

CTGATCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGC

AGCACAcccAGCGCCCTGGGAAAGCTGCAGGACGTGGTCAACcacAATGCCCAGGC

ACTGAACACCCTGGTCAAGCAGCTGTCCTCCaagTTCGGCGCCATCAGCTCTGTGC

TGAACGATATCttcAGCAGACTGGACccccctGAAGCCGAGGTGCAGATCGACAGACT

GATCACCGGAAGGCTGCAGTCCCTGCAGACCTACGTTACCCAGCAGCTGATCAG

AGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGT

GTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGGCAAGGGCTACCACTGATG

AGCTTCCCTCAGTCTGCCCCTCACGGCGTGGTGTTTCTGCACGTGACATACGTGC

CCGCTCAAGAGAAGAATTTCACCACCGCTCCAGCCATCTGCCACGACGGCAAAG

CCCACTTTCCTAGAGAAGGCGTGTTCGTGTCCAACGGCACCCATTGGTTCGTGAC

CCAGCGGAACTTCTACGAGCCCCAGATCATCACCACCGACAACACCTTCGTGTCT

GGCAACTGCGACGTCGTGATCGGCATTGTGAACAATACCGTGTACGACCCTCTGC

AGCCCGAGCTGGACAGCTTCAAAGAGGAACTGGATAAGTACTTTAAGAACCACA

CAAGCCCCGACGTGGACCTGGGCGATATCAGCGGAATCAATGCCAGCGTCGTGA

ACATCCAGAAAGAGATCGACCGGCTGAACGAGGTGGCCAAGAATCTGAACGAG

AGCCTGATCGACCTGCAAGAACTGGGGAAGTACGAGCAGTACATCAAGTGGCCC

Amino Acid Sequence of BA.1 S371 S375 (HXP-S ectodomain without signal peptide is

underlined; S371 S375 is in bold, italics and underlined): SEQ ID NO: 103

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGT

NGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE

FQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLRE

FVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT

PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFT

VEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADY

SVLYNSAPFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYN

YKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKP

CNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVK

NKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFG

GVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGC

LIGAEYVNNSYECDIPIGAGICASYQTQTKSHASVASQSIIAYTMSLGAENSVAYSNN

SIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGI

AVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLA

DAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWT

FGAGPALQIPFPMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSAL

GKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQS

LQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHG

VVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIIT

TDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINA

SVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

Amino Acid Sequence of Wuhan strain (Signal peptide is in bold and

underlined; Spike protein ectodomain is underlined):

SEQ ID NO: 104

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLP

FFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQ

SLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVS

QPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLP

IGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDA

VDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRF

ASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRG

DEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSN

LKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELL

HAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTD

AVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPT

WRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVAS

QSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTEC

SNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILP

DPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLT

DEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRENGIGVTQNVLYENQKLI

ANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDIL

SRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSK

RVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGV

FVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEEL

DKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYI

KWP

Amino Acid Sequence of Wuhan strain (Spike protein ectodomain without

signal peptide is underlined):

SEQ ID NO: 105

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVS

GTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIK

VCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQG

NFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLAL

HRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK

CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRIS

NCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTG

KIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY

QAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKK

STNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDI

TPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQ

TRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAEN

SVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQL

NRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLL

FNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLA

GTITSGWTFGAGAALQIPFAMQMAYRENGIGVTQNVLYENQKLIANQFNSAIGKIQD

SLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQID

RLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMS

FPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQR

NFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVD

LGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWP

TABLE 4

Other Sequences

Linker Sequence
GGGGS
SEQ ID NO: 24

SacII Restriction Sequence
CCGCGG
SEQ ID NO: 25

NDV Gene End Sequence
TTAGAAAAAA
SEQ ID NO: 26

NDV Gene Start Sequence
ACGGGTAGAA
SEQ ID NO: 27

Kozak Sequence
CCGCCACC
SEQ ID NO: 28

Signal Sequence
MFVFLVLLPLVSS
SEQ ID NO: 29

6. EXAMPLES
6.1 Example 1: Generation and Rescue of NDV-HXP-S

NDV-HXP-S expressing the spike protein of the Omicron variant were generated using the same approach as previously described (1-3). Briefly, Omicron BA. 1 sublineage specific mutations (A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F) were introduced into the HXP-S backbone, which has ⁶⁸²RRAR⁶⁸⁵changed to “A”, 6 Proline stabilizing mutations and the transmembrane domain (TM) and cytoplasmic tail (CT) from F protein (Table 5).

The viruses were rescued and passed once in eggs via limiting dilutions. The expression of the spike protein was examined by western blot (FIG. 1A). As compared to the Wuhan control, a degradation production below S0 was observed that could be identified by anti-S1 antibody. Based on previous structural work on SARS-COV spike with 2P (4), it is possible that such proteolysis event would not change the pre-fusion conformation due to the presence of 6 Proline stabilizing mutations. However, since it is not clear where the proteolysis occur and how it would affect the immunogenicity at this stage, different constructs were generated aiming to minimize the observed proteolysis event. One approach taken is to make more changes to the S1/S2 furin cleavage site. A previous study described a natural deletion and mutation at the furin cleavage site when the SARS-CoV-2 virus was passaged on Vero E6 cells (5). The changes include a larger portion of deletion at the furin cleavage site (⁶⁷⁹KSHRRARS⁶⁸⁶) and an adaptive V687I mutation (delCSV687I). It is also been reported that residues that are structurally close to the cleavage site might contribute to the S1/S2 cleavage such as H655Y, N679K and P681H/P (6). Therefore, the 655Y in the Omicron spike was changed back to the H655, and 679K and 681H have been deleted in the delCSV687I modifications. This construct was rescued and appeared to show some improvement to the S0 content (FIG. 1B). After assessing other candidates with a panel of different mutations, the proteolysis event might occur in the receptor binding domain (RBD) due to Omicron-specific mutations such as Q493R and Q498R which could introduce cleavage sites. Therefore, additional Omicron constructs with 493R and 498R changed back to Q493 and Q498 are being rescued and characterized (Table 5).

TABLE 5

NDV-HXP-S Omicron constructs
Mutations

NDV-HXP-S Omicron BA.1
A67V, HV69-70 deletion, T95I, G142D,

VYY143-145 deletion, N211 deletion, L212I,

ins214EPE, G339D, S371L, S373P, S375F,

K417N, N440K, G446S, S477N, T478K, E484A,

Q493R, G496S, Q498R, N501Y, Y505H, T547K,

D614G, H655Y, N679K, P681H, N764K, D796Y,

N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron BA.1
A67V, HV69-70 deletion, T95I, G142D,

(H655_delCSV687I)
VYY143-145 deletion, N211 deletion, L212I,

ins214EPE, G339D, S371L, S373P, S375F,

K417N, N440K, G446S, S477N, T478K, E484A,

Q493R, G496S, Q498R, N501Y, Y505H, T547K,

D614G, H655, NSPRRARS 679-686 deletion,

V6871, N764K, D796Y, N856K, Q954H, N969K,

L981F

NDV-HXP-S Omicron BA. 1
A67V, HV69-70 deletion, T95I, G142D,

(Q493 Q498)
VYY143-145 deletion, N211 deletion, L212I,

ins214EPE, G339D, S371L, S373P, S375F,

K417N, N440K, G446S, S477N, T478K, E484A,

Q493, G496S, Q498, N501Y, Y505H, T547K,

D614G, H655Y, N679K, P681H, N764K, D796Y,

N856K, Q954H, N969K, L981F

6.1.1 REFERENCES CITED EXAMPLE 1

1. Sun W, McCroskery S, Liu W C, Leist S R, Liu Y, Albrecht R A, Slamanig S, Oliva J, Amanat F, Schafer A, Dinnon K H, 3rd, Innis B L, Garcia-Sastre A, Krammer F, Baric R S, Palese P. 2020. A Newcastle Disease Virus (NDV) Expressing a Membrane-Anchored Spike as a Cost-Effective Inactivated SARS-CoV-2 Vaccine. Vaccines (Basel) 8.

2. Sun W, Liu Y, Amanat F, Gonzalez-Dominguez I, McCroskery S, Slamanig S, Coughlan L, Rosado V, Lemus N, Jangra S, Rathnasinghe R, Schotsaert M, Martinez J L, Sano K, Mena I, Innis B L, Wirachwong P, Thai D H, Oliveira R D N, Scharf R, Hjorth R, Raghunandan R, Krammer F, Garcia-Sastre A, Palese P. 2021. A Newcastle disease virus expressing a stabilized spike protein of SARS-CoV-2 induces protective immune responses. Nat Commun 12:6197.

3. Sun W, Leist S R, McCroskery S, Liu Y, Slamanig S, Oliva J, Amanat F, Schaefer A, Dinnon K, Garcia-Sastre A, Krammer F, Baric R S, Palese P. 2020. Newcastle disease virus (NDV) expressing the spike protein of SARS-CoV-2 as vaccine candidate. bioRxiv doi: 10.1101/2020.07.26.221861.

4. Kirchdoerfer R N, Wang N, Pallesen J, Wrapp D, Turner H L, Cottrell C A, Corbett K S, Graham B S, Mclellan J S, Ward A B. 2018. Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Sci Rep 8:15701.

5. Xia S, Lan Q, Su S, Wang X, Xu W, Liu Z, Zhu Y, Wang Q, Lu L, Jiang S. 2020. The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin. Signal Transduct Target Ther 5:92.

6 Escalera A, Gonzalez-Reiche A S, Aslam S, Mena I, Laporte M, Pearl R L, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins D A, Balaraman V, McDowell C, Richt J A, Bajic G, Sordillo E M, Dejosez M, Zwaka T P, Krogan N J, Simon V, Albrecht R A, van Bakel H, Garcia-Sastre A, Aydillo T. 2022. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 30:373-387 e7.

6.2 Example 2: Generation and Rescue of Additional NDV-HXP-S

NDV-HXP-S expressing the spike protein of the Omicron variant were generated using the same approach as described in previous work (1-3). Briefly, Omicron BA.1 sublineage specific mutations were introduced into the HXP-S backbone, which has ⁶⁸²RRAR⁶⁸⁵changed to “A”, 6 Proline stabilizing mutations and the transmembrane domain (TM) and cytoplasmic tail (CT) from F protein (Table 6).

The viruses were rescued and passed once in eggs via limiting dilutions. The expression of the spike protein was examined by western blot (FIG. 2A). As compared to the Wuhan control, a cleavage product below S0 that could be identified by anti-S1 antibody. Based on previous structural work on SARS-COV spike with 2P (4), it is possible that such a proteolysis event would not change the pre-fusion conformation due to the presence of 6 Proline stabilizing mutations. However, since it is not clear where the proteolysis occurs and how it would affect the immunogenicity at this stage, different constructs were generated aiming to minimize the observed proteolysis event. One approach taken was to make more changes to the S1/S2 furin cleavage site. It has been reported that residues that are structurally close to the cleavage site might contribute to the S1/S2 cleavage such as H655Y, N679K and P681H/P (5). Therefore, single, double and triple mutations focusing on these residues in different combinations were made, which turned out to be unsuccessful to show an improvement (data not shown) (sequences of the constructs tested are shown in Table 7). A previous study described a natural deletion and mutation at the furin cleavage site when the SARS-CoV-2 virus was passaged on Vero E6 cells (6). The changes included a larger deletion at the furin cleavage site (⁶⁷⁹KSHRRARS⁶⁸⁶) and an adaptive V687I mutation (delCSV687I). Therefore, the 655Y in the Omicron spike was changed back to the H655 and 679K and 681H were deleted in the delCSV687I modifications (Table 6). This construct was rescued and appeared to show some improvement to the S0 content (likely due to structural changes) but did not completely prevent cleavage (FIG. 2B). After assessing candidates with a panel of different mutations, it was suspected that the proteolysis event might occur in the RBD domain due to Omicron-specific mutations. The attention of the inventors was drawn two sites containing more than one Omicron spike specific mutations. One site contains Q493R and Q498R, while the other site contains S371L, S373P and S375F. Single or double mutations were made regarding Q493R and Q498R, but no improvement was observed (sequences of the constructs tested are shown in Table 7). However, mutating amino acid residues 371, 373 and 375 back to S (Table 6) prevented the cleavage of the Omicron spike (FIG. 2C). Therefore, it was concluded that one, two or three of amino acid residue S371L, S373P and S375F cause the cleavage of the spike protein.

TABLE 6

NDV-HXP-S Omicron Constructs

NDV-HXP-S Omicron

Constructs
Mutations

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y,

N679K, P681H, N764K, D796Y, N856K, Q954H, N969K,

L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(H655_delCSV687I)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655,

NSPRRARS 679-686 deletion, V6871, N764K, D796Y, N856K,

Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1 (S371 S373 S375)
N211 deletion, L212I, ins214EPE, G339D, S371, S373, S375,

K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S,

Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K,

P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

TABLE 7

Examples of other mutant constructs that are still cleaved

to a level similar to that of the NDV-HXP-S Omicron BA.1.

NDV-HXP-S Omicron

constructs
Mutations

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1 (N679)
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679,

P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1 (P681 N764)
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y,

N679K, P681, N764, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1 (N679K P681
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

N764)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679,

P681, N764, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(H655)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, N679K,

P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(P681)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y,

N679K, P681, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(N679 P681)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679,

P681, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(H655 P681)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, N679K,

P681, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(H655 N679 P681)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655, N679,

P681, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(Q493)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493,

G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y,

N679K, P681H, N764K, D796Y, N856K, Q954H, N969K,

L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(Q498)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R,

G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K,

P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion,

BA.1
N211 deletion, L212I, ins214EPE, G339D, S371L, S373P,

(Q493 Q498)
S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493,

G496S, Q498, N501Y, Y505H, T547K, D614G, H655Y, N679K,

P681H, N764K, D796Y, N856K, Q954H, N969K, L981F

6.2.1 REFERENCES CITED IN EXAMPLE 2

1. Sun W, McCroskery S, Liu W C, Leist S R, Liu Y, Albrecht R A, Slamanig S, Oliva J, Amanat F, Schafer A, Dinnon K H, 3rd, Innis B L, Garcia-Sastre A, Krammer F, Baric R S, Palese P. 2020. A Newcastle Disease Virus (NDV) Expressing a Membrane-Anchored Spike as a Cost-Effective Inactivated SARS-CoV-2 Vaccine. Vaccines (Basel) 8.

2. Sun W, Liu Y, Amanat F, Gonzalez-Dominguez I, McCroskery S, Slamanig S, Coughlan L, Rosado V, Lemus N, Jangra S, Rathnasinghe R, Schotsaert M, Martinez J L, Sano K, Mena I, Innis B L, Wirachwong P, Thai D H, Oliveira R D N, Scharf R, Hjorth R, Raghunandan R, Krammer F, Garcia-Sastre A, Palese P. 2021. A Newcastle disease virus expressing a stabilized spike protein of SARS-CoV-2 induces protective immune responses. Nat Commun 12:6197.

3. Sun W, Leist S R, McCroskery S, Liu Y, Slamanig S, Oliva J, Amanat F, Schaefer A, Dinnon K, Garcia-Sastre A, Krammer F, Baric R S, Palese P. 2020. Newcastle disease virus (NDV) expressing the spike protein of SARS-CoV-2 as vaccine candidate. bioRxiv doi: 10.1101/2020.07.26.221861.

4. Kirchdoerfer R N, Wang N, Pallesen J, Wrapp D, Turner H L, Cottrell C A, Corbett K S, Graham B S, McLellan J S, Ward A B. 2018. Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis. Sci Rep 8:15701.

5 Escalera A, Gonzalez-Reiche A S, Aslam S, Mena I, Laporte M, Pearl R L, Fossati A, Rathnasinghe R, Alshammary H, van de Guchte A, Farrugia K, Qin Y, Bouhaddou M, Kehrer T, Zuliani-Alvarez L, Meekins D A, Balaraman V, McDowell C, Richt J A, Bajic G, Sordillo E M, Dejosez M, Zwaka T P, Krogan N J, Simon V, Albrecht R A, van Bakel H, Garcia-Sastre A, Aydillo T. 2022. Mutations in SARS-CoV-2 variants of concern link to increased spike cleavage and virus transmission. Cell Host Microbe 30:373-387 e7.

6 Xia S, Lan Q, Su S, Wang X, Xu W, Liu Z, Zhu Y, Wang Q, Lu L, Jiang S. 2020. The role of furin cleavage site in SARS-CoV-2 spike protein-mediated membrane fusion in the presence or absence of trypsin. Signal Transduct Target Ther 5:92.

6.3 Example 3: Generation and Rescue of Additional NDV-HXP-S

With increased prevalence of BA.2 and BA.4/5 during this time (Table 8), NDV-HXP-S expressing the BA.2 spike protein was generated. Omicron BA.2 sublineage specific mutations were introduced into the HXP-S backbone, which has ⁶⁸²RRAR⁶⁸⁵changed to “A”, 6 Proline stabilizing mutations and the transmembrane domain (TM) and cytoplasmic tail (CT) from F protein. The virus was rescued and passed once in eggs via limiting dilutions. The expression of the spike protein was examined by western blot (FIG. 3). As compared to the Wuhan control, a cleavage product below S0 that could be identified by anti-S1 antibody. The BA.2 and BA4/5 spike protein both contain S371F, S373P and S375F mutations (see NDV-HXP-S Omicron BA.2 and NDV-HXP-S Omicron BA.4/5 in Table 8). Omicron BA.2 sublineage specific mutations are introduced into the HXP-S backbone, which has ⁶⁸²RRAR⁶⁸⁵changed to “A”, 6 Proline stabilizing mutations, the transmembrane domain (TM) and cytoplasmic tail (CT) from F protein, and serines are maintained at amino acid positions 371, 373 and 375. (See NDV-HXP-S Omicron BA.2 (S371 S373 S375) in Table 8.) Similarly, Omicron BA.4/5 sublineage specific mutations are introduced into the HXP-S backbone, which has ⁶⁸²RRAR⁶⁸⁵changed to “A”, 6 Proline stabilizing mutations, the transmembrane domain (TM) and cytoplasmic tail (CT) from F protein, and serines are maintained at amino acid positions 371, 373 and 375. (See NDV-HXP-S Omicron BA.4/5 (S371 S373 S375) in Table 8.)

TABLE 8

NDV-HXP-S Omicron

Constructs
Mutations

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, G142D, V213G, G339D, S371F,

BA.2
S373P, S375F. T376A, D405N, R408S, K417N, N440K, S477N,

T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y,

N679K, P681H, N764K, D796Y, Q954H, N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP),A27S, del69-70(HV), G142D, V213G,

BA.4/5
G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N,

N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y,

Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H,

N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, G142D, V213G, G339D, S371, S373,

BA.2
S375, T376A, D405N, R408S, K417N, N440K, S477N, T478K,

(S371 S373 S375)
E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K,

P681H, N764K, D796Y, Q954H, N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP),A27S, del69-70(HV), G142D, V213G,

BA.4/5
G339D, S371, S373, S375, T376A, D405N, R408S, K417N,

(S371 S373 S375)
N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y,

Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H,

N969K

6.4 Example 4: Generation and Rescue of Additional NDV-HXP-S

As previously disclosed in Example 2, S371 S373 and S375 in the BA.1 spike could stabilize the spike protein in its uncleaved form. It was hypothesized that the same amino acid composition at 371, 373, and 375 could also stabilize the BA.2 spike since the BA.2 wild-type spike (NDV-HXP-S Omicron BA.2) was observed to be cleaved when expressed by NDV vector (FIG. 4A). Indeed, when amino acid residues 371, 373 and 375 were reverted back to S371, S373 and S375 in the BA.2 SSS (NDV-HXP-S Omicron BA.2 SSS), the spike protein was stabilized (FIG. 4B). See Table 9 for the amino acid substitutions of BA.2 sequences relative to the ancestral HXP-S.

To develop a vaccine candidates for the BA.5, corresponding amino acid substitutions showed in Table 9 were added. Of note, G446S was added to represent an essential mutation in the BA.2.75.2 variant of concern (VOC) that was circulating at that time, which was also present in BA.1. As expected, the BA.5 spike was cleaved. Subsequently, S371, S373 and S375 were applied to the BA.5 construct, but surprisingly, they were not found sufficient to prevent cleavage of the spike (FIG. 5A). To determine which amino acid substitution(s) contributed to the cleavage of the spike in the presence of the SSS, four (4) essential changes from BA.2 were highlighted, including del69-70, G446S, L452R and F486V. Each substitution was reverted back individually to ancestral sequence designated as Add69-70, G446, L452 and F486 in the presence of SSS. It was found that L452R, but not del69-70, G446S, F486V, causes the cleavage of the spike as L452 stabilized the spike protein (FIG. 5B). BA.5 without the SSS but with L452 was still cleaved indicating both were needed to stabilize the spike proteins (FIGS. 5B and 5C). Therefore, BA.5 SSS L452 was pursued as the BA.5-like vaccine candidate.

TABLE 9

Amino acid substitutions of BA.2 and BA.5

sequences relative to the ancestral HXP-S

NDV-HXP-S Omicron

constructs
Mutations

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, G142D, V213G, G339D, S371F,

BA.2
S373P, S375F, T376A, D405N, R408S, K417N, N440K,

S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H,

D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H,

N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, G142D, V213G, G339D, S371,

BA.2 SSS
S373, S375, T376A, D405N, R408S, K417N, N440K, S477N,

T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G,

H655Y, N679K, P681H, N764K, D796Y, Q954H, N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP),A27S, del69-70(HV), G142D, V213G,

BA.5
G339D, S371F, S373P, S375F, T376A, D405N, R408S,

K417N, N440K, *G446S, S477N, L452R, T478K, E484A,

F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K,

P681H, N764K, D796Y, Q954H, N969K

NDV-HXP-S Omicron
T191, del24-26(LPP),A27S, del69-70(HV), G142D, V213G,

BA.5 SSS L452
G339D, S371, S373, S375, T376A, D405N, R408S, K417N,

N440K, *G446S, S477N, L452, T478K, E484A, F486V,

Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H,

N764K, D796Y, Q954H, N969K

Note:

*G446S was added for breadth since BA.2.75.2 was circulating as a variant of concern at the same time and G446S was one of the key mutations, which was also present in BA.1.

Additionally, NDV vectors expressing the BQ.1.1 variant spike protein or the XBB.1.5 variant spike protein were generated with corresponding amino acid substitutions based on the ancestral HXP-S expressed by the NDV (Table 10). Both BQ.1.1 (FIG. 6A) and XBB.1.5 (FIG. 6C) showed limited cleavage in the spike, which was likely influenced by novel strain-specific mutations in the receptor binding domain (RBD), that the cleavage sites were masked or eliminated. As sufficient uncleaved S0 was expressed (e.g., purified BQ.1.1 as shown in FIG. 6B), no additional modifications were needed for BQ.1.1 and XBB.1.5.

TABLE 10

Amino acid substitutions of BQ.1.1 and XBB.1.5 relative to the ancestral HXP-S

NDV-HXP-S Omicron

constructs
mutations

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, del69-70, G142D, V213G,

BQ.1.1
G339D,R346T, S371F, S373P, S375F, T376A, D405N, R408S,

K417N, N440K, K444T, L452R, N460K, S477N, T478K,

E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y,

N679K, P681H, N764K, D796Y, Q954H, N969K

NDV-HXP-S Omicron
T19I, del24-26(LPP), A27S, V83A, G142D, del144, H146Q,

XBB.1.5
Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P,

S375F, T376A, D405N, R408S, K417N, N440K, V445P,

G446S, N460K, S477N, T478K, E484A, F486P, F490S,

Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H,

N764K, D796Y, Q954H, N969K

6.5 Example 5: Immunization in Mice with NDV-HXP-S Vaccines

As previously identified in Example 2, changing amino acid residues of 371, 373 and 375 in the Omicron BA.1 spike protein back to ancestral S371 S373 and S375 (SSS) could stabilize the spike protein expressed by NDV (FIGS. 7A and 7B). In the process of characterizing how many mutations out of the three were necessary, S371 and S375 were observed to be sufficient to stabilize the BA. 1 spike without affecting the expression level of the protein (FIG. 7C). See Table 11 for mutations in NDV-HXP-S Omicron BA.1 (S371, S375).

TABLE 11

NDV-HXP-S Omicron Construct

NDV-HXP-S Omicron

Construct
Mutations

NDV-HXP-S Omicron
A67V, HV69-70 deletion, T95I, G142D, VYY143-145

BA.1 (S371, S375)
deletion, N211 deletion, L212I, ins214EPE, G339D, S371,

S373P, S375, K417N, N440K, G446S, S477N, T478K, E484A,

Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G,

H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H,

N969K, L981F

To compare the immunogenicity of the cleaved BA. 1 wild-type spike (NDV-HXP-S Omicron BA.1) and the stabilized BA.1 SSS spike (NDV-HXP-S Omicron BA.1 (S371, S373, S375). An immunization study in mice testing live vaccine via the intranasal route was performed. Briefly, female BALB/c mice were immunized intranasally with 106 EID50 of NDV-HXP-S (Wuhan), NDV-HXP-S (BA.1 WT), and NDV-HXP-S (BA.1 SSS) twice with a 4-week interval. Four weeks after the first and second dose, serum IgG against ancestral spike protein, ancestral RBD protein, BA. 1 spike protein, BA. 1 RBD protein, BA.4/5 spike protein, and BA.4/5 RBD protein were measured by ELISAs (FIG. 8A). After the first vaccination, mice that were vaccinated with the Wuhan vaccine developed high levels of ancestral spike and RBD-binding antibodies, which cross-reacted to BA. 1 and BA.4/5 spike and RBD to a much lower level. Mice that received either BA. 1 WT and BA.1 SSS developed high levels of BA. 1 spike and RBD binding antibodies, substantially higher than those induced by the Wuhan vaccine. With the BA. 1 spike-binding antibodies developed to a similar level of the two groups, the BA.1 SSS induced ˜2.4 fold BA.1 RBD-binding antibodies of that induced by the BA.1 WT vaccines. The difference of binding antibodies to the ancestral and BA.4/5 antigens was more pronounced, that BA. 1 SSS appeared to induce more cross-reactive antibodies than the BA. 1 WT vaccine (FIG. 8B). At four weeks after the booster dose, the Wuhan vaccine induced more binding antibodies to all three types of antigens overall following a similar binding profile as that of post-prime vaccination. Again, the second booster dose of BA. 1 WT and BA.1 SSS induced similar levels of BA.1 spike-binding antibodies, but the difference in BA.1 RBD-binding was still about 2.4 fold. It was also clear that BA.1 SSS vaccine induced substantially more ancestral and BA.4/5 RBD-binding antibodies. Even for cross-reactive antibodies to the BA.4/5 spike, the difference was more than 2 fold (FIG. 8C). These data indicate that as compared to the unstable BA.1 WT spike, the stabilized BA.1 SSS induced better strain-specific as well as cross-reactive antibody responses in vivo in naïve animals.

To investigate humoral responses using NDV-HXP-S ancestral and BA.1 SSS as a booster vaccine, a three-vaccination series study was first performed in naïve female BALB/c mice with NDV-based vaccines. Specifically, mice were vaccinated with NDV-HXP-S Wuhan strain twice with a 3-week interval between the first and second dose. Approximately 5 months later, a third booster with either the same ancestral NDV-HXP-S Wuhan vaccine or the NDV-HXP-S BA.1 SSS vaccine was given. This was essentially to mimic a primary vaccination series with NDV-based vaccine and use the NDV-based vaccine again as a third booster when antibodies waned, similar to the real-world COVID-19 booster strategy. Each vaccination was administered intranasally at the same dose (106 EID50) to each mouse. Antibodies induced by the following vaccinations were measured: two vaccinations of the NDV-HXP-S Wuhan (2×NDV-HXP-S), three vaccinations of NDV-HXP-S Wuhan (3×NDV-HXP-S), two vaccinations of NDV-HXP-S Wuhan followed by NDV-HXP-S BA.1 SSS booster, and two vaccinations of the vector (2×NDV WT) (FIG. 9A). Serum IgG titers were measured for all four conditions against the Wuhan spike, BA. 1 spike, Wuhan RBD, BA.1 RBD as well as the vector (inactivated whole virion of NDV WT) by ELISAs. It was observed that as compared to the 2×NDV-HXP-S Wuhan group, a third booster of NDV-HXP-S Wuhan was able to further increase antibody responses to all protein substrates (Wuhan S, BA.1 S, Wuhan RBD, BA.1 RBD) and the vector. Interestingly, as the NDV-HXP-S BA.1 SSS booster brought antibodies against the ancestral and BA. 1 spikes to a similar level as the ancestral booster, it induced more binding-antibodies towards both the ancestral RBD as well as the BA. 1 RBD (FIG. 9B). In the nasal wash, a booster effect of the third dose was also observed at increasing Wuhan spike-, BA.1 spike- and vector-targeting IgA titers, that BA.1 SSS vaccine appeared to increase the BA.1 spike binding antibodies more substantially than the ancestral vaccine (FIG. 9C). In conclusion, a third intransal (i.n.) booster of NDV-HXP-S can increase antibodies titers after a primary i.n. vaccination series with the same vector-based vaccines 5 month later in the mouse model at 106 EID50 per mouse. In this particular study, NDV-HXP-S BA. 1 SSS booster induced more BA. 1 strain specific antibodies than the Wuhan vaccine.

7. EMBODIMENTS

The following are exemplary embodiments:

1. A recombinant protein comprising a derivative of a SARS-CoV-2 Omicron spike protein ectodomain, wherein the derivative comprises the ectodomain of the amino acid sequence of SEQ ID NO: 104 without the signal peptide and with amino acid modifications, wherein the amino acid modifications comprise: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of SEQ ID NO: 104 to a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of SEQ ID NO: 104: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) two or more amino acid modifications to the amino acid sequence of the ectodomain of SEQ ID NO:104 to amino acid residues found at the corresponding amino acid positions in the Omicron spike protein ectodomain, wherein the two or more amino acid modifications comprise two or more amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and/or N969K.

2. The recombinant protein of embodiment 1, wherein the two or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: N440K, S477N, Y505H, N679K, N764K, D796Y, Q954H, and N969K.

3. The recombinant protein of any one of embodiments 1 or 2, wherein the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371 and 375 in SEQ ID NO:104.

4. The recombinant protein of any one of embodiments 1 or 2, wherein the two or more amino acid modifications does not include amino acid modifications at amino acid positions corresponding to amino acid positions of 371, 373, and 375 in SEQ ID NO:104.

5. The recombinant protein of any one of embodiments 1 to 4, wherein the two or more amino acid modifications further comprises the following amino acid modification at the amino acid position corresponding to the indicated amino acid positions of SEQ ID NO: 104: G339D or G339H.

6. The recombinant protein of any one of embodiments 1 to 5, wherein the two or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F.

7. The recombinant protein of any one of embodiments 1 to 5, wherein the two or more amino acid modifications further comprise one or more of the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), T376A, D405N, R408S, and/or Q498R.

8. The recombinant protein of any one of embodiment 1 to 5, wherein the two or more amino acid modifications further comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), T376A, D405N, R408S, and Q498R.

9 The recombinant protein of any one of embodiments 1 to 5, 7, or 8, wherein the two or more amino acid modifications further comprise the following amino acid modification at the amino acid position corresponding to the indicated amino acid position of SEQ ID NO: 104: V213G or V213E.

10. The recombinant protein of any one of embodiments 1 to 5, wherein the two or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

11. The recombinant protein of any one of embodiments 1 to 5, wherein the two or more amino acid modifications comprise the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

12. The recombinant protein of any one of embodiments 1 to 5, wherein the two or more amino acid modifications comprise the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO:104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

13. The recombinant protein of any one of embodiments 1 to 3, wherein the two or more amino acid modifications does not include amino acid modification at the amino acid position corresponding to amino acid position of 452 in SEQ ID NO: 104.

14. The recombinant protein of any one of embodiments 1 to 5, or 13, wherein the two or more amino acid modifications comprise the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

15. A recombinant protein comprising a derivative of a SARS-CoV-2 Omicron spike protein ectodomain, wherein the derivative comprises the ectodomain of the amino acid sequence of SEQ ID NO: 104 without the signal peptide and with amino acid modifications, wherein the amino acid modifications comprise: (1) an amino acid substitution at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of SEQ ID NO: 104 to a single alanine; (2) amino acid substitutions at amino acid residues corresponding to the following amino acid residues of SEQ ID NO: 104: F817P, A892P, A899P, A942P, K986P, and V987P; and (3) 18 or more amino acid modifications to the amino acid sequence of the ectodomain of SEQ ID NO: 104 to amino acid residues found at the corresponding amino acid positions in the Omicron spike protein ectodomain.

16. The recombinant protein of embodiment 15, wherein the 18 or more amino acid modifications do not include amino acid modifications at the amino acid positions corresponding to the amino acid positions 371 and 375 of SEQ ID NO:104.

17. The recombinant protein of embodiment 15, wherein the 18 or more amino acid modifications do not include amino acid modifications at the amino acid positions corresponding to the amino acid positions 371, 373, and 375 of SEQ ID NO: 104.

18. The recombinant protein of any one of embodiments 15 to 17, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO:104: A67V, HV69-70 deletion, T95I, G142D, VYY143-145 deletion, N211 deletion, L212I, ins214EPE, G339D, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, and L981F.

19. The recombinant protein of any one of embodiments 15 to 17, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

20. The recombinant protein of any one of embodiments 15 to 17, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO:104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

21. The recombinant protein of any one of embodiments 15 to 17, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

22. The recombinant protein of embodiment 15, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, del69-70, G142D, V213G, G339D, R346T, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

23. The recombinant protein of embodiment 15, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at the amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO: 104: T19I, del24-26 (LPP), A27S, V83A, G142D, del144, H146Q, Q183E, V213E, G252V, G339H, R346T, L368I, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, V445P, G446S, N460K, S477N, T478K, E484A, F486P, F490S, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

24. The recombinant protein of any one of embodiments 15 to 17, wherein the 18 or more amino acid modifications does not include amino acid modification at the amino acid position corresponding to amino acid position of 452 in SEQ ID NO: 104.

25. The recombinant protein of any one of embodiments 15 to 17, or 24, wherein the 18 or more amino acid modifications comprise the following amino acid modifications at amino acid positions corresponding to the indicated amino acid positions of SEQ ID NO:104: T19I, del24-26 (LPP), A27S, del69-70 (HV), G142D, V213G, G339D, T376A, D405N, R408S, K417N, N440K, S477N, L452R, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, N764K, D796Y, Q954H, and N969K.

26. The recombinant protein of embodiment 15, wherein the derivative of the ectodomain comprises the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, or 79.

27. A recombinant protein comprising a derivative of the ectodomain of a SARS-CoV-2 variant, wherein the ectodomain comprises an amino acid sequence that is at least 90% identical to the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, 79, 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95 or 101.

28. The recombinant protein of embodiment 27, wherein the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO: 104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO:104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K.

29 The recombinant protein of embodiment 27, wherein the ectodomain comprises the amino acid sequence of SEQ ID NO: 103, 35, 85, 47, 59, 91, 97, 19, 21, 23, 41, 53, 65, 71, 79, 33, 39, 45, 51, 57, 63, 69, 77, 83, 89, 95 or 101.

30. The recombinant protein of any one of embodiments 1 to 26, wherein the protein further comprises a signal peptide.

31. The recombinant protein of embodiment 27, wherein the signal peptide comprises the amino acid sequence of SEQ ID NO:29.

32. The recombinant protein of any one of embodiments 1 to 31, wherein the protein further comprises the transmembrane and cytoplasmic domains of NDV F protein.

33. The recombinant protein of any one of embodiments 1 to 32, wherein the protein further comprises a linker and the transmembrane and cytoplasmic domains of NDV F protein.

34. The recombinant protein of embodiment 32 or 33, wherein the transmembrane and cytoplasmic domains of NDV F protein comprises the amino acid sequence of SEQ ID NO: 5.

35. A polynucleotide comprising a nucleotide sequence encoding the protein of any one of embodiments 1 to 31.

36. The polynucleotide of embodiment 35, which comprises the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, 78, 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

37. A polynucleotide comprising a nucleotide sequence encoding the protein of any one of embodiments 32 to 33.

38. The polynucleotide of embodiment 37, which comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 7, 10, 11, 14, 15, 36, 48, 60 or 74.

39. The polynucleotide of embodiment 38, wherein the nucleotide sequence encodes the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 9, 12, 13, 16, 17, 37, 49, 61, or 75.

40. A vector comprising the polynucleotide of any one of embodiments 35 to 39.

41. The vector of embodiment 40, which is a plasmid or a viral vector.

42. A transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises:

- (a) the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75 without the signal peptide;
- (b) the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75;
- (c) an amino acid sequence that is at least 90% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75 without the signal peptide; or
- (d) an amino acid sequence that is at least 90% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

43. The transgene of embodiment 42, wherein the chimeric F protein comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75 without the signal peptide.

44. The transgene of embodiment 42, wherein the chimeric F protein comprises an amino acid sequence that is at least 90% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

45. The transgene of embodiment 42, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75 without the signal peptide.

46. The transgene of embodiment 42, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

47. The transgene of embodiment 42, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75 without the signal peptide.

48. The transgene of embodiment 42, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

49. A transgene comprising a nucleotide sequence encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises:

- (a) the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79;
- (b) the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77;
- (c) an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79; or
- (d) an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77.

50. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

51. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77.

52. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

53. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77.

54. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

55. The transgene of embodiment 49, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 33, 83, 101, 89, 95, 45, 57, 39, 51, 63, 69, or 77.

56. A transgene comprising:

- (a) the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide;
- (b) the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74;
- (c) a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide; or
- (d) a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

57. The transgene of embodiment 56, which comprises a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

58. The transgene of embodiment 56, which comprises a nucleotide sequence that is at least 80% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

59. The transgene of embodiment 56, which comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 44, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

60. The transgene of embodiment 56, which comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

61. The transgene of embodiment 56, which comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

62. The transgene of embodiment 56, which comprises the nucleotide sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

63. A transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises:

- (a) the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78;
- (b) the nucleotide sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76;
- (c) a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78; or
- (d) a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

64. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

65. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 80% identical to the nucleotide sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

66. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

67. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the nucleotide sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

68. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

69. The transgene of embodiment 63, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the nucleotide sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

70. A transgene comprising:

- (a) an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide;
- (b) an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74;
- (c) an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide; or
- (d) an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

71. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

72. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

73. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

74. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

75. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74 without the nucleotide sequence encoding the signal peptide.

76. The transgene of embodiment 70, which comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 30, 42, 54, 66, 80, 86, 92, 98, 6, 10, 14, 36, 48, 60, or 74.

77. A transgene comprising a polynucleotide encoding a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises:

- (a) an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78;
- (b) an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76;
- (c) an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78; or
- (d) an RNA sequence corresponding to the negative sense of the cDNA sequence of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

78. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

79. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 80% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

80. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

81. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of a nucleotide sequence that is at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% identical to the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

82. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 34, 84, 102, 90, 96, 46, 58, 18, 20, 22, 40, 52, 64, 70, or 78.

83. The transgene of embodiment 77, wherein the nucleotide sequence encoding the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 32, 82, 100, 88, 94, 44, 56, 38, 50, 62, 68, or 76.

84. The transgene of any one of embodiments 49 to 55, wherein the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

85. The transgene of embodiment 84, wherein the linker comprises the amino acid sequence of SEQ ID NO:24.

86. The transgene of any one of embodiments 77 to 82, wherein the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

87. The transgene of embodiment 82, wherein the linker comprises the amino acid sequence of SEQ ID NO:24.

88. The transgene of any one of embodiments 63 to 69, wherein the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

89. The transgene of embodiment 88, wherein the linker comprises the amino acid sequence of SEQ ID NO:24.

90. The transgene of any one of embodiments 56 to 69, 88 or 89, wherein the transgene further comprises a Newcastle Disease Virus (NDV) gene start sequence.

91. The transgene of any one of embodiments 56 to 69, 88, or 89, wherein the transgene further comprises a Newcastle Disease Virus (NDV) gene end sequence.

92. The transgene of any one of embodiments 56 to 69, 88, 89, or 91, wherein the transgene further comprises the nucleotide sequence of SEQ ID NO:26 and 27.

93. The transgene of any one of embodiments 56 to 69, 88, 89, 91, or 92, wherein the transgene further comprises the nucleotide sequence of SEQ ID NO: 25, SEQ ID NO:28, or SEQ ID NOS: 25 and 28.

94. The transgene of any one of embodiments 42 to 55, or 77 to 87, wherein the transgene further comprises a Newcastle Disease Virus (NDV) gene start sequence.

95. The transgene of any one of embodiments 42 to 55, 77 to 87, or 94, wherein the transgene further comprises a Newcastle Disease Virus (NDV) gene end sequence.

96. The transgene of any one of embodiments 42 to 55, 77 to 87, 94, or 95, wherein the transgene further comprises an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NO: 25, SEQ ID NO:28, or an RNA sequence corresponding to the negative sense of the cDNA sequence of SEQ ID NOS: 25 and 28.

97. A vector comprising the transgene of any one of embodiments 42 to 96.

98. A nucleotide sequence comprising the transgene of any one of embodiments 42 to 55, 70 to 87, or 94 to 96, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit.

99. A nucleotide sequence comprising the transgene of any one of embodiments 42 to 55, 70 to 87, or 94 to 96, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit, wherein the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain.

100. A nucleotide sequence comprising the transgene of any one of embodiments 56 to 69, or 88 to 93, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit.

101. A nucleotide sequence comprising the transgene of any one of embodiments 56 to 69, or 88 to 93, and (1) a NDV F transcription unit, (2) a NDV NP transcription unit, (3) a NDV M transcription unit, (4) a NDV L transcription unit, (5) a NDV P transcription unit, and (6) a NDV HN transcription unit, wherein the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain.

102. A vector comprising the nucleotide sequence of any one of embodiments 98 to 101.

103. A recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises the transgene of any one of embodiments 42 to 55, 70 to 87, or 94 to 96.

104. The recombinant NDV of embodiment 103, wherein the NDV virion comprises the chimeric F protein.

105. A recombinant Newcastle disease virus (NDV) comprising a packaged genome, wherein the packaged genome comprises a transgene, wherein the transgene encodes a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, or an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

106. The recombinant NDV of embodiment 105, wherein the derivative of the ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, and wherein the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO: 104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO: 104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K.

107. The recombinant NDV of embodiment 103 to 106, wherein the genome comprises a NDV F transcription unit, a NDV NP transcription unit, a NDV M transcription unit, a NDV L transcription unit, a NDV P transcription unit, and a NDV HN transcription unit.

108. The recombinant NDV of embodiment 103 to 106, wherein the genome comprises a NDV F transcription unit, a NDV NP transcription unit, a NDV M transcription unit, a NDV L transcription unit, a NDV P transcription unit, and a NDV HN transcription unit, and wherein the NDV F transcription unit encodes a NDV F protein comprising a leucine to alanine amino acid substitution at the amino residue corresponding to amino acid residue 289 of the LaSota NDV strain.

109. The recombinant NDV of any one of embodiments 103 to 108, wherein the transgene is between two NDV transcription units of the packaged genome.

110. The recombinant NDV of embodiment 109, wherein the two transcription units of the packaged genome are the transcription units for the NDV P gene and the NDV M gene.

111. The recombinant NDV of embodiment 109, wherein the two transcription units of the packaged genome are the transcription units for the NDV NP gene and the NDV P gene.

112. A recombinant NDV comprising a chimeric F protein, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75, or an amino acid sequence that is at least 90% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

113. The recombinant NDV of embodiment 112, wherein the chimeric F protein comprises an amino acid sequence that is at least 90%, identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

114. The recombinant NDV of embodiment 112, wherein the chimeric F protein comprises an amino acid sequence that is at least 95%, at least 98%, or at least 99% identical to SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

115. The recombinant NDV of embodiment 112, wherein the chimeric F protein comprises the amino acid sequence of SEQ ID NO: 31, 43, 55, 67, 81, 87, 93, 99, 8, 12, 16, 37, 49, 61, or 75.

116. A recombinant NDV comprising a protein, wherein the protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, or an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

117. The recombinant NDV of embodiment 116, wherein the derivative of the ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, and wherein the derivative of the ectodomain comprises: (1) alanine at amino acid residues corresponding to amino acid residues 682 to 685 (RRAR) of the amino acid sequence of SEQ ID NO: 104; (2) proline at amino acid residues corresponding to the following amino acid residues of the amino acid sequence of SEQ ID NO: 104: F817, A892, A899, A942, K986, and V987; and (3) two or more of the following amino acid residues at amino acid positions corresponding to the indicated amino acid positions of the amino acid sequence of SEQ ID NO: 104: 440K, 477N, 505H, 679K, 764K, 796Y, 954H, and/or 969K.

118. A recombinant NDV comprising a chimeric F protein, wherein the chimeric F protein comprises a derivative of a SARS-CoV-2 Omicron virus spike protein ectodomain and NDV F protein transmembrane and cytoplasmic domains, and wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79, or an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

119. The recombinant NDV of embodiment 118, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

120. The recombinant NDV of embodiment 118, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises an amino acid sequence at least 95%, at least 98%, or at least 99% identical to the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

121. The recombinant NDV of embodiment 118, wherein the derivative of the SARS-CoV-2 Omicron virus spike protein ectodomain comprises the amino acid sequence of SEQ ID NO: 35, 85, 103, 91, 97, 47, 59, 19, 21, 23, 41, 53, 65, 71, or 79.

122. The recombinant NDV of any one of embodiments 118 to 121, wherein the SARS-CoV-2 Omicron virus spike protein ectodomain is linked via a linker to the NDV F protein transmembrane and cytoplasmic domains.

123. The recombinant NDV of any one of embodiments 103 to 122, which comprises an NDV backbone which is lentogenic.

124. The recombinant NDV of any one of embodiments 103 to 122, which comprises an NDV backbone of LaSota strain.

125. The recombinant NDV of any one of embodiments 103 to 122, which comprises an NDV backbone of Hitchner B1 strain.

126. A composition comprising the recombinant NDV of any one of embodiments 103 to 125, or vector of any one of embodiments 40, 41, or 102.

127. An immunogenic composition comprising the recombinant NDV of any one of embodiments 103 to 125.

128. The immunogenic composition of embodiment 127, wherein the recombinant NDV is inactivated.

129. An immunogenic composition comprising the polynucleotide of any one of embodiments 35 to 39, or vector of any one of embodiments 40, 41, or 102.

130. The immunogenic composition of embodiment 127 or 129, further comprising an adjuvant.

131. A method for inducing an immune response to SARS-CoV-2 Omicron spike protein, comprising administering the immunogenic composition of any one of embodiments 127 to 130 to a subject.

132. A method for preventing COVID-19, or severe COVID-19, comprising administering the immunogenic composition of any one of embodiments 127 to 130 to a subject.

133. A method for immunizing a subject against SARS-CoV-2, comprising administering the immunogenic composition of any one of embodiments 127 to 130 to a subject.

134. The method of any one of embodiments 131 to 133, wherein the composition is administered to the subject intranasally or intramuscularly.

135. The method of any one of embodiments 127 to 134, wherein the subject is a human.

136. The method of any one of embodiments 127 to 135, wherein the subject has been previously vaccinated with a COVID-19 vaccine.

137. The method of any one of embodiments 127 to 136, wherein the subject is administered at least one booster of the immunogenic composition.

138. A kit comprising the recombinant NDV of any one of embodiments 103 to 125.

139. A kit comprising the transgene of any one of embodiments 42 to 96, the polynucleotide of any one of embodiments 35 to 39, the nucleotide sequence of any one of embodiments 98 to 101, the recombinant protein of any one of embodiments 1 to 34, or the vector of embodiment 40, 41, or 102.

140. A cell line, in vitro cell, or chicken embryonated egg comprising the recombinant NDV of any one of embodiments 103 to 125.

141. A cell line, in vitro cell, or chicken embryonated egg comprising the polynucleotide any one of embodiments 35 to 39, or vector of embodiment 40, 41, or 102, the transgene of any one of embodiments 42 to 96, or the nucleotide sequence of any one of embodiments 98 to 101.

142. A cell line, an in vitro cell, or chicken embryonated egg expressing the recombinant protein any one of embodiments 1 to 34.

143. A method for propagating the recombinant NDV of any one of embodiments 103 to 125, the method comprising culturing the cell line, in vitro cell, or embryonated egg of embodiment 140.

144. The method of embodiment 143, wherein the method further comprises isolating the recombinant NDV from the cell line or embryonated egg.

145. A method for detecting the presence of antibody specific to SARS-CoV-2 Omicron spike protein, comprising contacting a specimen with the recombinant NDV of any one of embodiments 103 to 125, or a recombinant protein of any one of embodiments 1 to 34, in an immunoassay.

146. The method of embodiment 145, wherein the specimen is a biological specimen.

147. The method of embodiment 146, wherein the biological specimen is blood, plasma or sera from a subject.

148. The method of embodiment 147, wherein the subject is human.

149. The method of embodiment 145, wherein the specimen is an antibody or antisera.

The invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described will become apparent to those skilled in the art from the foregoing description and accompanying Figures. Such modifications are intended to fall within the scope of the appended claims.

All references cited herein are incorporated herein by reference in their entirety and for all purposes to the same extent as if each individual publication or patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety for all purposes.

Number	Date	Country
63326877	Apr 2022	US
63346262	May 2022	US
63346260	May 2022	US

RECOMBINANT NEWCASTLE DISEASE VIRUSES AND IMMUNOGENIC COMPOSITIONS FOR USE IN IMMUNIZING AGAINST SARS-COV-2 OMICRON VARIANT

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