Patent Application
20240226271
The contents of the electronic sequence listing submitted herewith as file 18636_0020U1_Sequence_Listing.txt; Size: 854,569 bytes; and Date of Creation: Jul. 17, 2023, is herein incorporated by reference in its entirety.
The present disclosure relates to modified viral structural protein. The present invention also relates to virus-like particles (VLPs) comprising modified viral structural protein and methods of producing the VLPs in a host or host cells.
Coronaviruses (CoVs) are the largest group of viruses belonging to the Nidovirales order, which includes Coronaviridae, Arteriviridae, Mesoniviridae, and Roniviridae families. The Coronavirinae comprise one of two subfamilies in the Coronaviridae family, with the other being the Torovirinae. The Coronavirinae are further subdivided into four genera, the alpha, beta, gamma, and delta coronaviruses. Members of alpha coronavirus and beta coronavirus are found exclusively in mammals. The alphacoronavirus genus includes two human virus species, HCoV-229E and HCoV-NL63. Important animal alphacoronaviruses are transmissible gastroenteritis virus of pigs and feline infectious peritonitis virus.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, also known as 2019-nCoV and HCoV-19) is a novel lineage B betacoronavirus (Beta-CoV) and causes coronavirus disease 2019 (COVID-19), a respiratory illness with high mortality and morbidity resulting in major public health impacts worldwide. Outbreaks of SARS-CoV-2, such as the pandemic starting in 2020, are a paramount challenge for healthcare systems due to the incubation period and transmissibility of the virus. Treatments for COVID-19 are urgently needed, but long-term management of SARS-CoV-2 outbreaks will require an effective vaccine.
Coronavirus virions are spherical with diameters of approximately 118-140 nm as depicted in recent studies by cryo-electron tomography and cryo-electron microscopy.
The most prominent structural feature of coronaviruses is the club-shaped spike projections emanating from the surface of the virion. Coronavirus particles consist of a helical nucleocapsid structure, formed by the association between nucleocapsid (N) phosphoproteins and the viral genomic RNA, surrounded by a lipid bilayer where three or four types of structural proteins are inserted: the spike (S), the membrane (M), and the envelope (E) proteins and, for some coronaviruses only, the hemagglutinin-esterase (HE) protein (Masters PS. The molecular biology of coronaviruses. Adv Virus Res. 2006; 66:193-292.)
The membrane (M) protein is the most abundant structural protein in the virion. It is a small (˜25-30 kDa) protein with three transmembrane domains and is thought to give the virion its shape. The envelope (E) protein is a short, integral membrane protein of 76-109 amino acids, ranging from 8.4 to 12 kDa in size. The primary and secondary structure reveals that E has a short, hydrophilic amino terminus consisting of 7-12 amino acids, followed by a large hydrophobic transmembrane domain (TMD) of 25 amino acids, and ends with a long, hydrophilic carboxyl terminus, which comprises the majority of the protein. The E protein is involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis.
The spike (S) protein is a glycoprotein that is required for the recognition of host receptors for many coronaviruses as well as the fusion of viral and host cell membranes for viral entry into cells (Belouzard et al., Viruses 2012 June; 4(6):1011-33). As the primary glycoprotein on the surface of the viral envelope, S proteins of Coronaviridae are a major target of neutralizing antibodies elicited by natural infection, including SARS-CoV-2 infection, and are key antigens targeted in experimental vaccine candidates.
SARS-CoV-2 S protein, like S protein of other coronaviruses, is initially synthesized as a precursor protein. Individual precursor S protein forms a homotrimer and undergoes glycosylation within the Golgi compartment as well as processing to remove the signal peptide. The S protein requires a two-step, protease-mediated activation to facilitate membrane fusion. SARS-CoV-2 S protein is distinguished by a RRAR furin cleavage site at the S1/S2 junction that is presumably processed in the Golgi compartment to yield two separate polypeptides: the S1 and S2 polypeptide (or subunit), which remain non-covalently bound as S1/S2 protomers within the homotrimer in the prefusion conformation (Walls et al. Cell 2020 181(2) p 281-292; Li et al. eLife 2019; 8: e51230.). Furin cleavage at the S1/S2 junction and cleavage at the S2′ site, upstream of the fusion peptide, occurs during viral entry at the cell surface or in endosomes and can be mediated by several proteases.
This trimer is held in the prefusion conformation prior to binding to target receptors on a host cell via receptor binding domain (RBD) epitopes. Receptor binding destabilizes the prefusion trimer, resulting in shedding of the S1 subunit and transition of the S2 subunit to a stable post-fusion conformation through fusion of the virus to the cell membrane (Wrapp et al. Science, 13 Mar. 2020, Vol. 367, Issue 6483, pp. 1260-1263). Neutralizing antibodies from individuals infected with SARS-CoV-2 have been shown to target the RBD of the S1 subunit of the S protein (Premkumar, L., 2020 Science Immunology 11 Jun. 2020: Vol. 5, Issue 48).
Stabilization of the S protein ectodomain in the prefusion conformation tends to increase the recombinant expression yield, possibly by preventing triggering or misfolding that results from a tendency to adopt the more stable post-fusion structure (Hsieh et al. Science 2020, 369 p. 1501-1505).
Mutations to the S protein ectodomain have been shown to facilitate stabilization of the prefusion conformation. WO 2018/081318 and its companion publication by Pallesen, J. et al. (PNAS Aug. 29, 2017 114 (35)) disclose double proline substitutions at or near a junction between a heptad repeat 1 (HR1) and a central helix that stabilize the S ectodomain trimer of MERS-CoV spike protein in a prefusion conformation and substitutions to prevent protease cleavage at a S1/S2 cleavage site and the S2′ cleavage site of the S ectodomain. SARS-CoV-2 S protein stabilized with double proline substitutions at homologous amino acid residues have been used to determine high-resolution structures by cryo-EM (Wrapp et al Science 2020 367, 1260-1263; Walls et al. Cell 2020, 181, 281-292). Further, disruption of the furin recognition site is thought to retain S protein in a prefusion conformation (Wrapp et al Science 2020 367, 1260-1263). However, even with these substitutions, the SARS-CoV-2 S protein ectodomain remains unstable and difficult to produce reliably in mammalian cells, hindering development of effective and high-yield subunit vaccines (Hsieh et al. Science 2020, 369 p. 1501-1505).
Hsieh et al. (Science 2020, 369 p. 1501-1505) designed and expressed in mammalian cells over 100 structure-guided SARS-CoV-2 spike protein variants based upon previously determined cryo-EM structure. The variants were biochemically, biophysically and structurally characterized to identify substitutions that lead to an increase in yield and stability. Hsieh et al. reports multiple prolines, disulfide bonds, salt bridges, and cavity-filling substitutions that increase expression and/or stability of the spike relative to the double proline substitutions. The best identified variant, HexaPro, has six beneficial proline substitutions leading to 10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws.
The S2 subunit can be divided into three domains: a large ectodomain, a transmembrane domain (TM) and a cytoplasmic tail (CT). The cytoplasmic tail of the S protein has previously been shown to be required for assembly. Two distinct retention signals may be found in the CT of Coronaviridae: i) an endoplasmic reticulum retrieval signal (ERRS) and/or ii) a tyrosine-dependent localization signal (YxxI or YxxF motif). The ERRS comprises the dibasic KxHxx motif which binds to the coatomer complex I (COPI). The motif is required for the localization of the SARS S protein to the ERGIC/Golgi region when coexpressed with SARS membrane (M) protein, and localization can be disrupted by mutating the KxHxx motif (McBride et al. J. Virol. February 2007, 81 (5) 2418-2428). S proteins containing an ERRS are recruited into COPI vesicles and retrieved from the Golgi to the endoplasmic reticulum (ER) in retrograde. The repeated cycling of S proteins between the ER and the Golgi leads to S protein intracellular retention. S protein of Alphacoronavirus and Betacoronavirus both comprise an ERRS (Ujike et al. Journal of General Virology (2016), 97, 1853-1864).
S protein of Betacoronavirus, such as S protein of MERS-CoV, SARS-CoV and SARS-CoV 2, possess only an ERRS and cannot be retained intracellularly, resulting in the release of S protein into the plasma membrane. Mutant SARS-CoV S protein lacking the ERRS is transported to the plasma membrane, while native S protein, when coexpressed with M protein, interacts with the M protein near the budding site, leading to S protein intracellular retention, suggesting that the ERRS of SARS-CoV contributes to S protein accumulation specifically in the post-medial Golgi compartment by interaction with M protein, leading to S protein incorporation into VLPs (Ujike et al. Journal of General Virology (2016), 97, 1853-1864). Removal of the ERRS has recently been found to facilitate incorporation of SARS-CoV-2 S protein into lentiviral pseudovirons (Ou et al., 2020 Nature Communications volume 11, Article number: 1620).
Yu et al. (2020 Science) constructed a set of prototype DNA vaccines expressing six variants of the SARS-CoV-2 S protein with various deletions of the cytoplasmic tail, and transmembrane domain, which were assessed for their immunogenicity and protective efficacy against SARS-CoV-2 viral challenge in rhesus macaques. While the soluble fragments of the SARS-CoV-2 S protein ectodomain elicited reduced levels of sgmRNA (indicative of viral replication), optimal protection was achieved with the full-length S protein immunogen.
Broer et al. (2006 J. Virol. p. 1302-1310) studied the roles of the transmembrane and cytoplasmic domains of the S protein in the infectivity and membrane fusion activity of SARS-CoV, using a SARS-CoV S-pseudotyped retrovirus (SARSpp). SARSpp, in which the cytoplasmic domain of S was replaced by the cytoplasmic domain derived from vesicular stomatitis virus G protein (VSV-G), were infectious, up to 40% of wild type. In contrast, SARSpp containing both the TMD and the cytoplasmic domain of VSV-G, were severely impaired in infectivity (<5%). This shows that the TMD of S may be involved in the entry process of SARS-CoV.
Vaccination provides protection against disease by inducing a subject to mount an immune response to a likely agent prior to infection. Conventionally, this has been accomplished through the use of live attenuated or whole inactivated forms of the infectious agents as immunogens. To avoid the danger of using a whole virus (such as killed or attenuated viruses) as a vaccine, viral proteins or subunits, or recombinant versions thereof, have been pursued as vaccines. A major obstacle to employing viral proteins, either native or recombinant, as vaccine agents is ensuring that the conformation of the protein mimics the antigens in their natural environment. Suitable adjuvants and, in the case of peptides, carrier proteins, may be used to boost the immune response. In addition, viral proteins or subunits as vaccines may elicit primarily humoral responses and thus fail to evoke lasting immunity. Subunit vaccines may be ineffective for diseases in which whole inactivated virus can be demonstrated to provide superior protection.
Virus-like particles (VLPs) may be used in immunogenic compositions to express viral proteins in a preferred conformation with improved antigen presentation to the immune system. VLPs closely resemble mature virions, but they do not contain viral genomic material, and they are non-replicative which makes them safe for administration as a vaccine. In addition, VLPs can be engineered to express viral glycoproteins on the surface of the VLP, which is their native physiological configuration. Since VLPs resemble intact virions and are multivalent particulate structures, VLPs may be more effective in inducing neutralizing antibodies to the glycoprotein than soluble envelope protein antigens.
A variety of expression systems have been utilized to produce VLPs, including mammalian cell lines, bacteria, insect cell lines, yeast and plant cells. VLPs for over thirty different viruses have been generated in insect and mammalian systems for vaccine purposes (Noad, R. and Roy, P., 2003, Trends Microbiol 11: 438-44). VLPs have also been produced in plants (see WO2009/076778; WO2009/009876; WO 2009/076778; WO 2010/003225; WO 2010/003235; WO2010/006452; WO2011/03522; WO 2010/148511; WO2014153674, and WO2012/083445).
VLPs have been produced with native surface proteins from Severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1), including S protein, M protein, E protein in insect and mammalian cells (Liu et al., 2008, J Virol., p. 11318-11330). SARS-CoV-2 virus like particles (VLPs) have also been assembled by co-expressing viral surface proteins S, M, and E in mammalian cells (Xu et al. Front. Bioeng. Biotechnol., 30 Jul. 2020). Studies have further shown that the M protein is indispensable for virus-like particle (VLP) formation (Siu et al. Journal of Virology (2008) 82:11318-11330, Huang et al. Journal of Virology (2004) 78:12557-12565). In mammalian cells, expression of membrane protein (M) and small envelope protein (E) are essential for efficient formation and release of SARS-CoV-2 VLPs (Xu et al. Front. Bioeng. Biotechnol., 30 Jul. 2020)). Nevertheless, the minimal requirement for assembly of SARS-CoV VLPs is still controversial. Y. Huang et al. (Journal of Virology (2004) 78:12557-12565) described formation of VLPs in transfected human cells that only required co-expression of the M and N viral proteins, whereas Siu et al. (Journal of Virology (2008) 82:11318-11330) showed that both E and N proteins must be coexpressed with M protein for the efficient production and release of SARS-CoV VLPs in transfected mammalian cells.
WO2012/083445 discloses the production of SARS CoV S protein in plants, wherein the transmembrane domain and the cytosolic tail domain (TM/CT) of the S protein were replaced with TM/CT from an influenza HA protein.
A few groups have proposed immunization with SARS-CoV VLPs as an effective vaccine strategy. VLPs produced in insect cells or chimeric MHV/SARS-CoV VLPs produced in mammalian cells were used in these studies (Lokugamage et al. Vaccine 2008 Feb. 6; 26(6):797-808, Lu et al. 2007 Immunology 122496-5024).
However, effective scale-up and manufacture of SARS-CoV-2 VLPs at the quantity required to meet the need of widespread vaccination of the global population, requires efficient viral structural protein and VLP production.
The present invention relates to modified viral structural proteins. The present invention also relates to virus-like particles (VLPs) comprising modified viral structural protein and methods of producing the VLPs in a host or host cells. More specifically, the invention relates to modified coronavirus S proteins. The present invention also relates to virus-like particles (VLPs) comprising modified S proteins and methods of producing the VLPs in a host or host cells.
In one aspect it is provided a modified coronavirus S-protein comprising, in series,
The modified S-protein as described herein may form trimers. Accordingly it is also provided a trimer comprising modified coronavirus S-protein as described herewith.
In a further aspect, a virus like particle (VLP) comprising the modified S-protein or trimers comprising the modified S-protein as described above is provided. Accordingly, the VLP comprises a modified coronavirus S-protein or trimer that comprise the modified S-protein, the modified S-protein comprising
The VLP may further comprise plant lipids.
The TM may be directly fused to the CT. The TM may be derived from the coronavirus S-protein TM and the CT may be derived from the influenza HA protein CT. Furthermore, the TM may be a chimeric TM comprising a N terminal sequence derived from the coronavirus S-protein TM and a C terminal sequence derived from the influenza HA protein TM. The chimeric TM may comprise a N terminal sequence derived from the coronavirus S-protein TM comprising at least 20 amino acids corresponding to amino acids 1-20 of SEQ ID NO: 18 or SEQ ID NO: 169, or at least 21 amino acids corresponding to amino acids 1-21 of SEQ ID NO: 118 or 164, or at least 22 amino acids corresponding to amino acids 1-22 of SEQ ID NO: 123 and one or more than one amino acid from the C-terminal end of the influenza HA protein TM. The one or more than one amino acid from the C-terminal end of the influenza HA protein TM may be selected from AGL or conserved substitution of AGL, MAGL or conserved substitution of MAGL. The chimeric TM may comprise amino acids corresponding to amino acids of 1-20 of SEQ ID NO: 18.
The CT may be chimeric CT comprising a N terminal sequence derived from the coronavirus S-protein CT and a C terminal sequence derived from the influenza HA protein CT. The chimeric CT may comprise a C terminal sequence derived from influenza HA protein CT comprising at least 11 amino acids corresponding to amino acids 27-37 of SEQ ID NO: 18, 126, 127, 128, 129, 130 or 131 and one or more than one amino acid from the N-terminal end of the coronavirus S-protein CT. The one or more than one amino acid from the N-terminal end of the coronavirus S-protein CT may be selected from C or a conserved substitution of C, CC or a conserved substitution of CC, or CCM or a or a conserved substitution of CCM. The chimeric CT may comprise amino acids corresponding to amino acids of 27-37 of SEQ ID NO: 18, 126, 128, 129, 130 or 131; or amino acids 27-36 of SEQ ID NO: 127. In one aspect the chimeric TMCT may comprise a chimeric TM comprising amino acids corresponding to amino acids 1-20 of SEQ ID NO: 18 or SEQ ID NO: 169, or to amino acids 1-21 of SEQ ID NO: 118 or SEQ ID NO: 164, or amino acids 1-22 of SEQ ID NO: 123, a chimeric CT comprising amino acids corresponding to amino acids 27-37 of SEQ ID NO: 18, 126, 127, 128, 129, 130 or 131, or a combination thereof.
The CT or portion of the CT may comprise from 80% to 100% identity with the sequence of SEQ ID NO: 15, or with amino acids 35-50 of SEQ ID NO 6, 8, 7, 9, 10, 12, 13 or 14, or with amino acids 34-49 of SEQ ID NO 11, or with amino acids 553-568 of SEQ ID NO:3 or with amino acids 22-37 of SEQ ID NO:18, or with amino acids 21-40 of SEQ ID NO: 19, or with amino acids 21-39 of SEQ ID NO: 37, or with amino acids 25-36 of SEQ ID NO: 38 or with amino acids 24-34 of SEQ ID NO: 39, or amino acids 22-37 of SEQ ID NO: 126, 128, 129, 130 or 131; or amino acids 22-36 of SEQ ID NO: 127. The TM or portion of the TM may comprises from 80% to 100% identity with the sequence of SEQ ID NO: 132 or 133.
The TMCT may comprise a sequence having about 80% to about 100% identity with the sequence of SEQ ID NO: 18, 19, 37, 38, 39, 64, 126, 127, 128, 129, 130, 131, 118, 119, 120, 123, 124, 125, 134, 135 164, 165, 166, 169, 170, 171, 172 or 173.
The modified S protein may comprises an S1 subunit and an S2 subunit, wherein the S2 subunit comprises the chimeric TMCT.
The modified S-protein may be produced as a precursor protein, the precursor protein comprising the modified S-protein and a signal peptide. The precursor protein comprising the modified S-protein and a signal peptide may comprise from 80% to 100% identity with amino acids 1-1234 of SEQ ID 1, or with amino acids 1-1234 of SEQ ID NO: 5, amino acids 1-1219 of SEQ ID NO: 21 or with amino acids 1-1243 of SEQ ID NO: 30 and wherein the amino acid sequence of the CT comprises from 80% to 100% identity with the sequence of SEQ ID NO: 15, or with amino acids 35-50 of SEQ ID NO 6, 8, 7, 9, 10, 12, 13 or 14, or with amino acids 34-49 of SEQ ID NO 11, or with amino acids 553-568 of SEQ ID NO:3.
The signal peptide may be native or non-native to the S-protein. The non-native signal peptide may be derived from the signal peptide of protein disulfide-isomerase (PDI). The modified S-protein may further comprise plant specific N-glycans.
The CT or portion of the CT in the modified S-protein may be derived from an influenza hemagglutinin (HA) protein that is derived from influenza type B or influenza subtype H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, or H16. The influenza hemagglutinin (HA) protein may be derived from influenza type B or influenza subtype H1, H3, H5, H6, H7 or H9.
The ectodomain of the modified S-protein may be derived from SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43-CoV or 229E-CoV, the TM or the portion of the TM may be derived from SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43-CoV or 229E-CoV, or both the ectodomain and the TM or the portion of the TM may be derived from SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43-CoV or 229E-CoV.
In a further aspect, the modified S-protein may comprise one or more than one amino acid substitution when compared to a wild-type coronavirus amino acid sequence. The one or more than one substitution may maintain the S-protein in a pre-fusion state.
The one or more than one amino acid substitution may comprise i) substitutions that restricts the processing at a cleavage site between S1 and S2 subunit, ii) substitution of one or more than one amino acid to one or more than one proline, or iii) substitutions that restrict the processing at the cleavage site between the S1 and the S2 subunit and substitution of one or more than one amino acid to one or more than one proline.
The one or more than one substitution may maintain the S-protein in a pre-fusion state or produces are higher yield of the modified S-protein when expressed in a host or host cell, when compared to the yield of a corresponding S-protein without the one or more than one substitutions expressed in the host or host cell.
The one or more than one amino acid substitution may correspond to amino acids at positions 667, 668, 670, 802, 923, 927, 971, 972 or a combination thereof, when compared to reference amino acid sequence of SEQ ID NO: 2.
In one aspect, the one or more than one amino acid substitution correspond to amino acids at positions 971 and 972, when compared to reference amino acid sequence of SEQ ID NO: 2. In another aspect, the one or more than one amino acid substitution correspond to amino acids at positions 802, 927, 971 and 972, when compared to reference amino acid sequence of SEQ ID NO: 2. Furthermore, the modified S-protein may comprise one or more than one amino acid substitution corresponding to amino acids at positions 667, 668, 670, or a combination thereof, when compared to reference amino acid sequence of SEQ ID NO: 2. Accordingly, the modified S-protein may comprise substitutions that correspond to amino acids at positions 667, 668 and 670, when compared to reference amino acid sequence of SEQ ID NO: 2.
In one aspect, the one or more than one substitution may correspond to amino acids at positions 667, 668, 670, 971 and 972, when compared to reference amino acid sequence of SEQ ID NO: 2. The substitution of the amino acid corresponding to the amino acid at position 667 of SEQ ID NO: 2 may be to glycine or a conserved substitution of glycine, the substitution of the amino acid corresponding to position 668 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to position 670 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to the amino acid at position 971 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline and the substitution of the amino acid corresponding to the amino acid at position 972 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline. The modified S-protein as described above may further comprises an amino acid substitution corresponding to amino acid at position 923, when compared to reference amino acid sequence of SEQ ID NO: 2.
In another aspect the one or more than one amino acid substitution may correspond to amino acids at positions 667, 668, 670, 802, 927, 971 and 972, when compared to reference amino acid sequence of SEQ ID NO: 2. The substitution of the amino acid corresponding to the amino acid at position 667 of SEQ ID NO: 2 may be to glycine or a conserved substitution of glycine, the substitution of the amino acid corresponding to position 668 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to position 670 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to the amino acid at positions 802 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline, the substitution of the amino acid corresponding to the amino acid at positions 927 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline, the substitution of the amino acid corresponding to the amino acid at positions 971 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline and the substitution of the amino acid corresponding to the amino acid at positions 972 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline.
In another aspect the modified S-protein as described above may further comprises an amino acid substitution corresponding to amino acid at position 923, when compared to reference amino acid sequence of SEQ ID NO: 2. The substitution in the modified S-protein of the amino acid corresponding to the amino acid at position 667 of SEQ ID NO: 2 may be to glycine or a conserved substitution of glycine, the substitution of the amino acid corresponding to position 668 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to position 670 of SEQ ID NO: 2 may be to a serine or a conserved substitution of serine, the substitution of the amino acid corresponding to the amino acid at positions 802, 927, 971 and 972 of SEQ ID NO: 2 may be to a proline or a conserved substitution of proline and the substitution of the amino acid corresponding to position 923 of SEQ ID NO: 2 may be to phenylalanine or a conserved substitution of phenylalanine.
The modified the S-protein may comprise from 80% to 100% identity with amino acids of SEQ ID NO: 5, 21, 30, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 95, 96, 97, 108, 109, 110, 144, 145, 146, 155, 156 or 157, or with amino acids 24-1259 of SEQ ID NO: 47 amino acids 25-1259 of SEQ ID NO: 48, amino acids 25-1259 of SEQ ID NO: 49, amino acids 25-1259 of SEQ ID NO: 50, amino acids 25-1259 of SEQ ID NO: 51, amino acids 25-1259 of SEQ ID NO: 52, amino acids 25-1259 of SEQ ID NO: 53, amino acids 25-1259 of SEQ ID NO: 54, amino acids 25-1259 of SEQ ID NO: 55, amino acids 25-1259 of SEQ ID NO: 56, amino acids 25-1259 of SEQ ID NO: 57, amino acids 25-1259 of SEQ ID NO: 58, amino acids 25-1262 of SEQ ID NO: 59, amino acids 25-1261 of SEQ ID NO: 60, amino acids 25-1258 of SEQ ID NO: 61, or amino acids 25-1256 of SEQ ID NO: 62, amino acids 25-1243 of SEQ ID NO: 95, amino acids 25-1240 of SEQ ID NO: 96, amino acids 25-1243 of SEQ ID NO: 97, amino acids 25-1341 of SEQ ID NO: 108, amino acids 25-1338 of SEQ ID NO: 109, amino acids 25-1341 of SEQ ID NO: 110, amino acids 25-1351 of SEQ ID NO: 144, amino acids 25-1348 of SEQ ID NO: 145, amino acids 25-1351 of SEQ ID NO: 146, amino acids 25-1159 of SEQ ID NO: 155, amino acids 25-1156 of SEQ ID NO: 156, or amino acids 25-1159 of SEQ ID NO: 157.
In another aspect, it is provided a nucleic acid that comprises a nucleotide sequence that encodes the modified S-protein as described above.
In a further aspect a composition comprising an effective dose of the modified S-protein, the trimer comprising the modified S-protein or VLP comprising the modified S-protein as described above and a pharmaceutically acceptable carrier, adjuvant, vehicle or excipient is provided. In yet another aspect, it is provided a vaccine for inducing an immune response. The vaccine comprises an effective dose of the modified S protein, the trimer comprising the modified S-protein or VLP comprising the modified S-protein as described above as described above.
The composition further comprises a pharmaceutically acceptable carrier, adjuvant, vehicle or excipient. In a further aspect, it is provided a vaccine for inducing an immune response. The vaccine comprises an effective dose of the VLP comprising a modified coronavirus as described above. The vaccine may be a multivalent vaccine, comprising a mixture of VLP.
In yet another aspect a (non-human) host or host cell comprising the modified S-protein, trimer or VLP as described above is provided. In yet another aspect a host or host cell comprising the VLP as described above is provided. In another aspect it is provided a composition comprising an effective dose of the VLP comprising the modified S-protein as described above is provided.
In yet another aspect, a S-protein trimer is provided. The trimer comprises modified coronavirus S-protein, the modified S-protein comprising
In another aspect, it is provided a method for inducing immunity to a Coronavirus infection in a subject, the method comprising administering the composition or vaccines as described above. The composition or vaccine may be administered once to the subject or the composition or vaccine may be administered multiple times to the subject. The composition or vaccine may be administered as an initial dose and one or more than one subsequent doses may be administered between 1 day and 6 month from the administration of the initial dose. The subsequent dose may be administered after 21 days from the administration of the initial dose.
In another aspect an antibody or antibody fragment prepared using the composition or vaccine as described above are provided.
In yet another aspect, it is provided A) a method of producing a virus like particle (VLP) in a (non-human) host or host cell comprising:
In a further step c) the non-human host or host cell may be harvested.
In a further aspect, it is provided B) a method of increasing yield of production of a Coronavirus S-protein in a (non-human) host or host cell comprising:
In a further step c) the non-human host or host cell may be harvested.
In yet another aspect, it is provided C) a method of increasing yield of production of virus like particle (VLP) in a (non-human) host or host cell comprising:
In a further aspect, it is provided D) a method of producing a virus like particle (VLP) in a (non-human) host or host cell comprising:
In a further aspect the VLP of method A), B), C) or D) may further be extracted and purified from the host or host cell. The host or host cell may comprise a plant, a plant cell, a fungi, a fungi cell, an insect, an insect cell, an animal or an animal cell. The host or host cell of method A), B), C) or D) may be a plant, portion of a plant or plant cell.
In another aspect it is provided a VLP produced by the method of A), B), C) or D).
Furthermore, in yet another aspect it is provided a composition comprising an adjuvant and virus-like particles (VLP), the VLP comprising modified coronavirus S-protein, the modified S-protein comprising
In yet another aspect it is provided a composition comprising virus-like particle (VLP), the VLP comprising modified coronavirus S-protein, the modified S protein comprising
In a further aspect it is provided a composition comprising virus-like particle (VLP), the VLP comprising modified coronavirus S-protein, the modified S protein comprising the sequence of SEQ ID NO: 21. The composition may further comprise an adjuvant.
This summary of the invention does not necessarily describe all features of the invention.
These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein:
The following description is of a preferred embodiment.
As used herein, the terms “comprising,” “having,” “including” and “containing,” and grammatical variations thereof, are inclusive or open-ended and do not exclude additional, un-recited elements and/or method steps. The term “consisting essentially of” when used herein in connection with a use or method, denotes that additional elements and/or method steps may be present, but that these additions do not materially affect the manner in which the recited method or use functions. The term “consisting of” when used herein in connection with a use or method, excludes the presence of additional elements and/or method steps. A use or method described herein as comprising certain elements and/or steps may also, in certain embodiments, consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to. In addition, the use of the singular includes the plural, and “or” means “and/or” unless otherwise stated. The term “plurality” as used herein means more than one, for example, two or more, three or more, four or more, and the like. Unless otherwise defined herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. As used herein, the term “about” refers to an approximately +/−10% variation from a given value. It is to be understood that such a variation is always included in any given value provided herein, whether or not it is specifically referred to. The use of the word “a” or “an” when used herein in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one” and “one or more than one.”
The present description relates to modified viral structural protein and their production in a host or host cell. The modified viral structural protein comprises in series, an ectodomain, a transmembrane domain (TM) or portion of a TM, and a cytosolic tail (CT) domain or portion of a CT, wherein the ectodomain and the TM or portion of the TM are derived from a Coronaviridae, and the CT or portion of the CT is derived from an influenza hemagglutinin (HA) protein.
The modified viral structural protein may be a modified Coronavirus structural protein, wherein the cytosolic tail domain or portion of the cytosolic tail domain has been replaced with the cytosolic tail domain or portion of the cytosolic tail domain of an influenza hemagglutinin (HA) protein. For example, the modified viral structural protein may be a modified Coronavirus spike or surface (S) protein, wherein the cytosolic tail domain or portion of the cytosolic tail domain of the S protein has been replaced with the cytosolic tail domain or portion of the cytosolic tail domain of an influenza hemagglutinin (HA) protein.
The present disclosure provides modified viral structural protein, wherein the ectodomain and the transmembrane domain of the modified viral structural protein may be derived from the ectodomain and the transmembrane domain of a Coronavirus S protein and wherein the cytosolic tail domain is derived from the cytosolic tail domain of an influenza hemagglutinin (HA) protein.
The modified S-protein may be a chimeric modified S-protein or a chimeric S-protein. By “chimeric S-protein”, it is meant a protein or polypeptide that comprises amino acid sequences and/or protein domains or portions of protein domains from two or more than two sources that are fused as a single polypeptide. For example but not limited to, the ectodomain and the transmembrane domain (TM) or portion of the TM of the chimeric S-protein may be derived from a first viral structural protein, for example a Coronavirus S protein, and the cytoplasmic tail (CT) or portion of the CT may be derived from a second viral structural protein, for example the CT may be derived from influenza HA. Furthermore, the ectodomain may be derived from a first viral structural protein for example a first Coronavirus S protein, the TM or portion of the TM may be derived from a second viral structural protein, for example a second Coronavirus S protein and the CT or portion of the CT may be derived from a third viral structural protein, for example the CT may be derived from influenza HA. Accordingly, the modified S-protein or chimeric S-protein may comprise a chimeric transmembrane and cytosolic tail domain (TMCT).
The modified coronavirus S-protein may comprise, in series,
The TM or portion of the TM may directly be fused or joined to the CT or portion of the CT or the TM or portion of the TM may be fused or joined to the CT or portion of the CT by an intervening peptide sequence.
Furthermore, the TM may be a chimeric TM that may comprise a N terminal sequence derived from the coronavirus S-protein TM and a C terminal sequence derived from the influenza HA protein TM. The CT may be a chimeric CT that may comprise a N terminal sequence derived from the coronavirus S-protein CT and a C terminal sequence derived from the influenza HA protein CT.
Accordingly, the chimeric TMCT, may comprise a native coronavirus S-protein TM, a chimeric coronavirus S-protein/influenza HA TM, a native influenza HA CT, a chimeric influenza HA/coronavirus S-protein CT or a combination thereof. The chimeric coronavirus S-protein/influenza HA TM comprises sequences from the TM of coronavirus S-protein and sequences from the TM of influenza HA. Similarly, the chimeric influenza HA/coronavirus S-protein CT comprises sequences from the CT of influenza HA and sequences from the CT of coronavirus S-protein.
A “chimeric transmembrane and cytosolic tail domain” or “chimeric TMCT” refers to a TMCT that is not native to the coronavirus S-protein TMCT. The chimeric TMCT comprises sequences that are not found together in nature. Thus the TMCT may comprise sequences that are heterologous to the ectodomain of the coronavirus S-protein. The term “heterologous” refers to a sequence or domain originating from different biological or synthetic sources. For example, the chimeric TMCT may comprise a TM or portion of a TM that is derived from the same coronavirus S-protein as the ectodomain, i.e. the TM may be homologous to the ectodomain of the S-protein or the TM or portion of the TM may be derived from a different viral TM, for example a TM from a different coronavirus S-protein as the ectodomain, i.e. the TM may be heterologous to the ectodomain of the S-protein. The CT or portion of the CT may be derived from a CT that is heterologous to the ectodomain, the TM, or both the ectodomain and the TM of the modified S-protein.
The coronavirus S protein, the modified S protein or the ectodomain and the transmembrane domain or portion of the transmembrane domain of the modified coronavirus S protein may be derived from any member of the Coronaviridae family of viruses. For example the coronavirus S-protein, the modified S-protein or the ectodomain and the transmembrane domain of the modified coronavirus S-protein may for example be derived from a Coronavirus, such as an Alphacoronavirus (Alpha-CoV), a Betacoronavirus (Beta-CoV), a Gammacoronavirus (Gamma-CoV) or a Deltacoronavirus (Delta-CoV). For example, the Coronavirus may be an Alphacoronavirus (Alpha-CoV) or a Betacoronavirus (Beta-CoV). The Alphacoronavirus may be a Duvinacovirus, such as for example HCoV-229E (229E-CoV), or may be a Setracovirus, such as for example HCoV-NL63. In a preferred embodiment, the Coronavirus is a Betacoronavirus (Beta-CoV). The Betacoronavirus may be a lineage A Betacoronavirus, such as for example HCoV-OC43 (OC43-CoV) or HCoV-HKU1 (HKU1-CoV), a lineage B Betacoronavirus, such as for example SARS-CoV (also referred to as SARS-CoV-1) or SARS-CoV-2 and variants thereof or a lineage C Betacoronavirus, such as for example MERS-CoV.
The coronavirus S-protein, the modified S-protein or the ectodomain and the transmembrane domain or portion of the transmembrane domain of the modified coronavirus S-protein may further be derived from variants of the SARS-CoV-2 lineage, including but not limited to the B.1.1.7 strain (“Alpha” variant) (20I/501Y.V1, MW531680.1), the B.1.351 strain (“Beta” variant) (20H/501Y.V2), the P.1 strain (“Gamma” variant) (20J/501Y.V3), the B 1.617.2 strain (“Delta” variant), the B.1.525 strain, the B.1.429 strain (the “ETA” variant) or other variants of strains comprising mutations that arise naturally in the coronavirus S protein, or naturally occurring recombinant strains thereof.
In one embodiment the ectodomain and the transmembrane domain or portion of the transmembrane domain of the modified viral structural protein are derived from the spike protein (S) of a Coronavirus of the SARS-CoV-2 lineage (also referred to as SARS-CoV-2 variants). In other embodiments the ectodomain and the transmembrane domain or portion of the transmembrane domain of the modified viral structural protein are derived from the spike protein (S) of SARS-CoV-1, MERS-CoV, OC43-CoV or 229E-CoV or variants thereof.
With reference to modified viral structural protein, the term “modified” as used herein may refer to the replacement of the cytoplasmic tail domain (CT) or portion of the CT in a structural protein from Coronaviridae with the CT or portion of the CT of a heterologous virus. For example a modified viral structural protein may be a Coronavirus S protein wherein the CT or portion of the CT of the S protein has been replaced with the CT or portion of the CT of influenza hemagglutinin (HA).
Therefore the modified viral structural protein may be a modified coronavirus spike (S) protein comprising a transmembrane domain (TM) or portion of a TM, and a cytosolic tail (CT) or portion of a CT, wherein the CT or portion of the CT may be derived from an influenza hemagglutinin (HA) protein and wherein the TM or portion of the TM is heterologous to the CT or portion of the CT. Furthermore, the modified S protein comprises a transmembrane domain (TM) or portion of the TM, and a cytosolic tail (CT) or portion of the CT, wherein the CT or portion of the CT may be derived from an influenza hemagglutinin (HA) protein and wherein the CT or portion of the CT is heterologous to the TM or portion of the TM.
Therefore, in one aspect it is provided a modified coronavirus spike (S) protein comprising a transmembrane domain (TM) or portion of a TM, and a cytosolic tail (CT) or portion of a CT, wherein the CT or portion of the CT is derived from an influenza hemagglutinin (HA) protein and wherein the TM or portion of the TM is heterologous to the CT or portion of the CT. The modified coronavirus spike (S) protein is also referred to as modified S protein.
The cytoplasmic tail domain may also be referred to as “cytoplasmic tail”, “cytosolic tail”, “cytosolic tail domain”, “CT, “CTD”, “cytoplasmic domain”, “cytoplasm domain”, “CP, “CPD” or “C-terminal domain” and similar expressions. The cytoplasmic tail domain may also encompass portions of the cytoplasmic tail domain.
It has been found that the modified viral structural protein such as a modified S protein as disclosed herewith has improved characteristics as compared to the wild-type or unmodified viral structural protein (for example the S-protein). Examples of improved characteristics of the modified viral structural protein such as the modified S protein include but are not limited to: increased yield of the modified viral structural protein when expressed in a host or host cell as compared to the wild-type or unmodified viral structural protein; improved integrity, stability, or both integrity and stability, of the viral structural protein when expressed in a host or host cell as compared to the wild-type or unmodified viral structural protein; improved integrity, stability, or both integrity and stability, of virus like particles (VLPs) that are comprised of the modified viral structural protein as compared to the integrity, stability or integrity and stability of VLPs comprising to viral structural protein that does not comprise the modification as described herewith; increased yield of VLPs comprising modified viral structural protein when expressed in host cells as compared to the yield of VLPs that do not comprise the modified viral structural protein that are expressed in same or substantially similar host cells.
Furthermore, methods of producing virus like particle (VLP) comprising modified viral structural protein such as the modified S protein in a host or host cell are also described. It has been observed that when VLPs are produced that comprise a modified viral structural protein such as the modified S protein wherein the native or wild-type CT has been replaced with a CT of influenza HA as described herein, the yield of VLP production in a host is increased compared to the yield of VLP that comprise viral structural protein that either i) comprise the native CT or ii) comprise a modified viral structural protein wherein the transmembrane domain (TM) and the CT have been replaced with the TM and the CT of an influenza HA.
The transmembrane domain may also be referred to as “TM” or “TMD”. The transmembrane and cytoplasmic tail domain may be referred to as TMCT or TM/CT.
As further discussed in more detail below, similar results were obtained, wherein the modified S-protein comprises a SARS-CoV-1 S protein with a cytoplasmic tail from influenza HA (see
The present description provides a modified viral structural protein, wherein the modified viral structural protein may be a modified Coronavirus Spike or Surface Protein (S protein). The modified S protein comprising, in series, an ectodomain, a transmembrane domain (TM) or portion of a TM, and a cytosolic tail (CT) domain or portion of a CT, wherein the ectodomain and the transmembrane domain are derived from Coronavirus, and the CT or portion of the CT is derived from a CT of influenza hemagglutinin (HA) protein. The ectodomain and the transmembrane domain or portion of the TM may be derived from the same Coronavirus. Therefore, the ectodomain and the transmembrane domain or portion of the TM of the modified structural protein are homologues (i.e. not heterologous) to each other, whereas the CT or portion of the CT is heterologous to the ectodomain and the transmembrane domain.
Furthermore, the transmembrane domain (TM) or portion of the TM of the modified S protein may be derived from a different Coronavirus than the ectodomain. Therefore, the TM or portion of the TM in the modified S protein may be heterologous (not homologous) to both the ectodomain and the CT domain or portion of the CT of the modified S protein. Similarly, the ectodomain may be heterologous (not homologous) to the TM or portion of the TM and the CT domain or portion of the CT of the modified S protein. For example, the ectodomain of the modified S protein may be derived from a first Coronavirus, the TM or portion of the TM may be derived from a second Coronavirus and the CT or portion of the CT may be derived from an influenza HA. The first Coronavirus and the second Coronavirus may belong to different Coronavirus families, sub-groups, types, subtypes, lineages or strains. The first Coronavirus and second Coronavirus may therefore be heterologous to each other and also each heterologous to the virus family from which the CT or portion of the CT is derived.
For example, the first Coronavirus from which the S protein ectodomain is derived, may be from any Coronavirus such for example an Alphacoronavirus (Alpha-CoV) or a Betacoronavirus (Beta-CoV). A non-limiting example of the first coronavirus from which the ectodomain of the S protein may be derived is a Duvinacovirus, such for example HCoV-229E, a Setracovirus, such for example HCoV-NL63. a lineage A Betacoronavirus, such for example HCoV-OC43 or HCoV-HKU1, a lineage B Betacoronavirus, such for example SARS-CoV or SARS-CoV 2 or a lineage C Betacoronavirus such for example MERS-CoV. The second Coronavirus, from which the TM is derived, may belong to a different Coronavirus family, sub-group, type, subtype, lineage or strain than the first Coronavirus from which the ectodomain is derived. For example the second Coronavirus from which the S protein TM is derived, may be from any Coronavirus such for example an Alphacoronavirus (Alpha-CoV) or Betacoronavirus (Beta-CoV), as long as the second Coronavirus is heterologous to the first Coronavirus. A non-limiting example of the second coronavirus from which the TM of the S protein may be derived is a Duvinacovirus, such for example HCoV-229E (also referred to as 229E-CoV), a Setracovirus, such for example HCoV-NL63 (NL63-CoV), a lineage A Betacoronavirus, such for example HCoV-OC43 (also referred to as OC43-CoV) or HCoV-HKU1 (HKU1-CoV), a lineage B Betacoronavirus, such for example SARS-CoV (also referred to as SARS-CoV 1) or SARS-CoV 2 or a lineage C Betacoronavirus such for example MERS-CoV (also simply referred to as “MERS”).
The domains in a Coronavirus S protein, such as the SARS-CoV-1 S-protein, SARS-CoV-2 S-protein, MERS CoV S-protein, OC43-CoV S-protein, or 229E-CoV S-protein, may readily be identified by methods known within the art. For example, domains such as transmembrane domains, may be identified by determining the degree of hydrophobicity of an amino acid sequence of the protein, for example using a transmembrane prediction program (e.g. Expert Protein Analysis System; ExPASy.org, operated by the Swiss Institute of Bioinformatics; or the Dense Alignment Surface Method, Cserzo M., et al. 1997, Prot. Eng. vol. 10, no. 6, 673-676; Lolkema J. S. 1998, FEMS Microbiol Rev. 22, no 4, 305-322), by determining the hydropathy profile of the amino acid sequence of the protein (e.g. Kyte-Doolittle Hydropathy Profile), by determining the three-dimensional protein structure and identifying the structure that is thermodynamically stable in a membrane (e.g. a single alpha helix, a stable complex of several transmembrane alpha helices, a transmembrane beta barrel, a beta-helix, or any other structure that is thermodynamically stable in a membrane).
Furthermore, domains within a Coronavirus S protein may be determined by comparison to known protein sequences for example by sequence alignment. Methods of alignment of sequences for comparison are well-known in the art and as further described below.
Domains and domain organization of Coronavirus S protein are well known and have been described. All Coronavirus spike proteins (S protein) share the same organization in two subunits or domains: a N-terminal subunit (or domain) named S1 that is responsible for receptor binding and a C-terminal S2 subunit (or domain) responsible for virus attachment, membrane fusion and virus entry.
The transmembrane domain (TM) and the cytoplasmic tail domain (CT) are positioned at the C-terminal end of the S2 subunit. While these domains are conserved in all coronaviruses (see
For example, amino acids (aa): 1214-1234 may be assigned to the TM and aa 1235-1273 may be assigned to the CT in the S protein of SARS-CoV-2 (see for example UniProtKB-P0DTC2 (SPIKE_SARS2)). When aligning the sequence of SARS-CoV-2 (SEQ ID NO. 1) with the sequence of SARS-CoV-1 of Kirchdoerfer et al. (Nature 2016 Mar. 3; 531(7592):118-2) the SARS-CoV-2 TM corresponds to amino acids 1214-1236 and the SARS-CoV-2 CT corresponds to amino acids: 1237-1273.
For the purpose of this disclosure, the TM and CT of the native (unmodified) S protein corresponds to the following amino acids when aligned to a Coronavirus S protein reference sequence (SEQ ID NO: 1): TM: amino acids 1214-1234 and CT: amino acids: 1235-1273.
When 15 amino acids comprising the signal peptide (SP) are removed from the S protein, the TM corresponds to amino acids 1199-1219 of reference sequence SEQ ID NO: 2 and the CT corresponds to amino acids 1220-1258 of SEQ ID NO:2. (see also Table 1 for reference sequences and numbering).
The TM of Coronavirus S-protein has a highly conserved N-terminal aromatic rich stretch, followed by a hydrophobic sequence (see
For example, the Coronavirus S-protein TM domain consensus sequence may be:
1numbering excludes signal peptide, CT is derived from influenza HA
2numbering includes signal peptide, CT is native
3numbering excludes signal peptide, CT is native
While there are differences in the numbering of the residues assigned to the TM and CT domain, a person of skill in the art will be able to determine the borders or boundaries of these domains in a Coronavirus S-protein by using known methods as for example described below.
In the modified Coronavirus S protein, the heterologous CT or portion of the CT that may be derived from influenza HA may be directly fused to the C-terminal end of the TM or portion of the TM of the Coronavirus S protein, or the heterologous CT or portion of the CT may be fused to the C-terminal end of the TM or portion of the TM of the Coronavirus S protein with an intervening peptide sequence (also referred to as a linker or linker sequence). Accordingly, the modified S-protein may comprise a intervening peptide, wherein the intervening peptide sequence fuses the CT or portion of the CT to the C-terminal end of the TM or portion of the TM.
The heterologous CT, portion of the CT or the intervening peptide sequence with the heterologous CT may be fused to an amino acid in the C-terminal portion of the TM domain (for example within 4 amino acids of the C-terminus of the TM domain as defined in Table 1 with reference to SEQ ID NO: 1, 2, 21, 114, 115, 160 or 161) or the N-terminal portion of the CT domain (for example within 4 amino acids of the N-terminus of the CT domain as defined in Table 1 with reference to SEQ ID NO: 1, 2, 21, 114, 115, 160 or 161).
For example, the Coronavirus TM may end at an amino acid residue that corresponds to any one of amino acids 1230-1238 of SEQ ID NO: 1. Accordingly, the C-terminal end of the Coronavirus TM may be an amino acid that corresponds to any one of amino acids 1230-1238 of SEQ ID NO: 1. In one example the Coronavirus TM may end at an amino acid residue that corresponds to amino acid 1230 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1231 in SEQ ID NO: 1. In a further example, the TM may end at an amino acid residue that corresponds to amino acid 1232 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1233 in SEQ ID NO: 1. In a further example, the TM may end at an amino acid residue that corresponds to amino acid 1234 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1235 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1236 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1237 in SEQ ID NO: 1. In another example, the TM may end at an amino acid residue that corresponds to amino acid 1238 in SEQ ID NO: 1. In a preferred embodiment the TM may end at an amino acid residue that corresponds to amino acid 1234 in SEQ ID NO: 1.
In another example, the Coronavirus TM or portion of the TM may end at an amino acid residue that corresponds to any one of amino acids 1215-1219 of SEQ ID NO: 2 or 21. Accordingly, the C-terminal end of the Coronavirus TM or portion of the TM may be an amino acid that corresponds to any one of amino acids 1215-1224 of SEQ ID NO: 2 or 21. In one example the Coronavirus TM or portion of the TM may end at an amino acid residue that corresponds to amino acid 1215 in SEQ ID NO: 2 or 21. In another example, the TM or portion of the TM may end at an amino acid residue that corresponds to amino acid 1216 in SEQ ID NO: 2 or 21. In a further example, the TM or portion of the TM may end at an amino acid residue that corresponds to amino acid 1217 in SEQ ID NO: 2 or 21. In another example, the TM or portion of the TM may end at an amino acid residue that corresponds to amino acid 1218 in SEQ ID NO: 2 or 21. In another example, the TM or portion of the TM may end at an amino acid residue that corresponds to amino acid 1219 in SEQ ID NO: 2 or 21.
The intervening peptide sequence that may fuse the heterologous CT to the C-terminal end of the TM or portion of the TM from the Coronavirus S protein may have a length from 0-10 amino acids. Accordingly, the intervening peptide sequence may have a length of 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids. The intervening peptide sequence may be derived from a Coronavirus protein, for example the intervening peptide sequence may be derived from the C-terminal end of the TM from a Coronavirus S protein or from the N-terminal end of the CT of a Coronavirus S protein or both. The intervening peptide sequence may further be derived from an influenza HA protein, for example the intervening peptide sequence may be derived from the C-terminal end of the TM from influenza HA protein or from the N-terminal end of the CT of influenza HA protein, or both. Furthermore, the intervening peptide sequence may be heterologous to the Coronavirus and/or the HA portion of the modified S protein or the intervening peptide sequence may be an artificial sequence.
Non-limiting examples of sequences of the TM/CT domain (also referred to as chimeric TMCT) of the modified S protein are as shown below. The sequence of the TM domain from Coronavirus S-protein is underlined and the CT domain derived from influenza HA is shown in bold. Sequences in italic and bold are sequences derived from the TM of influenza HA. Sequences in italic and underlined are sequences derived from the CT of Coronavirus S-protein.
WYIWLGFIAGLIAIVMVTIML
SLWMCSNGSLQCRICI (wtTM/H5iCT)
WYIWLGFIAGLIAIVMVTIM
MAGLS
LWMCSNGSLQCRICI (wtTM/
WYIWLGFIAGLIAIVMVTIM
AGLS
LWMCSNGSLQCRICI (wtTM/
WYIWLGFIAGLIAIVMVTIMLCCM
CSNGSLQCRICI (wtTM/H5ICT
WYIWLGFIAGLIAIVMVTIMLCC
SNGSLQCRICI (wtTM/H5iCT V4)
WYIWLGFIAGLIAIVMVTIML
SFWMCSNGSLQCRICI (wtTM/HliCT)
WYIWLGFIAGLIAIVMVTIML
MWACQKGNIRCNICI (wtTM/H3iCT)
WYIWLGFIAGLIAIVMVTIML
GLWMCSNGSMQCRICI (wtTM/H6iCT)
WYIWLGFIAGLIAIVMVTIML
VFICVKNGNMRCTICI (wtTM/H7iCT)
WYIWLGFIAGLIAIVMVTIML
LEWAMSNGSCRCNICI (wtTM/H9iCT)
WYIWLGFIAGLIAIVMVTIML
VVYMVSRDNVSCSICL (wtTM/BiCT)
WYVWLGFIAGLIAIVMVTILL
SLWM CSNGSLQCRICI (wtTM/
WYVWLGFIAGLIAIVMVTILLCC
SNGSLQCRICI (wtTM/H5ICT V4)
WYVWLGFIAGLIAIVMVTILL
SFWM CSNGSLQCRICI (wtTM/
WYIWLGFIAGLVALALCVFFIL
SLWMCSNGSLQCRICI (wtTM/
WYIWLGFIAGLVALALCVFFILCC
SNGSLQCRICI (wtTM/H5iCT
WYIWLGFIAGLVALALCVFFIL
SFWMCSNGSLQCRICI (wtTM/
WYVWLLICLAGVAMLVLLFFI
SLWMCSNGSLQCRICI (wtTM/H5iCT)
WYVWLLICLAGVAMLVLLFFICC
SNGSLQCRICI (wtTM/H5ICT V4)
WYVWLLICLAGVAMLVLLFFI
SFWMCSNGSLQCRICI (wtTM/
WWVWLCISVVLIFVVSMLLL
SLWMCSNGSLQCRICI (wtTM/H5iCT)
WWVWLCISVVLIFVVSMLLLCC
SNGSLQCRICI (wtTM/H5ICT V4)
WWVWLCISVVLIFVVSMLLL
SFWMCSNGSLQCRICI (wtTM/H1cCT)
The modified coronavirus S-protein may comprise a chimeric TMCT. For example, the chimeric TMCT may comprise N-terminal sequences derived from coronavirus S-protein and C-terminal sequence derived from influenza HA protein as indicated in Table 1B. The TM may comprise the sequences as indicated in the column labeled as “S-protein TM sequences” and the CT may comprise the sequences as indicated in the column labeled as “HA protein CT sequence”. The CT and TM may be joined by the sequences as indicated in columns labeled as “S-protein CT sequence” and/or “HA protein TM sequence” (also referred to as intervening sequences or linker, as further described below).
For example, the N-terminal sequence derived from coronavirus S-protein TM may comprise at least the following:
The N-terminal sequence derived from the coronavirus S-protein TM may comprise at least 20 amino acids corresponding to amino acids 1-20 of SEQ ID NO: 18 or 169, or at least 21 amino acids corresponding to amino acids 1-21 of SEQ ID NO: 118 or 164, or at least 22 amino acids corresponding to amino acids 1-22 of SEQ ID NO: 123 and one or more than one amino acid from the C-terminal end of the influenza HA protein TM. The N-terminal sequence derived from the coronavirus S-protein TM may comprise at least 20 amino acids corresponding to amino acids 1-20 of SEQ ID NO: 18 or 169, or at least 21 amino acids corresponding to amino acids 1-21 of SEQ ID NO: 118 or 164, or at least 22 amino acids corresponding to amino acids 1-22 of SEQ ID NO: 123 and one or more than one amino acid from the C-terminal end of the influenza HA protein TM. The one or more than one amino acid from the C-terminal end of the influenza HA protein TM may comprise 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acids. For example the one or more than one amino acid may be 2, 3 or 4 amino acids. The one or more than one amino acid from the C-terminal end of the influenza HA protein TM may be A, C, G, L, S, M, W or conserved substitution of A, C, G, L, S, M, W, or a combination thereof. In one example the one or more than one amino acid from the C-terminal end of the influenza HA protein TM may be selected from AG or conserved substitution of AG, AGL or conserved substitution of AGL, MAGL or conserved substitution of MAGL.
The modified coronavirus S-protein may also comprise a chimeric CT comprising a N-terminal sequence derived from the coronavirus S-protein CT and a C-terminal sequence derived from the influenza HA protein CT.
The N-terminal sequence derived from the coronavirus S-protein CT may comprise one or more than one amino acid. The one or more than one amino acid from the N terminal end of the coronavirus S-protein CT may comprise 0, 1, 2, 3, 4 or 5 amino acids. For example the one or more than one amino acid may be 1, 2 or 3 amino acids. The one or more than one amino acid from the N-terminal end of the coronavirus S-protein CT may be C or M or conserved substitutions of C or M. In one example the one or more than one amino acids from the N-terminal end of the coronavirus S-protein may be selected from C or a conserved substitution of C, CC or a conserved substitution of CC, or CCM or a or a conserved substitution of CCM.
The C-terminal sequence derived from the influenza HA protein CT may comprise at least 11 amino acids corresponding to amino acids 27-37 of SEQ ID NO: 18.
The N-terminal sequence derived from the influenza HA protein CT may further comprise at least 12 amino acids corresponding to amino acids 26-37 of SEQ ID NO: 18, at least 13 amino acids corresponding to amino acids 25-37 of SEQ ID NO: 18, at least 14 amino acids corresponding to amino acids 24-37 of SEQ ID NO: 18, at least 15 amino acids corresponding to amino acids 23-37 of SEQ ID NO: 18, or at least 16 amino acids corresponding to amino acids 22-37 of SEQ ID NO: 18.
In another example, the C-terminal sequence derived from the influenza HA protein CT may comprise at least the following:
For example the CT may comprise the sequences as indicated in Table 1B (HA protein CT sequence). For example the CT may comprise amino acids 22-37 of SEQ ID NO: 18, 126, 128, 129, 130, 131, 118, 120, 164 or 166; or amino acids 25-40 of SEQ ID NO: 19; or amino acids 24-39 of SEQ ID NO: 37; or amino acids 25-36 of SEQ ID NO: 38; or amino acids 24-34 of SEQ ID NO: 39 or 119; or amino acids 22-36 of SEQ ID NO: 127; or amino acids 22-37 of SEQ ID NO: 118 or 164; or amino acids 23-38 of SEQ ID NO: 123 or 125; or amino acids 25-35 of SEQ ID NO: 124; or amino acids 24-34 of SEQ ID NO: 165; or amino acids 21-36 of SEQ ID NO: 169; or amino acids 23-33 of SEQ ID NO: 170; or amino acids of SEQ ID NO: 21-36.
The influenza CT or portion of the CT may be fused or joined to the TM or portion of the TM of the S-protein with an intervening peptide sequence. For example, the intervening peptide sequence may be derived from the influenza CT, the S-protein TM or a combination thereof or the intervening peptide sequence may be an artificial sequence. The intervening peptide sequence may be of varying length. For example, the intervening peptide sequence may be 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid long, preferably the intervening peptide sequence is between 2 and 8 amino acids long. In one example the intervening peptide sequence is 2 amino acid long and may for example comprise the sequence LC. In another example the intervening peptide sequence is 4 amino acids long and may for example comprise the sequence LCCM. In another example the intervening peptide sequence may be 5 amino acids long and may for example comprise the sequence LSLWM. In another example the intervening peptide sequence may be 7 amino acids long and may for example comprise the sequence AGLSLWM. In a further example the intervening peptide sequence may be 8 amino acids long and may for example comprise the sequence MAGLSLWM.
For example the TMCT of the modified S-protein may comprise the following sequence or a sequence that has 90-100%, or any amount therebetween sequence identity, or sequence similarity to:
Non-limiting intervening peptide sequences (X)n may include the following:
Similarly, a modified S protein comprising a SARS-CoV-1 S protein with a wtTM/H5iCT V4 version of the TMCT (
Accordingly, the modified S protein may comprise a TM and CT domain (TM/CT), wherein the CT or a portion of the CT is fused to the C-terminal end of the TM or portion of the TM via a intervening peptide sequence, wherein the intervening peptide sequence comprises the sequence Xn.
Furthermore, the modified S protein may comprise a TM and CT domain (TM/CT) comprising a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 18, 19, 37, 38, 39, 64, 126, 127, 128, 129, 130, 131, 118, 119, 120, 123, 124, 125, 134, 135, 164, 165, 166, 169, 170, 171, 172 or 173.
The modified S protein may comprise a CT or portion of the CT comprising a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with amino acids 22-37 of SEQ ID NO:18, amino acids 21-40 of SEQ ID NO: 19, amino acids 21-39 of SEQ ID NO: 37, amino acids 25-36 of SEQ ID NO: 38 or amino acids 24-34 of SEQ ID NO: 39, amino acids 22-37 of SEQ ID NO:126, amino acids 22-36 of SEQ ID NO:127, amino acids 22-37 of SEQ ID NO:128, amino acids 22-37 of SEQ ID NO:129, amino acids 22-37 of SEQ ID NO:130, or amino acids 22-37 of SEQ ID NO:131.
The modified S protein may comprise a TM or portion of the TM comprising a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with amino acids 1-20 of SEQ ID NO:18, amino acids 1-20 of SEQ ID NO: 19, amino acids 1-20 of SEQ ID NO: 37, amino acids 1-24 of SEQ ID NO: 38, amino acids 1-23 of SEQ ID NO: 39, amino acids 1-21 of SEQ ID NO: 118, amino acids 1-23 of SEQ ID NO: 119, amino acids 1-22 of SEQ ID NO: 123, amino acids 1-24 of SEQ ID NO: 124, amino acids 1-21 of SEQ ID NO: 164, amino acids 1-23 of SEQ ID NO: 165, amino acids 1-20 of SEQ ID NO: 169, or amino acids 1-22 of SEQ ID NO: 170. Furthermore, the modified S protein as described herewith may comprise a TM or portion of TM that comprises from 80% to 100% identity with the sequence of SEQ ID NO: 132 or 133.
Furthermore, the modified the S-protein may comprise from 70% to 100% sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 59, 60, 61, 62, 95, 96, 97, 108, 109 or 110, for example the modified S protein may comprise a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 59, 60, 61, 62, 95, 96, 97, 108, 109 or 110.
The cytoplasmic tail domain (CT) or portion of the CT of a viral structural protein such as for example a Coronavirus S protein, may be replaced with the CT or portion of the CT from an influenza hemagglutinin (HA) as described below, the resulting protein is referred to as modified viral structural protein. Accordingly, a coronavirus S protein wherein the native CT or portion of the native CT has been replaced with the CT or portion of the CT from HA may be referred to as modified coronavirus S-protein or modified S-protein. As further described above the HA CT or portion of the HA CT may either be directly fused to the N-terminal end of the Coronavirus TM domain or may be fused to the N-terminal end of the Coronavirus TM or portion of the TM via a intervening peptide sequence. Therefore, the HA CT or a portion of a HA CT may be fused to the C-terminal end of the S-protein TM or portion of the S-protein TM via an intervening peptide sequence.
Influenza “hemagglutinin” or “HA” is a homotrimeric membrane type I glycoprotein, generally comprising a signal peptide, an HA1 domain, and an HA2 domain comprising a membrane-spanning anchor site at the C-terminus and a small cytoplasmic tail (see for example
While different references and groups assign different length to the CT of HA, it has been shown that the N-terminal sequence of the CT is conserved among HA from different influenza subtypes and strains and that at least five residues have sequence identity for at least 10 of 13 HA subtypes (Simpson and Lamb 1992, Journal of Virology, 790-803).
CT sequences that correspond to the HA cytoplasmic tail domain consensus sequence may be fused to the C-terminal end of the TM of Coronavirus S protein either directly or via an intervening peptide sequence (linker sequence) as discussed above.
Furthermore, amino acid residues located in N-terminal or C-terminal from the native influenza HA TM/CT boundary may also be included in the CT sequence that is fused either directly or via an intervening peptide sequence to the TM or a portion of the TM of the modified Coronavirus S protein.
Therefore the sequence of the CT or a portion of the CT may for example start at an amino acid residue that corresponds to any one of amino acids 30-40 of SEQ ID NO: 14. Accordingly, the N-terminal end of the CT sequence may be an amino acid that corresponds to any one of amino acids 30-40 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In one example the CT sequence may start at an amino acid residue that corresponds to amino acid 30 in SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In another example, the CT sequence may start at an amino acid residue that corresponds to amino acid 31 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In a further example, the CT sequence may start at an amino acid residue that corresponds to amino acid 32 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In another example, the CT sequence may start at an amino acid residue that corresponds to amino acid 33 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In a further example, the CT sequence may start at an amino acid residue that corresponds to amino acid 34 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In another example, the CT sequence may start at an amino acid residue that corresponds to amino acid 35 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In a further example, the CT sequence may start at an amino acid residue that corresponds to amino acid 36 of SEQ ID NOs: 6-13 or 14. In another example, the CT sequence may start at an amino acid residue that corresponds to amino acid 37 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In a further example, the CT sequence may start at an amino acid residue that corresponds to amino acid 38 of SEQ ID NOs: 6-13 or 14. In another example, the CT sequence may start at an amino acid residue that corresponds to amino acid 39 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14. In a further example, the CT sequence may start at an amino acid residue that corresponds to amino acid 40 of SEQ ID NOs: 6, 7, 8, 9, 10, 11, 12, 13 or 14.
The cytoplasmic tail (CT) or portion of the CT of the modified S protein may be derived from a CT or portion of the CT of hemagglutinin (HA) of any one influenza type, subtype or strain. For example the CT may be derived from an HA from influenza type A or influenza type B. For example the CT may be derived from an HA of influenza subtype H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, or H16. The CT may for example be derived from a HA of subtype H1, H2, H3, H5, H6, H7 or H9. Furthermore, the CT or portion of the CT may be derived from an HA of influenza type B. The type B influenza may be from the lineage B/Yamagata or B/Victoria.
For example, the CT or portion of the CT of the modified S protein may be derived from a CT of hemagglutinin (HA) influenza H1, H3, H5, H6, H7, H9 or B strain. Non limiting examples of influenza stains from which the HA CT might be derived are influenza H1 California/7/2009, H2 A/Singapore/1/1957, H3 A/Minnesota/41/2019, H5 A/Indonesia/5/05, H6 A/Teal/Hong Kong/W312/97, H7 A/Guangdong/17SF003/2016, H9 A/Hong Kong/1073/99 or B/Washington/02/2019. Non limiting examples of amino acid sequences of the HA CT are shown in
As shown in
Similar results were obtained, when the native cytoplasmic tail (CT) of SARS-CoV-1 S protein, the native CT of MERS S protein, or the native CT of OC43 CoV S protein was replaced with the CT from influenza HA H1 California/7/2009 (H1cCT) (see
Accordingly, the cytoplasmic tail domain (CT) or portion of the CT may have about 70, 75, 80, 85, 86, 87, 88, 89, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 15, or with amino acids 30-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 31-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 32-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 33-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 34-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 35-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 36-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 37-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 38-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 39-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 40-50 of SEQ ID NO 6, 7, 8, 9, 10, 12, 13, 14, or with amino acids 31-49 of SEQ ID NO 11, or with amino acids 32-49 of SEQ ID NO 11, or with amino acids 33-49 of SEQ ID NO 11, or with amino acids 34-49 of SEQ ID NO 11, or with amino acids 35-49 of SEQ ID NO 11, or with amino acids 36-49 of SEQ ID NO 11, or with amino acids 37-49 of SEQ ID NO 11, or with amino acids 38-49 of SEQ ID NO 11, or with amino acids 39-49 of SEQ ID NO 11, or with amino acids 548-568 of SEQ ID NO:3, or with amino acids 549-568 of SEQ ID NO:3, or with amino acids 550-568 of SEQ ID NO:3, or with amino acids 551-568 of SEQ ID NO:3, or with amino acids 552-568 of SEQ ID NO:3, or with amino acids 553-568 of SEQ ID NO:3, or with amino acids 554-568 of SEQ ID NO:3, or with amino acids 555-568 of SEQ ID NO:3, or with amino acids 556-568 of SEQ ID NO:3, or with amino acids 557-568 of SEQ ID NO:3, or with amino acids 558-568 of SEQ ID NO:3.
Furthermore, the modified S-protein may comprise from 70% to 100% sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 53, 54, 55, 56, 57 or 58, for example the modified S protein may comprise a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 53, 54, 55, 56, 57 or 58 or with amino acids 25-1259 of SEQ ID NO: 53, amino acids 25-1259 of SEQ ID NO: 54, amino acids 25-1259 of SEQ ID NO: 55, amino acids 25-1259 of SEQ ID NO: 56, amino acids 25-1259 of SEQ ID NO: 57 or amino acids 25-1259 of SEQ ID NO: 58.
In further embodiments, the modified S protein ectodomain and/or transmembrane domain may be obtained from a coronavirus S protein other than SARS-CoV-2 S protein, for example from SARS-CoV-1 S protein, MERS-CoV S protein, OC43-CoV S protein, 229E-CoV S protein and the like.
As shown in
Similar results were obtained for modified MERS-CoV S protein (see
As further shown in
Furthermore, MERS-CoV S-protein, OC43-CoV S-protein, and 229E-CoV S-protein with a TMCT from influenza H5 HA (H5iTMCT), a CT from influenza H5 HA (H5iCT), or a CT from influenza H1 HA were observed to form VLPs as shown in
The present disclosure therefore provides a “modified viral structural protein”, a “viral structural fusion protein” or a “chimeric viral structural protein”, wherein the ectodomain and the transmembrane domain (TM) of the viral structural protein or a portion of the TM are derived from a Coronavirus and the cytosolic tail (CT) or a portion of the CT is derived from an influenza protein. For example, the ectodomain and the transmembrane domain may be derived from a Coronavirus Spike (S) protein and the cytosolic tail (CT) or a portion of the CT may be derived from influenza HA protein. Modified S protein may comprise, in series i) an ectodomain derived from a coronavirus S-protein (comprising the S1 subunit and the FP, HR1 and HR2 domains of the S2 subunit), ii) a Coronavirus transmembrane domain (TM) or a portion of a Coronavirus TM and iii) an influenza HA cytoplasmic tail domain (CT) or a portion of a HA CT. Therefore, in the modified S protein, the CT or portion of the CT is heterologous to the TM and the ectodomain. Similarly, the TM (and the ectodomain) of the modified S protein are heterologous to the CT. The ectodomain and the transmembrane domain (TM) may be derived from the same Coronavirus (i.e. the ectodomain and the TM may be homologous to each other) or the ectodomain may be derived from a first Coronavirus and the TM may be derived from a second Coronavirus (i.e. the ectodomain and the TM are heterologous to each other).
By “chimeric protein”, or “chimeric polypeptide”, also referred to as a “fusion protein”, it is meant a protein or polypeptide that comprises amino acid sequences from two or more than two sources, for example but not limited to an ectodomain and a transmembrane domain derived from a first viral structural protein for example derived from Coronavirus S protein and a cytoplasmic tail (CT) derived from a second viral structural protein for example a CT from influenza HA, that are fused as a single polypeptide.
The modified coronavirus S-protein may comprise a transmembrane and cytosolic tail domain (TMCT), wherein the TMCT is a chimeric TMCT. The chimeric TMCT may comprise a transmembrane domain (TM), wherein the TM or a portion of the TM is derived from a coronavirus S-protein and a cytosolic tail (CT), wherein the CT or a portion of the CT is derived from an influenza hemagglutinin (HA) protein. Furthermore the chimeric TMCT may comprise a native coronavirus S-protein TM, a chimeric coronavirus S-protein/influenza HA TM, a native influenza HA CT, a chimeric influenza HA/coronavirus S-protein CT or a combination thereof. For example, the modified coronavirus S-protein may comprise a chimeric TMCT with a native influenza HA CT and a chimeric TM, wherein the chimeric TM comprises a N-terminal sequence which is derived from the TM of the coronavirus S-protein and a C-terminal sequence which is derived from the TM of influenza HA protein. In another example the modified coronavirus S-protein may comprise a chimeric TMCT with a native coronavirus S-protein TM and a chimeric CT, wherein the chimeric CT comprises a N-terminal sequence derived from the coronavirus S-protein and a C-terminal sequence derived from the influenza HA protein. In a further example, the modified coronavirus S-protein may comprise a chimeric TMCT with a chimeric TM, wherein the chimeric TM comprises a N-terminal sequence which is derived from the TM of the coronavirus S-protein and a C-terminal sequence which is derived from the TM of influenza HA protein and a chimeric CT, wherein the chimeric CT comprises a N-terminal sequence derived from the coronavirus S-protein and a C-terminal sequence derived from the influenza HA protein.
When referring to a modified S-protein or modified coronavirus spike (S)-protein in the present disclosure, it is meant a modified coronavirus spike (S)-protein comprising a transmembrane domain (TM) or portion of a S-protein TM, and a cytosolic tail (CT) or a portion of a CT, wherein the CT is derived from an influenza hemagglutinin (HA) protein and wherein the TM is heterologous to the CT.
The modified the S-protein may comprise from 70% to 100% sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 21, 30, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 95, 96, 97, 108, 109, 110, 144, 145, 146, 155, 156 or 157, for example the modified S protein may comprise a sequence having about 70, 75, 80, 85, 87, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 5, 21, 30, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 95, 96, 97, 108, 109, 110, 144, 145, 146, 155, 156 or 157, or with amino acids 25-1259 of SEQ ID NO: 47, amino acids 25-1259 of SEQ ID NO: 48, amino acids 25-1259 of SEQ ID NO: 49, amino acids 25-1259 of SEQ ID NO: 50, amino acids 25-1259 of SEQ ID NO: 51, amino acids 25-1259 of SEQ ID NO: 52, amino acids 25-1259 of SEQ ID NO: 53, amino acids 25-1259 of SEQ ID NO: 54, amino acids 25-1259 of SEQ ID NO: 55, amino acids 25-1259 of SEQ ID NO: 56, amino acids 25-1259 of SEQ ID NO: 57, amino acids 25-1259 of SEQ ID NO: 58, amino acids 25-1262 of SEQ ID NO: 59, amino acids 25-1261 of SEQ ID NO: 60, amino acids 25-1258 of SEQ ID NO: 61, amino acids 25-1256 of SEQ ID NO: 62, amino acids 25-1243 of SEQ ID NO: 95, amino acids 25-1240 of SEQ ID NO: 96, amino acids 25-1243 of SEQ ID NO: 97, amino acids 25-1341 of SEQ ID NO: 108, amino acids 25-1338 of SEQ ID NO: 109, amino acids 25-1341 of SEQ ID NO: 110, amino acids 25-1351 of SEQ ID NO: 144, amino acids 25-1348 of SEQ ID NO: 145, amino acids 25-1351 of SEQ ID NO: 146, amino acids 25-1159 of SEQ ID NO: 155, amino acids 25-1156 of SEQ ID NO: 156, or amino acids 25-1159 of SEQ ID NO: 157.
The modified S-protein may further be produced or synthesized as modified S-protein precursor (also referred to as precursor S-protein), wherein the S-protein precursor comprises the modified S-protein and a signal peptide, wherein the signal peptide is native to Coronavirus (i.e. homologues to the ectodomain) or the signal peptide might be non-native or heterologous to the ectodomain. In a non-limiting example, the native signal peptide may be replaced with the signal peptide from protein disulfide isomerase (PDI).
The modified S-protein precursor may comprise a signal peptide that is non-native or heterologous to the ectodomain. The non-native signal peptide may replace the entire native signal peptide or may replace a portion of the native signal peptide of the Coronavirus S protein. Furthermore, the non-native or heterologous signal peptide may be directly fused to the N-terminus of the modified S protein or the non-native or heterologous signal peptide may be fused to the N-terminus of the modified S protein with an intervening peptide sequence.
A signal peptide (also referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide present at the N-terminus of the majority of newly synthesized proteins that are destined toward the secretory pathway. The signal peptide is responsible for targeting proteins to the endomembrane system, including the endoplasmic reticulum and the Golgi apparatus, where it is co-translationally removed by a signal peptidase located within the ER lumen and the mature proteins are generated. Since experimental methods for identification of targeting sequences are time-consuming and laborious, different computational approaches predicting targeting signals were developed, and are well known within the art. Signal peptides generally have low sequence similarity, but share some characteristic features. For predicting the signal sequence and its cleavage site, many prediction methods have been developed which take these characteristic features into account, such for example SignalP (Bendtsen et al., J Mol Biol. 2004 Jul. 16; 340(4):783-95.; Petersen et al., Nature Methods volume 8, pages 785-786(2011), Signal-CF (Chou and Shen, Biochem Biophys Res Commun. 2007 Jun. 8; 357(3):633-40), and Signal-BLAST (Frank and Sippl, Bioinformatics, 2008 Oct. 1; 24(19):2172-6), which are herewith incorporated by reference.
Using the SignalP prediction program, a signal peptide cleavage site for the SARS-CoV-2 S protein is predicted between position 15 and 16 of the sequence corresponding to the sequence of SEQ ID NO:1. However, a signal peptide cleavage site for the SARS-CoV-2 S protein may be predicted or occur between other consecutive positions of the sequence corresponding to the sequence of SEQ ID NO:1. For example, a signal peptide cleavage site for the SARS-CoV-2 S protein may also be predicted or may occur between position 13 and 14 of the sequence corresponding to the sequence of SEQ ID NO:1.
The N-terminal region of the native SARS-CoV-2 S protein (including the native signal peptide sequence) is shown below:
MFVFLVLLPLV
QLPPAYTNS
A predicted signal peptide sequence (SP) is underlined. The sequence shaded in grey corresponds to the sequence depicted in Table 2. The first amino acid residue of the mature SARS-CoV-2 S protein may be Valine (V) with its position designated as 1 (+1), which corresponds to V16 of the precursor S protein (native SARS-CoV-2 S protein with the native signal peptide). The first amino acid residue of the mature SARS-CoV-2 S protein may be at other residues of SEQ ID NO:1 or SEQ ID NO: 63 as indicated in Table 2. For example, the first amino acid residue of the mature SARS-CoV-2 S protein may be Glutamine (Q) with its position designated as 14 (-2).
Signal peptides or peptide sequences for directing localization of an expressed protein or polypeptide to the apoplast include, but are not limited to, a native (with respect to the protein) signal or leader sequence, or a heterologous signal sequence, for example but not limited to, a rice amylase signal peptide (McCormick 1999, Proc Natl Acad Sci USA 96:703-708) or a protein disulfide isomerase signal peptide (PDI). Therefore, as described herein, the modified S protein may be produced as precursor protein comprising a modified S-protein and a heterologous amino acid signal peptide sequence. For example, the modified S protein precursor may comprise the signal peptide from Protein disulphide isomerase (PDI SP; nucleotides 32-103 of Accession No. Z11499).
The present disclosure therefore also provides for a modified S protein precursor comprising a modified S-protein and a native, or a non-native signal peptide, and nucleic acids encoding such protein.
The modified viral structural protein may be a modified S protein, wherein the modified S protein is a monomeric or single chain modified S protein. The monomeric or single chain modified S protein may include an S1 domain (subunit) and an S2 domain (subunit), wherein the S2 domain (subunit) has been modified to replace the native CT of the S protein with the CT of influenza HA protein and wherein the modified S protein is a single contiguous polypeptide chain. Monomeric or single chain modified S protein may trimerize to form a trimer, referred to as a trimeric modified S protein. A trimer is a macromolecular complex formed by three, usually non-covalently bound proteins.
The S protein is cleaved at a conserved activation cleavage site into 2 polypeptide chains, the S1 subunit and S2 subunit, which remain associated as S1/S2 protomers within the homotrimer. Without wishing to be bound by theory, the cleavage of the S protein into subunits may be important for virus infectivity, but it may not be essential for the trimerization of the protein.
The modified S protein may further comprise one or more than one substitution, replacement or mutation. For example, the modified S protein may comprise one or more than one substitution, replacement or mutation in the ectodomain to increase expression, yield, stability or to increase expression, yield and stability of the modified S protein in a suitable expression system.
For example the modified S protein, may comprise substitutions or mutations to the S1/S2 and/or S2′ protease cleavage sites to prevent protease cleavage at these sites. Therefore, when produced in a host or host cells, the modified S protein is not cleaved into separate S1 and S2 subunits or polypeptide chains.
The modified viral structural protein, such as the modified S protein, may further assemble into trimers of modified viral structural protein. It is therefore further provided a Coronavirus protein trimer comprising the modified S protein as described herein. The trimer may comprise single chain modified S protein wherein the single chain modified S protein comprises an S1 subunit and an S2 subunit, wherein the CT of the S2 subunit has been replaced with the CT of influenza hemagglutinin (HA).
The trimer may further be stabilized in a prefusion conformation. The modified viral structural protein, such as the modified S protein, therefore may further comprise one or more than one substitution, replacement or mutation to inhibit a conformational change in the S protein from the prefusion conformation to the post-fusion conformation, and thereby stabilizing the S protein or S protein trimer in the prefusion conformation.
By “amino acid substitution” or “substitution” it is meant the replacement of an amino acid in the amino acid sequence of a protein with a different amino acid. The terms amino acid, amino acid residue or residue are used interchangeably in the disclosure. One or more amino acids may be replaced with or substituted with one or more amino acids that are different than the original or wild-type amino acid at this position, without changing the overall length of the amino acid sequence of the protein.
For example, the modified viral structural protein, such as the modified S protein may be stabilized by proline substitutions, substitutions allowing the formation of disulfide bonds and salt bridges, and/or cavity-filling substitutions.
Hsieh et al. (Science 2020, 369 p. 1501-1505 which is incorporated herein by reference) designed and expressed a variety of SARS-CoV-2 spike protein variants in mammalian cells. An S protein variant with six proline substitutions, referred to as HexaPro, expressed 9.8× higher than S protein compared to variant that only had a double proline substitutions, had ˜5° C. increase in Tm, and retained the trimeric prefusion conformation in mammalian cell lines. The HexaPro variant is considered the best variant by Hsieh et al.
In the current disclosure, the highest yields were observed with combinations of four proline substitutions corresponding to positions 802, 927, 971 and 972 (“4P”) of SEQ ID NO: 2 and an additional single amino acid substitution at position 923. Furthermore, higher yields were also observed with combinations of six proline substitutions corresponding to positions 802, 877, 884, 927, 971 and 972 (“6P”) and an additional single amino acid substitution at position 923.
As provided herewith, the modified S protein may further comprise one or more than one substitution, replacement or mutation to increase stability, yield or stability and yield of the modified protein in a host or cost cell, such for example in a plant or plant cells.
The modified S protein as described herein may comprise one or more than one mutation, modification, or substitution in its amino acid sequence at any one or more amino acid that corresponds to an amino acid within a reference sequence as described below.
By “correspond to an amino acid”, “corresponding to an amino acid” “or “corresponding to the sequence” and the like, it is meant that an amino acid (or nucleotide) corresponds to an amino acids (or nucleotide) in a sequence alignment with a reference Coronavirus sequence as described below. The corresponding amino acid positions in Coronavirus sequence may be determined by alignment to known sequences of Coronavirus S protein. Methods of alignment of sequences for comparison are well-known in the art and are further described below. Examples of corresponding amino acids are shown in Table 3.
1numbering excludes signal peptide (SP)
2numbering includes signal peptide (SP)
For example, the modified S protein may have one or more than one (for example two consecutive) proline substitutions at or near the boundary between a HR1 domain and a central helix domain that stabilize the S ectodomain trimer in the prefusion conformation, as described for example in WO 2018/081318, which is herein incorporated by reference. Furthermore, the one or more than one substitution may restrict and/or may prevent the processing or cleavage at the cleavage site between the S1 and the S2 subunit.
The modified S protein may comprise one or more than one substitution at a position as indicated in Table 3. For example the modified S protein may comprise one or more than one substitution at a position that corresponds to position 667, 668, 670, 802, 877, 884, 923, 927, 971, 972, or a combination thereof in reference sequence of SEQ ID NO: 2 (SARS-CoV-2). Corresponding positions in S-proteins of SARS-CoV-1, MERS-CoV, OC43-CoV and 229E-CoV are indicated in Table 3. Corresponding amino acid positions in S-protein from other Coronavirus may be determined by methods know within the art.
For example, the modified S protein may have one or more than one substitution at one or more than one amino acid corresponding to amino acid at positions 667, 668, 670, 971 or 972 of amino acid sequence of SEQ ID NO: 2.
In one aspect, the modified S protein may comprise a substitution, modification or mutation, corresponding to positions 667, 668, 670 or a combination thereof (numbering in accordance with SEQ ID NO: 2). For example, the amino acid corresponding to position 667 may be substituted for glycine (G) or a conserved substitution of glycine (G), the amino acid corresponding to position 668 may be substituted for serine (S) or a conserved substitution of serine (S), and the amino acid corresponding to position 670 may be substituted for serine (S) or a conserved substitution of serine (S).
The modified S protein may further comprise a substitution, modification or mutation, corresponding to positions 971, 972 or at positions 971 and 972 (numbering in accordance with SEQ ID NO: 2). For example, the amino acid corresponding to position 971 and/or 972 may be substituted for proline (P) or a conserved substitution of proline (P).
The modified S protein may comprise one or more than one substitution wherein the one or more than one substitutions comprise or consist of one or more than one substitution of an amino acid corresponding to amino acid at positions 667, 668, 670, 971, 972 of SEQ ID NO: 2. The modified S protein with one or more than one substitutions may be stabilized in a prefusion confirmation. Furthermore, the modified S protein may form trimer that are stabilized in a prefusion confirmation.
For example, the modified S protein may comprise the following substitutions (numbering in accordance with SEQ ID NO: 2): R667G, R668S, R670S (herein referred to as “GSAS”). The modified S protein may also have the following substitutions (numbering in accordance with SEQ ID NO: 2): K971P and V972P (herein referred to as “2P”). Furthermore the modified S protein may have the following substitutions (numbering in accordance with SEQ ID NO: 2): R667G, R668S, R670S, K971P and V972P (herein referred to as “GSAS-2P”).
For example the modified S protein may have an amino acid sequence that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 47 sequence or with amino acids 25-1259 of SEQ ID NO: 47, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at position 668, serine (S) or a conserved substitution of serine (S) at position 670, proline (P) or a conserved substitution of proline (P) at positions 971 and 972, wherein the modified S protein, when expressed, forms VLP.
In another example, the modified S protein may have one or more than one substitution at one or more than one amino acid corresponding to amino acid at positions 654, 955 or 956 of amino acid sequence of SEQ ID NO: 114 or at positions 730, 733, 1043 or 1044 of amino acid sequence of SEQ ID NO: 115.
For example, the modified S protein may comprise the following substitutions: R654A (numbering in accordance with SEQ ID NO: 114) or R730A and/or R733G (numbering in accordance with SEQ ID NO: 115). The modified S protein may also have the following substitutions: K955P and/or V956P (numbering in accordance with SEQ ID NO: 114) or V1043P and/or L1044P (numbering in accordance with SEQ ID NO: 115). Furthermore the modified S protein may have the following substitutions: R654A, K955P and V956P (numbering in accordance with SEQ ID NO: 114) or R730A, R733G, V1043P, L1044P (numbering in accordance with SEQ ID NO: 115).
The modified S protein may further have substitution at amino acids corresponding to amino acid at positions 667, 668, and 670 and further one or more than one substitution at one or more than one residue corresponding to positions 802, 927, 971 and 972 (numbering in accordance with SEQ ID NO: 2). For example, the amino acid corresponding to positions 802, 927, 971 and 972 may be substituted for proline (P) or a conserved substitution of proline (P).
As shown in
Accordingly, the modified S protein may comprise one or more than one substitution wherein the one or more than one substitution comprise or consist of one or more than one substitution of an amino acid corresponding to amino acid at positions 667, 668, 670, 802, 927, 971 and 972 of SEQ ID NO: 2.
For example the modified S protein may have an amino acid sequence that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 48 or with amino acids 25-1259 of SEQ ID NO: 48, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at position 668, serine (S) or a conserved substitution of serine (S) at position 670, proline (P) or a conserved substitution of proline (P) at positions 802, 927, 971 and 972, wherein the modified S protein, when expressed, forms VLP.
In another example, the modified S protein may have one or more than one substitution at one or more than one amino acid corresponding to amino acid at positions 654, 786, 911, 955 or 956 of amino acid sequence of SEQ ID NO: 114 or at positions 730, 733, 872, 999, 1043 or 1044 of amino acid sequence of SEQ ID NO: 115.
For example, the modified S protein may comprise the following substitutions: R654A (numbering in accordance with SEQ ID NO: 114) or R730A and/or R733G (numbering in accordance with SEQ ID NO: 115). The modified S protein may also have the following substitutions: F786P, S911P, K955P and/or V956P (numbering in accordance with SEQ ID NO: 114) or A872P, N999P, V1043P and/or L1044P (numbering in accordance with SEQ ID NO: 115). Furthermore the modified S protein may have the following substitutions: R654A, F786P, S911P, K955P and V956P (numbering in accordance with SEQ ID NO: 114) or R730A, R733G, A872P, N999P, V1043P, L1044P (numbering in accordance with SEQ ID NO: 115).
The modified S protein may further have substitution at amino acids corresponding to amino acid at positions 667, 668, and 670 and further one or more than one substitution at one or more than one residue corresponding to positions 802, 877, 884, 927, 971, and 972 (numbering in accordance with SEQ ID NO: 2). For example, the amino acid corresponding to position 802, 877, 884, 927, 971, and 972 may be substituted for proline (P) or a conserved substitution of proline (P) (numbering in accordance with SEQ ID NO: 2).
As shown in
Accordingly, the modified S protein may comprise one or more than one substitution wherein the one or more than one substitution comprise or consist of one or more than one substitution of an amino acid corresponding to amino acid at positions 667, 668, 670, 802, 877, 884, 927, 971 and 972 of SEQ ID NO: 2.
For example the modified S protein may have an amino acid sequence that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 49 or with amino acids 25-1259 of SEQ ID NO: 48, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at position 668, serine (S) or a conserved substitution of serine (S) at position 670, proline (P) or a conserved substitution of proline (P) at position 802, 802, 877, 884, 927, 971 and 972, wherein the modified S protein when expressed forms VLP.
In another example, the modified S protein may have one or more than one substitution at one or more than one amino acid corresponding to amino acid at positions 654, 786, 861, 868, 911, 955 or 956 of amino acid sequence of SEQ ID NO: 114 or at positions 730, 733, 872, 949, 956, 999, 1043 or 1044 of amino acid sequence of SEQ ID NO: 115.
For example, the modified S protein may comprise the following substitutions: R654A (numbering in accordance with SEQ ID NO: 114) or R730A and/or R733G (numbering in accordance with SEQ ID NO: 115). The modified S protein may also have the following substitutions: F786P, A861P, A868P, S911P, K955P and/or V956P (numbering in accordance with SEQ ID NO: 114) or A872P, S949P, A956P, N999P, V1043P and/or L1044P (numbering in accordance with SEQ ID NO: 115). Furthermore the modified S protein may have the following substitutions: R654A, F786P, A861P, A868P, S911P, K955P and V956P (numbering in accordance with SEQ ID NO: 114) or R730A, R733G, A872P, S949P, A956P, N999P, V1043P and L1044P (numbering in accordance with SEQ ID NO: 115).
The modified S protein as described herewith may further comprise a substitution, modification, or mutation, corresponding to position 923 (numbering in accordance with SEQ ID NO: 2). For example the amino acid corresponding to position 923 may be substituted for phenylalanine (F) or a conserved substitution of phenylalanine (F).
As shown in
Accordingly, the modified S protein may comprise one or more than one substitution wherein the one or more than one substitution comprises or consists of one or more than one substitution of an amino acid corresponding to amino acids at positions 667, 668, 670, 927, 971, 972, 802, 877, 884, 923 or a combination thereof of SEQ ID NO: 2. For example the modified S-protein may comprise one or more than one substitution wherein the one or more than one substitution comprises or consists of one or more than one substitution of an amino acid corresponding to amino acids at positions 667, 668, 670, 971, 972, 923, or a combination thereof of SEQ ID NO: 2 (GSAS-2P-923), 667, 668, 670, 927, 971, 972, 802 923, or a combination thereof of SEQ ID NO: 2 (GSAS-4P-923) or 667, 668, 670, 927, 971, 972, 802, 877, 884, 923 or a combination thereof of SEQ ID NO: 2 of SEQ ID NO: 2 (GSAS-6P-923).
For example, the modified S protein may comprise one or more than one substitution wherein the one or more than one substitution comprises or consists of one or more than one substitution of an amino acid corresponding to amino acids at positions
For example, the modified S protein may have an amino acid sequence that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 50 or amino acids 25-1259 of SEQ ID NO: 50, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at positions 668 and 670, proline (P) or a conserved substitution of proline (P) at positions 971 and 972, and phenylalanine (F) or a conserved substitution of phenylalanine (F) at position 923; SEQ ID NO: 51 or amino acids 25-1259 of SEQ ID NO: 51, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at positions 668 and 670, proline (P) or a conserved substitution of proline (P) at positions 927, 971, 972 and 802, and phenylalanine (F) or a conserved substitution of phenylalanine (F) at position 923; or SEQ ID NO: 52 or amino acids 25-1259 of SEQ ID NO: 52, wherein the amino acid sequence has glycine (G) or a conserved substitution of glycine (G) at position 667, serine (S) or a conserved substitution of serine (S) at positions 668 and 670, proline (P) or a conserved substitution of proline (P) at positions 927, 971, 972, 802, 877 and 884, and phenylalanine (F) or a conserved substitution of phenylalanine (F) at position 923, wherein the modified S protein when expressed forms VLP.
Accordingly, it is provided a modified coronavirus S-protein which may comprise:
As used herein, the term “conserved substitution” or “conservative substitution” and grammatical variations thereof, refers to an amino acid that is different from an reference amino acid (substitution), but is in the same class of amino acid as the described substitution or described residue (i.e., a nonpolar residue replacing a nonpolar residue, an aromatic residue replacing an aromatic residue, a polar-uncharged residue replacing a polar-uncharged residue, a charged residue replacing a charged residue). Further information about conservative substitutions can be found, for instance, in Sahin-Toth et al. (Protein ScL, 3:240-247, 1994), Hochuli et al (Bio/Technology, 6:1321-1325, 1988) Henikoff S, and Henikoff JG (Proc. Natl. Acad. Sci. USA 89: 10915-10919, 1992) and in widely used textbooks of genetics and molecular biology.
The modified viral structural protein may further be glycosylated. Coronavirus S protein, Coronavirus M protein and Coronavirus E protein are glycosylated and both N-linked glycosylation and O-linked glycosylation occur.
The modified viral structural protein may comprise glycosylation pattern that are unique to the host or host cell in which the modified viral structural protein is expressed. For example, when expressed in plants or plant cells, the modified viral structural protein may comprise plant-specific N-glycans. Therefore, it is also provided modified viral structural protein having plant specific N-glycans.
As described herein, the cytosolic tail domain (CT) of the modified viral structural protein may be replaced with the CT from influenza hemagglutinin (HA). The ectodomain and the transmembrane domain (TM) of the viral structural protein as described above are fused to an influenza HA cytosolic tail domain (CT) such that the CT is heterologous with respect to the ectodomain and the transmembrane domain of the viral structural protein, such as the S protein. The modified S protein may self-assemble into virus-like particles (VLPs).
The present description therefore further relates to virus-like particles (VLPs). More specifically, the present description is directed to VLPs comprising modified viral structural proteins such as modified S-protein, and methods of producing VLPs with modified viral structural proteins such as modified S-protein in a host or host cell. The VLPs comprise a modified viral structural protein such as modified S-protein as described herewith.
As shown in
Furthermore, as shown in
In addition, as shown in
Furthermore, as shown in
The term virus-like particle” (VLP), or “virus-like particles” or “VLPs” refers to virus-like structures that are generally morphologically and antigenically similar to virions produced in an infection, but lack genetic information sufficient to replicate and thus are non-infectious. VLPs are structures that self-assemble and comprise one or more structural proteins such as for example modified viral structural proteins, for example but not limited to a modified S protein. Therefore, the VLP may comprise modified S protein. The VLP may further comprise viral structural proteins, wherein the viral structural proteins consist of modified S protein. Therefore, in some embodiments the VLP may lack or be free of the Coronavirus M protein and/or Coronavirus E protein. In some embodiments the VLPs produced from the modified viral structural protein as described herewith, therefore do not comprise a Coronavirus M protein, a Coronavirus E protein or Coronavirus M protein and Coronavirus E protein. Furthermore, in some embodiment the VLP do not comprise structural or non-structural proteins from viruses that are heterologous to Coronaviridae or influenza virus, for example the VLP do not comprise structural and non-structural protein from viruses that are not from Coronaviridae.
In another embodiment the VLP may comprise Coronavirus E protein, Coronavirus M protein and modified Coronavirus S protein. In another embodiment the VLP may comprise Coronavirus E protein and modified Coronavirus S protein. In another embodiment the VLP may comprise Coronavirus M protein and modified Coronavirus S protein. Furthermore, the VLP may comprise Coronavirus E protein, modified Coronavirus M protein and modified Coronavirus S protein. The VLP may further comprise modified Coronavirus E protein, modified Coronavirus M protein and modified Coronavirus S protein. In another embodiment the VLP may comprise modified Coronavirus E protein and modified Coronavirus S protein. In another embodiment the VLP may comprise modified Coronavirus M protein and modified Coronavirus S protein.
VLPs may be produced in suitable host or host cells including plants and plant cells. Following extraction from the host or host cell and upon isolation and further purification under suitable conditions, VLPs may be recovered as intact structures.
The VLPs may be purified or extracted using any suitable method for example chemical or biochemical extraction. VLPs are relatively sensitive to desiccation, heat, pH, surfactants and detergents. Therefore it may be useful to use methods that maximize yields, minimize contamination of the VLP fraction with cellular proteins, maintain the integrity of the proteins, or VLPs, and, where required, the associated lipid envelope or membrane, methods of loosening the cell wall to release the proteins, or VLP. Minimizing or eliminating the use of detergence or surfactants such for example SDS or Triton™ X-100 may be beneficial for improving the yield of VLP extraction. VLPs may be then assessed for structure and size by, for example, electron microscopy (see
For enveloped viruses, such as Coronavirus, it may be advantageous for a lipid layer or membrane to be retained by the virus. The composition of the lipid may vary with the system (e.g. a plant-produced enveloped virus would include plant lipids or phytosterols in the envelope), and may contribute to an improved immune response.
Therefore, the VLPs that are produced in a host or host cell, may comprise lipids from the plasma membrane of the host or host cell. For example VLPs produced in plants may contain lipids of plant origin (“plant lipids”), VLPs produced in insect cells may comprise lipids from the plasma membrane of insect cells (generally referred to as “insect lipids”), and VLPs produced in mammalian cells may comprise lipids from the plasma membrane of mammalian cells (generally referred to as “mammalian lipids”).
The plant lipids or plant-derived lipids may be in the form of a lipid bilayer, and may further comprise an envelope surrounding the VLP. The plant-derived lipids may comprise lipid components of the plasma membrane of the plant where the VLP is produced, including phospholipids, tri-, di- and monoglycerides, as well as fat-soluble sterol or metabolites comprising sterols. Examples include phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol, phosphatidylserine, glycosphingolipids, phytosterols or a combination thereof. Examples of phytosterols include campesterol, stigmasterol, ergosterol, brassicasterol, delta-7-stigmasterol, delta-7-avenasterol, daunosterol, sitosterol, 24-methylcholesterol, cholesterol or beta-sitosterol. As one of skill in the art would understand, the lipid composition of the plasma membrane of a cell may vary with the culture or growth conditions of the cell or organism, or species, from which the cell is obtained. Generally, beta-sitosterol is the most abundant phytosterol.
Without wishing to be bound by theory, plant-made VLPs comprising plant derived lipids, may induce a stronger immune reaction than VLPs made in other manufacturing systems and the immune reaction induced by these plant-made VLPs may be stronger when compared to the immune reaction induced by live or attenuated whole virus vaccines.
Furthermore, in addition to the potential adjuvant effect of the presence of plant lipids, the ability of plant N-glycans to facilitate the capture of glycoprotein antigens by antigen presenting cells, may be advantageous of the production of VLPs in plants.
The VLP produced within a plant may comprise a modified viral structural protein comprising plant-specific N-glycans. Therefore, this disclosure also provides for a VLP comprising modified viral structural protein having plant specific N-glycans. Furthermore, it is provided VLP comprising plant lipids and modified viral structural protein having plant specific N-glycans.
Methods of producing virus like particle (VLP) comprising modified structural protein in a host or host cell are also provided. Furthermore, methods of increasing yield of production of virus like particle (VLP) comprising modified structural protein in a host or host cell are also provided. The methods comprise the introduction of a nucleic acid comprising a sequence that encodes a modified structural protein into the host or host cell, and incubating the host or host cell under conditions that permit the expression of the nucleic acid, thereby producing the VLP. The modified viral structural protein may be produced at a higher yield compared to a host or host cell expressing the unmodified viral structural protein.
For example, as shown in
The yield of the modified viral structural protein (such as modified S protein) or the yield of a VLP comprising modified viral structural protein produced in a host or host cell, such for example a plant or plant cells, may be increased by 1.1-10 fold, or any amount therebetween when compared to the yield of a corresponding unmodified viral structural protein or the yield of VLP that comprises the corresponding unmodified viral structural protein. For example the yield of the modified viral structural protein (such as modified S protein) or the yield of a VLP (comprising the modified viral structural protein) in a host or host cell may be increased by 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.6, 5.7, 5.8, 5.9, 6, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10 fold or any amount therebetween, compared to the yield of a corresponding unmodified viral structural protein or the yield of a VLP wherein the VLP comprises a corresponding unmodified viral structural protein, when produced in a host or host cell under identical conditions.
The modified viral structural protein described herewith includes modified S proteins with amino acid sequences that have about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 1, 2, 5, 21, 30, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 95, 96, 97, 108, 109, 110, 112, 113, 114, 115, 144, 145, 146, 155, 156, 157, 158, 159, 160, or 161, or with amino acids 25-1259 of SEQ ID NO: 47, amino acids 25-1259 of SEQ ID NO: 48, amino acids 25-1259 of SEQ ID NO: 49, amino acids 25-1259 of SEQ ID NO: 50, amino acids 25-1259 of SEQ ID NO: 51, amino acids 25-1259 of SEQ ID NO: 52, amino acids 25-1259 of SEQ ID NO: 53, amino acids 25-1259 of SEQ ID NO: 54, amino acids 25-1259 of SEQ ID NO: 55, amino acids 25-1259 of SEQ ID NO: 56, amino acids 25-1259 of SEQ ID NO: 57, amino acids 25-1259 of SEQ ID NO: 58, amino acids 25-1262 of SEQ ID NO: 59, amino acids 25-1261 of SEQ ID NO: 60, amino acids 25-1258 of SEQ ID NO: 61, amino acids 25-1256 of SEQ ID NO: 62, amino acids 25-1243 of SEQ ID NO: 95, amino acids 25-1240 of SEQ ID NO: 96, amino acids 25-1243 of SEQ ID NO: 97, amino acids 25-1341 of SEQ ID NO: 108, amino acids 25-1338 of SEQ ID NO: 109, amino acids 25-1341 of SEQ ID NO: 110, amino acids 25-1351 of SEQ ID NO: 144, amino acids 25-1348 of SEQ ID NO: 145, amino acids 25-1351 of SEQ ID NO: 146, amino acids 25-1159 of SEQ ID NO: 155, amino acids 25-1156 of SEQ ID NO: 156, or amino acids 25-1159 of SEQ ID NO: 157, and wherein modified S proteins when expressed in a host or host cell form VLP. The amino acid sequence of the ectodomain and the transmembrane domain of the modified S proteins has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with amino acids 1-1234 of SEQ ID NO:1, with amino acids 1-1219 of SEQ ID NO: 2, with amino acids 1-1234 of SEQ ID NO: 5, with amino acids 1-1219 of SEQ ID NO: 21, with amino acids 1-1243 of SEQ ID NO: 30, with the amino acids 25-1243 of SEQ ID NO: 47, with the amino acids 25-1243 of SEQ ID NO: 48, with the amino acids 25-1243 of SEQ ID NO: 49, with the amino acids 25-1243 of SEQ ID NO: 50, with the amino acids 25-1243 of SEQ ID NO: 51, with the amino acids 25-1243 of SEQ ID NO: 52, with the amino acids 25-1243 of SEQ ID NO: 53, with the amino acids 25-1243 of SEQ ID NO: 54, with the amino acids 25-1243 of SEQ ID NO: 55, with the amino acids 25-1243 of SEQ ID NO: 56, with the amino acids 25-1243 of SEQ ID NO: 57, with the amino acids 25-1243 of SEQ ID NO: 58, with the amino acids 25-1242 of SEQ ID NO: 59, with the amino acids 25-1242 of SEQ ID NO: 60, with the amino acids 25-1246 of SEQ ID NO: 61, or with the amino acids 25-1245 of SEQ ID NO: 62, amino acids 25-1227 of SEQ ID NO: 95, amino acids 25-1227 of SEQ ID NO: 96, amino acids 25-1227 of SEQ ID NO: 97, amino acids 25-1325 of SEQ ID NO: 108, amino acids 25-1325 of SEQ ID NO: 109, amino acids 25-1325 of SEQ ID NO: 110, amino acids 25-1335 of SEQ ID NO: 144, amino acids 25-1335 of SEQ ID NO: 145, amino acids 25-1335 of SEQ ID NO: 146, amino acids 25-1143 of SEQ ID NO: 155, amino acids 25-1143 of SEQ ID NO: 156, or amino acids 25-1143 of SEQ ID NO: 157, and the amino acid sequence of the cytoplasmic tail domain (CT) of the modified S protein has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 15, or with amino acids 35-50 of SEQ ID NO 6, 8, 7, 9, 10, 12, 13, 14, or with amino acids 34-49 of SEQ ID NO 11, or with amino acids 553-568 of SEQ ID NO:3 and wherein modified S proteins when expressed in a host or host cell form VLP.
Furthermore, the modified viral structural protein may be encoded by a nucleotide sequence that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the nucleotide sequence according to SEQ ID NO: 22, 26, 29, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 90, 91, 92, 95, 96, 97, 103, 104, 105, 139, 140, 141, 150, 151, or 152 and wherein the nucleotide sequence encodes modified S proteins that when expressed in a host or host cell form VLP.
It is further provided nucleotide sequence encoding a modified S proteins with amino acid sequences that have about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 1, 2, 5, 21, 30, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 95, 96, 97, 108, 109, 110, 144, 145, 146, 155, 156 or 157, and wherein modified S proteins when expressed in a host or host cell form VLP. The nucleotide sequence may encode an amino acid sequence of the ectodomain and the transmembrane domain of the modified S proteins that has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with amino acids 1-1234 of SEQ ID NO:1, with amino acids 1-1219 of SEQ ID NO: 2, with amino acids 1-1234 of SEQ ID NO: 5, with amino acids 1-1219 of SEQ ID NO: 21 or with amino acids 1-1243 of SEQ ID NO: 30, with the amino acids 25-1243 of SEQ ID NO: 47, with the amino acids 25-1243 of SEQ ID NO: 48, with the amino acids 25-1243 of SEQ ID NO: 49, with the amino acids 25-1243 of SEQ ID NO: 50, with the amino acids 25-1243 of SEQ ID NO: 51, with the amino acids 25-1243 of SEQ ID NO: 52, with the amino acids 25-1243 of SEQ ID NO: 53, with the amino acids 25-1243 of SEQ ID NO: 54, with the amino acids 25-1243 of SEQ ID NO: 55, with the amino acids 25-1243 of SEQ ID NO: 56, with the amino acids 25-1243 of SEQ ID NO: 57, with the amino acids 25-1243 of SEQ ID NO: 58, with the amino acids 25-1242 of SEQ ID NO: 59, with the amino acids 25-1242 of SEQ ID NO: 60, with the amino acids 25-1246 of SEQ ID NO: 61, with the amino acids 25-1245 of SEQ ID NO: 62, amino acids 25-1227 of SEQ ID NO: 95, amino acids 25-1227 of SEQ ID NO: 96, amino acids 25-1227 of SEQ ID NO: 97, amino acids 25-1325 of SEQ ID NO: 108, amino acids 25-1325 of SEQ ID NO: 109, amino acids 25-1325 of SEQ ID NO: 110, amino acids 25-1335 of SEQ ID NO: 144, amino acids 25-1335 of SEQ ID NO: 145, amino acids 25-1335 of SEQ ID NO: 146, amino acids 25-1143 of SEQ ID NO: 155, amino acids 25-1143 of SEQ ID NO: 156, or amino acids 25-1143 of SEQ ID NO: 157, and the amino acid sequence of the cytoplasmic tail domain of the modified S protein has about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence identity, or sequence similarity, with the sequence of SEQ ID NO: 15, or with amino acids 35-50 of SEQ ID NO 6, 8, 7, 9, 10, 12, 13, 14, or with amino acids 34-49 of SEQ ID NO 11, or with amino acids 553-568 of SEQ ID NO:3 and wherein modified S proteins when expressed in a host or host cell form VLP.
It is further provided a nucleotide sequence encoding a modified S proteins with amino acid sequences that have about 70, 75, 80, 85, 87, 90, 91, 92, 93 94, 95, 96, 97, 98, 99, 100% or any amount therebetween, sequence identity, or sequence similarity, with the amino acid sequence of SEQ ID NO: 5, 21, 30, or 47-62, or with amino acids 24-1259 of SEQ ID NO: 47 amino acids 25-1259 of SEQ ID NO: 48, amino acids 25-1259 of SEQ ID NO: 49, amino acids 25-1259 of SEQ ID NO: 50, amino acids 25-1259 of SEQ ID NO: 51, amino acids 25-1259 of SEQ ID NO: 52, amino acids 25-1259 of SEQ ID NO: 53, amino acids 25-1259 of SEQ ID NO: 54, amino acids 25-1259 of SEQ ID NO: 55, amino acids 25-1259 of SEQ ID NO: 56, amino acids 25-1259 of SEQ ID NO: 57, amino acids 25-1259 of SEQ ID NO: 58, amino acids 25-1262 of SEQ ID NO: 59, amino acids 25-1261 of SEQ ID NO: 60, amino acids 25-1258 of SEQ ID NO: 61, or amino acids 25-1256 of SEQ ID NO: 62, amino acids 25-1243 of SEQ ID NO: 95, amino acids 25-1240 of SEQ ID NO: 96, amino acids 25-1243 of SEQ ID NO: 97, amino acids 25-1341 of SEQ ID NO: 108, amino acids 25-1338 of SEQ ID NO: 109, amino acids 25-1341 of SEQ ID NO: 110, amino acids 25-1351 of SEQ ID NO: 144, amino acids 25-1348 of SEQ ID NO: 145, amino acids 25-1351 of SEQ ID NO: 146, amino acids 25-1159 of SEQ ID NO: 155, amino acids 25-1156 of SEQ ID NO: 156, or amino acids 25-1159 of SEQ ID NO: 157, and wherein modified S proteins when expressed in a host or host cell form VLP.
The terms “percent similarity”, “sequence similarity”, “percent identity”, or “sequence identity”, when referring to a particular sequence, are used for example as set forth in the University of Wisconsin GCG software program, or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology, Ausubel et al., eds. 1995 supplement). Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, using for example the algorithm of Smith & Waterman, (1981, Adv. Appl. Math. 2:482), by the alignment algorithm of Needleman & Wunsch, (1970, J. Mol. Biol. 48:443), by the search for similarity method of Pearson & Lipman, (1988, Proc. Natl. Acad. Sci. USA 85:2444), by computerized implementations of these algorithms (for example: GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.).
An example of an algorithm suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., (1977, Nuc. Acids Res. 25:3389-3402) and Altschul et al., (1990, J. Mol. Biol. 215:403-410), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the disclosure. For example the BLASTN program (for nucleotide sequences) may use as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program may use as defaults a word length of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (see URL: ncbi.nlm.nih.gov/).
A nucleic acid sequence or nucleotide sequence referred to in the present disclosure, may be “substantially homologous”, “substantially similar” or “substantially identical” to a sequence, or a compliment of the sequence if the nucleic acid sequence or nucleotide sequence hybridise to one or more than one nucleotide sequence or a compliment of the nucleic acid sequence or nucleotide sequence as defined herein under stringent hybridisation conditions. Sequences are “substantially homologous” “substantially similar” “substantially identical” when at least about 70%, or between 70 to 100%, or any amount therebetween, for example 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100%, or any amount therebetween, of the nucleotides match over a defined length of the nucleotide sequence providing that such homologous sequences exhibit one or more than one of the properties of the sequence, or the encoded product as described herein.
Many organisms display a bias for use of particular codons to code for insertion of a particular amino acid in a growing peptide chain. Codon preference or codon bias, differences in codon usage between organisms, is afforded by degeneracy of the genetic code, and is well documented among many organisms. Codon bias often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, inter alia, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. The process of optimizing the nucleotide sequence coding for a heterologously expressed protein may be an important step for improving expression yields. The optimization requirements may include steps to improve the ability of the host to produce the foreign protein.
There are different codon-optimization techniques known in the art for improving, the translational kinetics of translationally inefficient protein coding regions. These techniques mainly rely on identifying the codon usage for a certain host organism. If a certain gene or sequence should be expressed in this organism, the coding sequence of such genes and sequences will then be modified such that one will replace codons of the sequence of interest by more frequently used codons of the host organism.
“Codon optimization” is defined as modifying a nucleic acid sequence for enhanced expression in a host or host cell of interest by replacing at least one, more than one, or a significant number, of codons of the native sequence with codons that may be more frequently or most frequently used in the genes of another organism or species. Various species exhibit particular bias for certain codons of a particular amino acid.
The present disclosure includes synthetic polynucleotide sequences that have been codon optimized for example the sequences have been optimized for human codon usage or plant codon usage. The codon optimized polynucleotide sequences may then be expressed in the host for example plants. More specifically the sequences optimized for human codon usage or plant codon usage may be expressed in plants. Without wishing to be bound by theory, it is believed that the sequences optimized for human codon increases the guanine-cytosine content (GC content) of the sequence and improves expression yields when plants are used as host.
The term “construct”, “vector” or “expression vector”, as used herein, refers to a recombinant nucleic acid for transferring exogenous nucleotide sequences (for example a nucleotide sequences encoding the modified viral structural protein as described herewith) into host cells (e.g. plant cells) and directing expression of the exogenous nucleic acid sequences in the host cells. “Expression cassette” refers to a nucleic acid comprising a nucleotide sequence of interest under the control of, and operably (or operatively) linked to, an appropriate promoter or other regulatory elements for transcription of the nucleic acid of interest in a host cell. As one of skill in the art would appreciate, the expression cassette may comprise a termination (terminator) sequence that is any sequence that is active the host cell (e.g. plant host). For example in plants, the termination sequence may be derived from the RNA-2 genome segment of a bipartite RNA virus, e.g. a comovirus, the termination sequence may be a NOS terminator, or terminator sequence may be obtained from the 3′UTR of the alfalfa plastocyanin gene.
The nucleic acid comprising a nucleotide sequence encoding a modified viral structural protein, as described herein may further comprise sequences that enhance expression of the viral structural protein in the host, portion of the host or host cell. Sequences that enhance expression may include, a 5′ UTR enhancer element, or a plant-derived expression enhancer, in operative association with the nucleic acid encoding the modified viral structural protein. The sequence encoding the modified viral structural protein may also be optimized to increase expression by for example optimizing for human codon usage, increased GC content, or a combination thereof.
By “regulatory region” “regulatory element” or “promoter” it is meant a portion of nucleic acid typically, but not always, upstream of the protein coding region of a gene, which may be comprised of either DNA or RNA, or both DNA and RNA. When a regulatory region is active, and in operative association, or operatively linked, with a nucleotide sequence of interest, this may result in expression of the nucleotide sequence of interest. A regulatory element may be capable of mediating organ specificity, or controlling developmental or temporal gene activation. A “regulatory region” includes promoter elements, core promoter elements exhibiting a basal promoter activity, elements that are inducible in response to an external stimulus, elements that mediate promoter activity such as negative regulatory elements or transcriptional enhancers. “Regulatory region”, as used herein, also includes elements that are active following transcription, for example, regulatory elements that modulate gene expression such as translational and transcriptional enhancers, translational and transcriptional repressors, upstream activating sequences, and mRNA instability determinants. Several of these latter elements may be located proximal to the coding region.
In the context of this disclosure, the term “regulatory element” or “regulatory region” typically refers to a sequence of DNA, usually, but not always, upstream (5′) to the coding sequence of a structural gene, which controls the expression of the coding region by providing the recognition for RNA polymerase and/or other factors required for transcription to start at a particular site. However, it is to be understood that other nucleotide sequences, located within introns, or 3′ of the sequence may also contribute to the regulation of expression of a coding region of interest. An example of a regulatory element that provides for the recognition for RNA polymerase or other transcriptional factors to ensure initiation at a particular site is a promoter element. Most, but not all, eukaryotic promoter elements contain a TATA box, a conserved nucleic acid sequence comprised of adenosine and thymidine nucleotide base pairs usually situated approximately 25 base pairs upstream of a transcriptional start site. A promoter element may comprise a basal promoter element, responsible for the initiation of transcription, as well as other regulatory elements that modify gene expression.
There are several types of regulatory regions, including those that are developmentally regulated, inducible or constitutive. A regulatory region that is developmentally regulated, or controls the differential expression of a gene under its control, is activated within certain organs or tissues of an organ at specific times during the development of that organ or tissue. However, some regulatory regions that are developmentally regulated may preferentially be active within certain organs or tissues at specific developmental stages, they may also be active in a developmentally regulated manner, or at a basal level in other organs or tissues within the plant as well. Examples of tissue-specific regulatory regions, for example see-specific a regulatory region, include the napin promoter, and the cruciferin promoter (Rask et al., 1998, J. Plant Physiol. 152: 595-599; Bilodeau et al., 1994, Plant Cell 14: 125-130). An example of a leaf-specific promoter includes the plastocyanin promoter (see U.S. Pat. No. 7,125,978, which is incorporated herein by reference).
An inducible regulatory region is one that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer. In the absence of an inducer the DNA sequences or genes will not be transcribed. Typically the protein factor that binds specifically to an inducible regulatory region to activate transcription may be present in an inactive form, which is then directly or indirectly converted to the active form by the inducer. However, the protein factor may also be absent. The inducer can be a chemical agent such as a protein, metabolite, growth regulator, herbicide or phenolic compound or a physiological stress imposed directly by heat, cold, salt, or toxic elements or indirectly through the action of a pathogen or disease agent such as a virus. A plant cell containing an inducible regulatory region may be exposed to an inducer by externally applying the inducer to the cell or plant such as by spraying, watering, heating or similar methods. Inducible regulatory elements may be derived from either plant or non-plant genes (e.g. Gatz, C. and Lenk, I. R. P., 1998, Trends Plant Sci. 3, 352-358). Examples, of potential inducible promoters include, but not limited to, tetracycline-inducible promoter (Gatz, C., 1997, Ann. Rev. Plant Physiol. Plant Mol. Biol. 48, 89-108), steroid inducible promoter (Aoyama, T. and Chua, N. H., 1997, Plant J. 2, 397-404) and ethanol-inducible promoter (Salter, M. G., et al, 1998, Plant Journal 16, 127-132; Caddick, M. X., et al, 1998, Nature Biotech. 16, 177-180) cytokinin inducible IB6 and CKI1 genes (Brandstatter, I. and Kieber, J. J., 1998, Plant Cell 10, 1009-1019; Kakimoto, T., 1996, Science 274, 982-985) and the auxin inducible element, DR5 (Ulmasov, T., et al., 1997, Plant Cell 9, 1963-1971).
A constitutive regulatory region directs the expression of a gene throughout the various parts of a plant and continuously throughout plant development. Examples of known constitutive regulatory elements include promoters associated with the CaMV 35S transcript. (p 35S; Odell et al., 1985, Nature, 313: 810-812; which is incorporated herein by reference), the rice actin 1 (Zhang et al, 1991, Plant Cell, 3: 1155-1165), actin 2 (An et al., 1996, Plant J., 10: 107-121), or tms 2 (U.S. Pat. No. 5,428,147), and triosephosphate isomerase 1 (Xu et. al., 1994, Plant Physiol. 106: 459-467) genes, the maize ubiquitin 1 gene (Cornejo et al, 1993, Plant Mol. Biol. 29: 637-646), the Arabidopsis ubiquitin 1 and 6 genes (Holtorf et al, 1995, Plant Mol. Biol. 29: 637-646), the tobacco translational initiation factor 4A gene (Mandel et al, 1995 Plant Mol. Biol. 29: 995-1004), the Cassava Vein Mosaic Virus promoter, pCAS, (Verdaguer et al., 1996); the promoter of the small subunit of ribulose biphosphate carboxylase, pRbcS: (Outchkourov et al., 2003), the pUbi (for monocots and dicots).
The term “constitutive” as used herein does not necessarily indicate that a nucleotide sequence under control of the constitutive regulatory region is expressed at the same level in all cell types, but that the sequence is expressed in a wide range of cell types even though variation in abundance is often observed.
One or more of the genetic constructs of the present disclosure may also include further enhancers, either translation or transcription enhancers, as may be required. Enhancers may be located 5′ or 3′ to the sequence being transcribed. Enhancer regions are well known to persons skilled in the art, and may include an ATG initiation codon, adjacent sequences or the like. The initiation codon, if present, may be in phase with the reading frame (“in frame”) of the coding sequence to provide for correct translation of the transcribed sequence.
The term “5′UTR” or “5′ untranslated region”, “5′ leader sequence” or “5′ UTR enhancer element” refers to regions of an mRNA that are not translated. The 5′UTR typically begins at the transcription start site and ends just before the translation initiation site or start codon of the coding region. The 5′ UTR may modulate the stability and/or translation of an mRNA transcript.
The term “plant-derived expression enhancer”, as used herein, refers to a nucleotide sequence obtained from a plant, the nucleotide sequence encoding a 5′UTR. Examples of a plant derived expression enhancer are described in U.S. Provisional Patent Application No. 62/643,053 (Filed Mar. 14, 2018) and International Application No. PCT/CA2019/050319 (Filed Mar. 14, 2019); which are incorporated herein by reference) or in Diamos A. G. et al. (2016, Front Plt Sci. 7:1-15; which is incorporated herein by reference). The plant-derived expression enhancer may be selected from nbEPI42, nbSNS46, nbCSY65, nbHEL40, nbSEP44, nbMT78, nbATL75, nbDJ46, nbCHP79, nbEN42, atHSP69, atGRP62, atPK65, atRP46, nb30S72, nbGT61, nbPV55, nbPPI43, nbPM64 and nbH2A86 as described in U.S. 62/643,053 and PCT/CA2019/050319. The plant derived expression enhancer may be used within a plant expression system comprising a regulatory region that is operatively linked with the plant-derived expression enhancer sequence and a nucleotide sequence of interest, for example a nucleotide sequence encoding a modified S protein.
Stability and/or translation efficiency of an RNA may further be improved by the inclusion of a 3′ untranslated region (3′UTR). The one or more genetic constructs of the present description may therefore further comprise a 3′ UTR.
A 3′ untranslated region may contain a polyadenylation signal and any other regulatory signals capable of effecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by effecting the addition of polyadenylic acid tracks to the 3′ end of the mRNA precursor. Polyadenylation signals are commonly recognized by the presence of homology to the canonical form 5′ AATAAA-3′ although variations are not uncommon. Non-limiting examples of suitable 3′ regions are the 3′ transcribed non-translated regions containing a polyadenylation signal of Agrobacterium tumor inducing (Ti) plasmid genes, such as the nopaline synthase (Nos gene) and plant genes such as the soybean storage protein genes, the small subunit of the ribulose-1, 5-bisphosphate carboxylase gene (ssRUBISCO; U.S. Pat. No. 4,962,028; which is incorporated herein by reference), the promoter used in regulating plastocyanin expression, described in U.S. Pat. No. 7,125,978 (which is incorporated herein by reference), 3′ UTR derived from a Arracacha virus B isolate gene (AvB) (SEQ ID NO: 40), 3′UTR derived from Beet necrotic yellow vein virus (trBNYVV) (SEQ ID NO: 41), 3′UTR derived from Southern bean mosaic virus (SBMV) (SEQ ID NO: 42), 3′UTR derived from Turnip ringspot virus (TuRSV) (SEQ ID NO: 43), 3′ UTR derived from Cowpea Mosaic Virus (CPMV) (SEQ ID NO: 44), 3′UTR derived from Broad bean true mosaic virus (BBTMV) (SEQ ID NO: 45) or 3′UTR derived from Ourmia melon virus (trOUMV) (SEQ ID NO: 46). The 3′UTR might be used in conjunction with 5′UTR derived from heterologous sequences to modulate expression levels.
It is therefore provided a “construct”, “vector”, “expression vector” or “expression cassette” that comprises a nucleic acid comprising a nucleotide sequence of interest (such as a modified viral structural protein) under the control of, and operably (or operatively) linked to a 3′UTR. Furthermore, the nucleic acid may comprise a 3′UTR operably (or operatively) linked to a nucleotide sequence of interest (such as a modified viral structural protein).
The modified viral structural protein may be targeted to any intracellular or extracellular space, organelle or tissue of a host of host cell such as plant or plant cell as desired. In order to localize the expressed protein to a particular location, the nucleic acid encoding the protein may be linked to a nucleic acid sequence encoding a signal peptide or leader sequence. A signal peptide may alternately be referred to as a transit peptide, signal sequence, leader sequence, targeting signal, localization signal, localization sequence, transit peptide, or leader peptide.
The one or more than one modified genetic constructs of the present description may be expressed in any suitable host or host cell that is transformed by the nucleic acids, or nucleotide sequence, or constructs, or vectors of the present disclosure. The host or host cell may be from any source including plants, fungi, bacteria, insect and animals for example mammals. Therefore the host or host cell may be selected from a plant or plant cell, a fungi or a fungi cell, a bacteria or bacteria cell, an insect or an insect cell, and animal or an animal cell. The mammal or animal may not be a human. In a preferred embodiment the host or host cell is a plant, portion of a plant or plant cell.
The term “plant”, “portion of a plant”, “plant portion”, “plant matter”, “plant biomass”, “plant material”, plant extract”, or “plant leaves”, as used herein, may comprise an entire plant, tissue, cells, or any fraction thereof, intracellular plant components, extracellular plant components, liquid or solid extracts of plants, or a combination thereof, that are capable of providing the transcriptional, translational, and post-translational machinery for expression of one or more than one nucleic acids described herein, and/or from which an expressed protein or VLP may be extracted and purified. Plants may include, but are not limited to, herbaceous plants. The herbaceous plants may be annuals, biennials or perennials plants. Plants may further include, but are not limited to agricultural crops including for example canola, Brassica spp., maize, Nicotiana spp., (tobacco) for example, Nicotiana benthamiana, Nicotiana rustica, Nicotiana, tabacum, Nicotiana alata, Arabidopsis thaliana, alfalfa, potato, sweet potato (Ipomoea batatus), ginseng, pea, oat, rice, soybean, wheat, barley, sunflower, cotton, corn, rye (Secale cereale), Sorghum (Sorghum bicolor, Sorghum vulgare), safflower (Carthamus tinctorius).
The term “plant portion”, as used herein, refers to any part of the plant including but not limited to leaves, stem, root, flowers, fruits, a plant cell obtained from leaves, stem, root, flowers, fruits, a plant extract obtained from leaves, stem, root, flowers, fruits, or a combination thereof. In one embodiment the plant portion refers to the areal portion of a plant such as for example leaves, stem, flowers and fruits. The term “plant extract”, as used herein, refers to a plant-derived product that is obtained following treating a plant, a portion of a plant, a plant cell, or a combination thereof, physically (for example by freezing followed by extraction in a suitable buffer), mechanically (for example by grinding or homogenizing the plant or portion of the plant followed by extraction in a suitable buffer), enzymatically (for example using cell wall degrading enzymes), chemically (for example using one or more chelators or buffers), or a combination thereof. A plant extract may be further processed to remove undesired plant components for example cell wall debris. A plant extract may be obtained to assist in the recovery of one or more components from the plant, portion of the plant or plant cell, for example a protein (including protein complexes, protein surprastructures and/or VLPs), a nucleic acid, a lipid, a carbohydrate, or a combination thereof from the plant, portion of the plant, or plant cell. If the plant extract comprises proteins, then it may be referred to as a protein extract. A protein extract may be a crude plant extract, a partially purified plant or protein extract, or a purified product, that comprises one or more proteins, protein complexes such for example protein trimers, protein suprastructures, and/or VLPs, from the plant tissue. If desired a protein extract, or a plant extract, may be partially purified using techniques known to one of skill in the art, for example, the extract may be subjected to salt or pH precipitation, centrifugation, gradient density centrifugation, filtration, chromatography, for example, size exclusion chromatography, ion exchange chromatography, affinity chromatography, or a combination thereof. A protein extract may also be purified, using techniques that are known to one of skill in the art.
The constructs of the present disclosure can be introduced into plant cells using Ti plasmids, Ri plasmids, plant virus vectors, direct DNA transformation, micro-injection, electroporation, etc. For reviews of such techniques see for example Weissbach and Weissbach, Methods for Plant Molecular Biology, Academy Press, New York VIII, pp. 421-463 (1988); Geierson and Corey, Plant Molecular Biology, 2d Ed. (1988); and Miki and Iyer, Fundamentals of Gene Transfer in Plants. In Plant Metabolism, 2d Ed. DT. Dennis, DH Turpin, DD Lefebvre, DB Layzell (eds), Addison Wesly, Langmans Ltd. London, pp. 561-579 (1997). Other methods include direct DNA uptake, the use of liposomes, electroporation, for example using protoplasts, micro-injection, microprojectiles or whiskers, and vacuum infiltration. See, for example, Bilang, et al. (Gene 100: 247-250 (1991), Scheid et al. (Mol. Gen. Genet. 228: 104-112, 1991), Guerche et al. (Plant Science 52: 111-116, 1987), Neuhause et al. (Theor. Appl Genet. 75: 30-36, 1987), Klein et al., Nature 327: 70-73 (1987); Howell et al. (Science 208: 1265, 1980), Horsch et al. (Science 227: 1229-1231, 1985), DeBlock et al., Plant Physiology 91: 694-701, 1989), Methods for Plant Molecular Biology (Weissbach and Weissbach, eds., Academic Press Inc., 1988), Methods in Plant Molecular Biology (Schuler and Zielinski, eds., Academic Press Inc., 1989), Liu and Lomonossoff (J Virol Meth, 105:343-348, 2002), U.S. Pat. Nos. 4,945,050; 5,036,006; and 5,100,792, U.S. patent application Ser. No. 08/438,666, filed May 10, 1995, and Ser. No. 07/951,715, filed Sep. 25, 1992, (all of which are hereby incorporated by reference).
As described below, transient expression methods may be used to express the constructs of the present disclosure (see Liu and Lomonossoff, 2002, Journal of Virological Methods, 105:343-348; which is incorporated herein by reference). Alternatively, a vacuum-based transient expression method, as described by Kapila et al., 1997, which is incorporated herein by reference) may be used. These methods may include, for example, but are not limited to, a method of Agro-inoculation or Agroinfiltration, syringe infiltration, however, other transient methods may also be used as noted above. With Agro-inoculation, Agroinfiltration, or syringe infiltration, a mixture of Agrobacteria comprising the desired nucleic acid enter the intercellular spaces of a tissue, for example the leaves, aerial portion of the plant (including stem, leaves and flower), other portion of the plant (stem, root, flower), or the whole plant. After crossing the epidermis the Agrobacteria infect and transfer t-DNA copies into the cells. The t-DNA is episomally transcribed and the mRNA translated, leading to the production of the protein of interest in infected cells, however, the passage of t-DNA inside the nucleus is transient.
To aid in identification of transformed plant cells, the constructs of this disclosure may be further manipulated to include plant selectable markers. Useful selectable markers include enzymes that provide for resistance to chemicals such as an antibiotic for example, gentamycin, hygromycin, kanamycin, or herbicides such as phosphinothrycin, glyphosate, chlorosulfuron, and the like. Similarly, enzymes providing for production of a compound identifiable by colour change such as GUS (beta-glucuronidase), or luminescence, such as luciferase or GFP, may be used.
Also considered part of this disclosure are transgenic plants, plant cells or seeds containing the gene construct of the present disclosure that may be used as a platform plant suitable for transient protein expression described herein. Methods of regenerating whole plants from plant cells are also known in the art (for example see Guerineau and Mullineaux (1993, Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed) Oxford, BIOS Scientific Publishers, pp 121-148). In general, transformed plant cells are cultured in an appropriate medium, which may contain selective agents such as antibiotics, where selectable markers are used to facilitate identification of transformed plant cells. Once callus forms, shoot formation can be encouraged by employing the appropriate plant hormones in accordance with known methods and the shoots transferred to rooting medium for regeneration of plants. The plants may then be used to establish repetitive generations, either from seeds or using vegetative propagation techniques. Transgenic plants can also be generated without using tissue culture. Methods for stable transformation, and regeneration of these organisms are established in the art and known to one of skill in the art. Available techniques are reviewed in Vasil et al. (Cell Culture and Somatic Cell Genetics of Plants, Vol I, Il and III, Laboratory Procedures and Their Applications, Academic Press, 1984), and Weissbach and Weissbach (Methods for Plant Molecular Biology, Academic Press, 1989). The method of obtaining transformed and regenerated plants is not critical to the present disclosure.
If plants, plant portions or plant cells are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the Agrobacterium in a single transfection event so that the nucleic acids are pooled, and the bacterial cells transfected. Alternatively, the constructs may be introduced serially. In this case, a first construct is introduced into the Agrobacterium as described, the cells are grown under selective conditions (e.g. in the presence of an antibiotic) where only the singly transformed bacteria can grow. Following this first selection step, a second nucleic acid construct is introduced into the Agrobacterium as described, and the cells are grown under double-selective conditions, where only the double-transformed bacteria can grow. The double-transformed bacteria may then be used to transform a plant, portion of the plant or plant cell as described herein, or may be subjected to a further transformation step to accommodate a third nucleic acid construct.
Alternatively, if plants, plant portions, or plant cells are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the plant by co-infiltrating a mixture of Agrobacterium cells with the plant, plant portion, or plant cell, each Agrobacterium cell may comprise one or more constructs to be introduced within the plant. In order to vary the relative expression levels within the plant, plant portion or plant cell, of a nucleotide sequence of interest within a construct, during the step of infiltration, the concentration of the various Agrobacteria populations comprising the desired constructs may be varied.
The modified viral surface protein or VLP comprising modified viral surface protein as described herewith, may be used to elicit an immune response in a subject.
An “immune response” generally refers to a response of the adaptive immune system of a subject. The adaptive immune system generally comprises a humoral response, and a cell-mediated response. The humoral response is the aspect of immunity that is mediated by secreted antibodies, produced in the cells of the B lymphocyte lineage (B cell). Secreted antibodies bind to antigens on the surfaces of invading microbes (such as viruses or bacteria), which flags them for destruction. Humoral immunity is used generally to refer to antibody production and the processes that accompany it, as well as the effector functions of antibodies, including Th2 cell activation and cytokine production, memory cell generation, opsonin promotion of phagocytosis, pathogen elimination and the like. The terms “modulate” or “modulation” or the like refer to an increase or decrease in a particular response or parameter, as determined by any of several assays generally known or used, some of which are exemplified herein.
A cell-mediated response is an immune response that does not involve antibodies but rather involves the activation of macrophages, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen. Cell-mediated immunity is used generally to refer to some Th cell activation, Tc cell activation and T-cell mediated responses. Cell mediated immunity may be of particular importance in responding to viral infections.
For example, the induction of antigen specific CD8 positive T lymphocytes may be measured using an ELISPOT assay; stimulation of CD4 positive T-lymphocytes may be measured using a proliferation assay. Anti-Coronavirus antibody titers may be quantified using an ELISA assay; isotypes of antigen-specific or cross-reactive antibodies may also be measured using anti-isotype antibodies (e.g. anti-IgG, IgA, IgE or IgM). Methods and techniques for performing such assays are well-known in the art.
Cytokine presence or levels may also be quantified. For example a T-helper cell response (Th1/Th2) will be characterized by the measurement of IFN-γ and TL-4 secreting cells using by ELISA (e.g. BD Biosciences OptEIA kits). Peripheral blood mononuclear cells (PBMC) or splenocytes obtained from a subject may be cultured, and the supernatant analyzed. T lymphocytes may also be quantified by fluorescence-activated cell sorting (FACS), using marker specific fluorescent labels and methods as are known in the art.
A microneutralization assay may also be conducted to characterize an immune response in a subject, see for example the methods of Rowe et al., 1973. Virus neutralization titers may be quantified in a number of ways, including: enumeration of lysis plaques (plaque assay) following crystal violent fixation/coloration of cells; microscopic observation of cell lysis in in vitro culture; and 2) ELISA and spectrophotometric detection of Coronavirus.
The term “epitope” or “epitopes”, as used herein, refers to a structural part of an antigen to which an antibody specifically binds.
A method of producing an antibody or antibody fragment is provided, the method comprises administering the modified viral structural protein, a trimer or trimeric modified viral structural protein or VLP comprising the modified viral structural protein as described herewith to a subject, or a host animal, thereby producing the antibody or the antibody fragment. Antibodies or the antibody fragments produced by the method are also provided.
The present disclosure therefore also provides the use of a viral structural protein or VLP comprising the modified viral structural protein, as described herein, for inducing immunity to a Coronavirus infection in a subject. Also disclosed herein is an antibody or antibody fragment, prepared by administering the modified viral structural protein or VLP comprising the modified viral structural protein, to a subject or a host animal.
Further provided is a composition comprising an effective dose of modified viral structural protein or VLP comprising the modified viral structural protein, as described herein, and a pharmaceutically acceptable carrier, adjuvant, vehicle, or excipient, for inducing an immune response in a subject. Also provided is a vaccine for inducing an immune response again Coronavirus in a subject, wherein the vaccine comprises an effective dose of the modified viral structural protein or VLP comprising the modified viral structural protein.
Further provided is a composition that may comprise a mixture of VLPs provided that at least one of the VLPs within the composition comprises modified coronavirus S protein as described herein. For example, each coronavirus S protein including one or more than one modified S protein, from each of one or more than one Coronavirus family, sub-group, type, subtype, lineage or strain may be expressed and the corresponding VLPs purified. Virus like particles obtained from two or more than two Coronavirus families, sub-groups, types, subtypes, lineages or strains (for example, two, three, four, five, six, seven, eight, nine, 10 or more Coronavirus families, sub-groups, types, subtypes, lineages or strains) may be combined as desired to produce a mixture of VLPs, provided that one or more than one VLP in the mixture of VLPs comprises a modified S protein as described herein. The VLPs may be combined or produced in a desired ratio, for example about equivalent ratios, or may be combined in such a manner that one Coronavirus family, sub-group, type, subtype, lineage or strain comprises the majority of the VLPs in the composition. It is further provided a composition of VLPs comprising one or more than one modified S protein with ectodomain and/or TM or portion of a TM derived from each of one or more than one Coronavirus family, sub-group, type, subtype, lineage or strain, such that a mixture of different modified S protein as provided for in this disclosure may be present in any individual VLP of the composition.
The composition or vaccine may comprise VLP comprising the modified viral structural protein, such as the modified S protein from one type of Coronavirus family, sub-group, type, subtype, lineage or strain, or the composition or vaccine may comprise multiple VLP types, wherein each VLP type comprises modified S protein, wherein the modified S proteins in the same VLP are derived from one type of Coronavirus family, sub-group, type, subtype, lineage or strain i.e. the composition or vaccine may comprise a mixture of different Coronavirus VLP, wherein each VLP may comprise a modified S protein from the same Coronavirus family, sub-group, type, subtype, lineage or strain. For example the composition or vaccine may comprise a first VLP comprising a first modified S protein from a first Coronavirus family, sub-group, type, subtype, lineage or strain and a second VLP comprising a second modified S protein from a second Coronavirus family, sub-group, type, subtype, lineage or strain. Furthermore the composition may also comprise a third VLP comprising a third modified S protein from a third Coronavirus family, sub-group, type, subtype, lineage or strain and/or the composition or vaccine may comprise a fourth VLP comprising a fourth modified S protein from a fourth Coronavirus family, sub-group, type, subtype, lineage or strain. Accordingly, the description also provides compositions or vaccines that are monovalent (univalent), or multivalent (polyvalent). The monovalent composition or vaccine may immunize a subject against a single type of Coronavirus strain, whereas the multivalent composition or vaccine may immunize a subject against more than one Coronavirus strain. For example, the composition or vaccine may be a bivalent composition or vaccine, which upon administration, may immunize a subject against two different types of Coronavirus families, sub-groups, types, subtypes, lineages or strains. Furthermore, the composition or vaccine may be a trivalent composition, or the vaccine or composition may be a tetravalent or quadrivalent composition or vaccine.
Furthermore, the multivalent composition may comprise VLP comprising one or more than one modified S proteins with different HA cytoplasmic tails. For example, the multivalent composition may comprise a VLP or plurality of VLPs comprising two or more modified S proteins, each comprising a S protein ectodomain, a S protein transmembrane domain, and a cytoplasmic tail derived from HA from an influenza H1, H3, H5, H6, H7, H9 or B strain. Non-limiting examples of influenza strains are for example H1 California/7/2009, H3 A/Minnesota/41/2019, H5 A/Indonesia/5/05, H6 A/Teal/Hong Kong/W312/97, H7 A/Guangdong/17SF003/2016, H9 A/Hong Kong/1073/99 or B/Washington/02/2019.
The multivalent composition or vaccine with multiple type VLPs may further comprise a pharmaceutically acceptable carrier, adjuvant, vehicle, or excipient, for inducing an immune response in a subject.
Adjuvant systems to enhance a subject's immune response to a vaccine antigen are well known and may be used in conjunction with the vaccine or pharmaceutical composition as described herewith. There are many types of adjuvants that may be used. Common adjuvants for human use are aluminum hydroxide, aluminum phosphate and calcium phosphate. There are also a number of adjuvants based on oil emulsions (oil in water or water in oil emulsions such as Freund's incomplete adjuvant (FIA), Montanide™, Adjuvant 65, and Lipovant™), products from bacterial (or their synthetic derivatives), endotoxins, fatty acids, paraffinic, or vegetable oils, cholesterols, and aliphatic amines or natural organic compounds such for example squalene. Non-limiting adjuvants that might be used include for example oil-in water emulsions of squalene oil (for example MF-59 or AS03), adjuvant composed of the synthetic TLR4 agonist glucopyranosyl lipid A (GLA) integrated into stable emulsion (SE) (GLA-SE) or CpG 1018 a toll-like receptor (TLR9) agonist adjuvant.
Therefore the vaccine or pharmaceutical composition may comprise one or more than one adjuvant. For example the vaccine or pharmaceutical composition may comprise aluminum hydroxide, aluminum phosphate, calcium phosphate, an oil in water or water in oil emulsions, an emulsion comprising squalene (for example MF-59 or AS03), an emulsion comprising GLA-SE, or CpG 1018 adjuvant.
The pharmaceutical compositions, vaccines or formulations of the present description may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or tableting processes.
The pharmaceutical compositions, vaccines or formulations may be produced by mixing or premixing of any constituent components before administration, for example by manual or mechanically-aided mixing of two or more vaccine suspensions, pharmaceutically acceptable carriers, adjuvants, vehicles, or excipients as a step performed before the final formulation, vaccine, or pharmaceutical composition is administered.
The pharmaceutical compositions, vaccines or formulations may be administered to a subject orally, intradermally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Suitable excipients are, for example, water, saline, dextrose, mannitol, lactose, lecithin, albumin, sodium glutamate, cysteine hydrochloride, and the like. In addition, if desired, the injectable pharmaceutical compositions may contain minor amounts of nontoxic auxiliary substances, such as wetting agents, pH buffering agents, and the like. Physiologically compatible buffers include, but are not limited to, Hanks's solution, Ringer's solution, or physiological saline buffer. If desired, absorption enhancing preparations (for example, liposomes), may be utilized.
The composition or vaccine may be administered to a subject once (single dose). Furthermore, the vaccine or composition may be administered to a subject multiple times (multi-dose). Therefore the composition, formulation, or vaccine may be administered to a subject in a single dose to illicit an immune response or the composition, formulation, or vaccine may be administered multiple time (multi dosages). For example a dose of the composition or vaccine may be administered 2, 3, 4 or 5 times. Accordingly, the composition or vaccine may be administered to a subject in an initial dose and one or more than one doses may subsequently be administered to the subject. Administration of the doses may be separated in time from each other. For example after the administration of an initial dose, one or more than one subsequent dose may be administered 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 1 month, 2 months, 3 months, 4 months, 5 months or 6 months or any time in between from the administration of the initial dose. Furthermore, the composition or vaccine may be administered annually. For example the composition or vaccine may be administered as a seasonal vaccine.
The disclosure further provides the following sequences.
The present invention will be further illustrated in the following examples.
The SARS-CoV-2 S protein constructs were produced using techniques well known within the art. For example SARS-COV-2 Spike Protein with wtTMCT (Constructs number 8586, 8589, 8591, see
SARS-COV-2 Spike Protein with wtTMCT (Constructs Number 8586, 8589, 8591)
A sequence encoding mature SARS-CoV-2 Spike (S) protein 2 (SEQ ID NO: 23) with GSAS+K971P+V972P ectodomain mutations and with native transmembrane domain and native cytoplasmic tail (wtTMCT) from SARS-CoV-2, fused to alfalfa PDI secretion signal peptide (PDISP) was cloned into three different expression systems using the following PCR-based method. A fragment containing the SARS-COV-2 Spike protein (wtTMCT) coding sequence was amplified using primers IF(PDI)-CoV(opt2).c (SEQ ID NO: 24) and IF(AVB)-CoV(opt2).r (SEQ ID NO: 25), using PDISP-SARS-COV-2 Spike Protein with wtTMCT gene sequence (SEQ ID NO: 22) as template. The PCR product was cloned into three different expression systems using In-Fusion cloning system (Clontech, Mountain View, CA).
For the first expression system, construct number 8501 (
For the second expression system, construct number 8500 (
For the third expression system, construct number 8716 (
SARS-COV-2 Spike Protein with H5iTMCT (Constructs Number 8592, 8595, 8597)
A sequence encoding mature Spike (S) protein from SARS-CoV-2 (SEQ ID NO: 27) with GSAS+K971P+V972P ectodomain mutations, and with transmembrane domain and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iTMCT), was fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same three expression systems described above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). Construct number 8592 (
SARS-COV-2 Spike Protein with H5iCT (Constructs Number 8610, 8611, 8671)
A sequence encoding mature Spike (S) protein from SARS-CoV-2 (SEQ ID NO: 30) with GSAS+K971P+V972P ectodomain mutations, and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT), was fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same three expression systems as described above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). Construct number 8610 (
SARS-COV-2 Spike Protein with Alternative TM CT Fusion Sequences (Constructs Number 8980, 8981, 8982, 8983)
A sequence encoding mature Spike (S) protein from SARS-CoV-2 with GSAS+K971P+V972P ectodomain mutations, and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT), as depicted in SEQ ID NO: 19, was fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 8671, yielding construct 8980 (
SARS-COV-2 Spike Protein with CT from Other HA Strains (Constructs Number 7390, 7391, 7392, 7393, 7394, and 7395)
A sequence encoding mature Spike (S) protein from SARS-CoV-2 with GSAS+K971P+V972P ectodomain mutations, and cytoplasmic tail from H1 A/California/7/2009 HA (H1CT), was fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 8671 above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). The resulting construct 7390 thus encodes a modified S protein comprising a H1 A/California/7/2009 HA cytoplasmic tail (H1CT) (
SARS-COV-2 Spike Protein with Substitutions (Constructs Numbers 8933, 8960, 8947)
Modified SARS-CoV-2 S protein constructs comprising combinations of mutations in the S protein, such as R667G, R668S, R670S, F802P, A877P, A884P, A927P, K971P, V972P, and L923F were produced using techniques well known within the art and basically as described above. The constructs have the following substitutions: Construct 8933: R667G, R668S, R670S, K971P, V972P and L923F (“GSAS-2P-923”); construct 8960: R667G, R668S, R670S, F802P, A927P, K971P, V972P and L923F (“GSAS-4P-923”) and construct 8947: R667G, R668S, R670S, F802P, A877P, A884P, A927P, K971P, V972P and L923F (“GSAS-6P-923”).
SARS-COV-1 Spike Protein with wtTMCT and Modified TMCT (Constructs Number 9231, 9232, 9233, 9234, 9235)
A sequence encoding mature SARS-CoV-1 Spike (S) protein (SEQ ID NO: 88) with R654A+K955P+V956P ectodomain mutations and with native transmembrane domain and native cytoplasmic tail (wtTMCT) from SARS-CoV-1, fused to alfalfa PDI secretion signal peptide (PDISP) was cloned into the following expression system by a PCR-based method. A fragment containing the PDISP-SARS-COV-1 Spike protein (wtTMCT) coding sequence was amplified using primers IF(nbHEL40)-PDI.c (SEQ ID NO: 86) and IF(AvB+wtCT).r (SEQ ID NO: 87), using PDISP-SARS-COV-1 Spike Protein with wtTMCT gene sequence (SEQ ID NO: 88) as template. The PCR product was cloned into the following expression system using In-Fusion cloning system (Clontech, Mountain View, CA).
Construct number 7147 (
A sequence encoding mature Spike (S) protein from SARS-CoV-1 with R654A+K955P+V956P ectodomain mutations, and either i) transmembrane domain and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iTMCT), ii) cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT and variation H5iCT(V4)), or iii) cytoplasmic tail from H1 A/California/7/2009 HA (H1cCT), were fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 9231 above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). The resulting constructs 9232, 9233, 9234, 9235 thus encode a modified S protein comprising a H5 A/Indonesia/5/05 TMCT (H5iTMCT) (
MERS-CoV Spike Protein with wtTMCT and Modified TMCT (Constructs Number 9246, 9247, 9249, 9250, 9251)
A sequence encoding mature MERS-CoV Spike (S) protein (SEQ ID NO: 101) with R730A+R733G+V1043P+L1044P ectodomain mutations and with native transmembrane domain and native cytoplasmic tail (wtTMCT) from MERS-CoV, fused to alfalfa PDI secretion signal peptide (PDISP) was cloned into the following expression system by a PCR-based method. A fragment containing the PDISP-MERS-COV Spike protein (wtTMCT) coding sequence was amplified using primers IF(nbHEL40)-PDI.c (SEQ ID NO: 86) and IF(AvB+wtCT-MERS).r (SEQ ID NO: 98), using PDISP-MERS-COV Spike Protein with wtTMCT gene sequence (SEQ ID NO: 101) as template. The PCR product was cloned into the following expression system using In-Fusion cloning system (Clontech, Mountain View, CA).
Construct number 7147 (
A sequence encoding mature Spike (S) protein from MERS-CoV with R730A+R733G+V1043P+L1044P ectodomain mutations, and either i) transmembrane domain and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iTMCT), ii) cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT and variation H5iCT(V4)), or iii) cytoplasmic tail from H1 A/California/7/2009 HA (H1cCT), were fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 9246 above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). The resulting constructs 9247, 9249, 9250, 9251 thus encode a modified MERS-COV S protein comprising a H5 A/Indonesia/5/05 TMCT (H5iTMCT) (
OC43-CoV Spike Protein with wtTMCT and Modified TMCT (Constructs Number 9269, 9270, 9272, 9273 and 9274)
A sequence encoding mature OC43-CoV Spike (S) protein (SEQ ID NO: 137) with R761G+R762G+R764G+R765S+A1077P+L1078P ectodomain mutations and with native transmembrane domain and native cytoplasmic tail (wtTMCT) from OC43-CoV, fused to alfalfa PDI secretion signal peptide (PDISP) was cloned into the following expression system by a PCR-based method. A fragment containing the PDISP-OC43-COV Spike protein (wtTMCT) coding sequence was amplified using primers IF(nbHEL40)-PDI.c (SEQ ID NO: 86) and IF(AvB+wtCT-OC43).r (SEQ ID NO: 136), using PDISP-OC43-COV Spike Protein with wtTMCT gene sequence (SEQ ID NO: 137) as template. The PCR product was cloned into the following expression system using In-Fusion cloning system (Clontech, Mountain View, CA).
Construct number 7147 (
A sequence encoding mature Spike (S) protein from OC43-CoV with R761G+R762G+R764G+R765S+A1077P+L1078P ectodomain mutations, and either i) transmembrane domain and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iTMCT), ii) cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT and variation H5iCT(V4)), or iii) cytoplasmic tail from H1 A/California/7/2009 HA (H1cCT), were fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 9269 above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). The resulting constructs 9270, 9272, 9273 and 9274 thus encode a modified OC43-COV S protein comprising a H5 A/Indonesia/5/05 TMCT (H5iTMCT) (
229E-CoV Spike Protein with wtTMCT and Modified TMCT (Constructs Number 9310, 9311, 9312, 9313 and 9314)
A sequence encoding mature 229E-CoV Spike (S) protein (SEQ ID NO: 148) with R567A+T871P+I872P ectodomain mutations and with native transmembrane domain and native cytoplasmic tail (wtTMCT) from 229E-CoV, fused to alfalfa PDI secretion signal peptide (PDISP) was cloned into the following expression system by a PCR-based method. A fragment containing the PDISP-229E-COV Spike protein (wtTMCT) coding sequence was amplified using primers IF(nbHEL40)-PDI.c (SEQ ID NO: 86) and IF(CoV229EwtCT).r (SEQ ID NO: 147), using PDISP-OC43-COV Spike Protein with wtTMCT gene sequence (SEQ ID NO: 148) as template. The PCR product was cloned into the following expression system using In-Fusion cloning system (Clontech, Mountain View, CA).
Construct number 7147 (
A sequence encoding mature Spike (S) protein from 229E-CoV with R567A+T871P+I872P ectodomain mutations, and either i) transmembrane domain and cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iTMCT), ii) cytoplasmic tail from H5 A/Indonesia/5/05 HA (H5iCT and variation H5iCT(V4)), or iii) cytoplasmic tail from H1 A/California/7/2009 HA (H1cCT), were fused to alfalfa PDI secretion signal peptide (PDISP) and cloned into the same expression system as described for construct 9310 above by a similar PCR-based method (see table 5 for primers and Example 3 for sequences used). The resulting constructs 9311, 9312, 9313 and 9314 thus encode a modified 229E-COV S protein comprising a H5 A/Indonesia/5/05 TMCT (H5iTMCT) (
Agrobacterium tumefaciens Transfection
Agrobacterium tumefaciens strain AGL1 was transfected by electroporation with the SARS-CoV-2 modified S protein expression vectors using the methods described by D'Aoust et al., 2008 (Plant Biotech. J 6:930-40). Transfected Agrobacterium were grown in YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (MES), 20 μM acetosyringone, 50 μg/ml kanamycin and 25 μg/ml of carbenicillin pH5.6 to an OD600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl2 and 10 mM MES pH 5.6).
N. benthamiana plants were grown from seeds in flats filled with a commercial peat moss substrate. The plants were allowed to grow in the greenhouse under a 16/8 photoperiod and a temperature regime of 25° C. day/20° C. night. Three weeks after seeding, individual plantlets were picked out, transplanted in pots and left to grow in the greenhouse for three additional weeks under the same environmental conditions.
Agrobacteria transfected with each expression vector were grown in a YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (MES), 20 μM acetosyringone, 50 μg/ml kanamycin and 25 μg/ml of carbenicillin pH 5.6 until they reached an OD600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl2 and 10 mM MES pH 5.6) and stored overnight at 4° C. On the day of infiltration, culture batches were diluted in 2.5 culture volumes and allowed to warm before use. Whole plants of N. benthamiana were placed upside down in the bacterial suspension in an air-tight stainless steel tank under a vacuum of 20-40 Torr for 2-min. Plants were returned to the greenhouse for a 6 or 9 day incubation period until harvest.
Following incubation, the aerial part of plants was harvested, frozen at −80° C. and crushed into pieces. Total soluble proteins were extracted by mechanically homogenizing (Polytron) each sample of frozen-crushed plant material in two volumes of cold 50 mM Tris buffer at pH 8.0+500 mM NaCl, 0.4 μg/ml metabisulfite and 1 mM phenylmethanesulfonyl fluoride. After homogenization, the slurries were centrifuged at 10,000 g for 10 min at 4° C. and these clarified crude extracts (supernatant) kept for analysis.
The total protein content of clarified crude extracts was determined by the Bradford assay (Bio-Rad, Hercules, California) using bovine serum albumin as the reference standard. Proteins were separated by SDS-PAGE under reducing conditions using Criterion™ TGX Stain-Free™ precast gels (Bio-Rad Laboratories, Hercules, CA). Proteins were visualized by staining the gels with Coomassie Brilliant Blue. Alternatively, proteins were visualized with Gel Doc™ EZ imaging system (Bio-Rad Laboratories, Hercules, CA) and electrotransferred onto polyvinylene difluoride (PVDF) membranes (Roche Diagnostics Corporation, Indianapolis, Indiana) for immunodetection. Prior to immunoblotting, the membranes were blocked with 5% skim milk and 0.1% Tween-20 in Tris-buffered saline (TBS-T) for 16-18 h at 4° C.
For VLP purification, proteins were extracted from frozen biomass by mechanical extraction using a blender with two volumes of extraction buffer (50 mM Tris buffer at pH 7.0+500 mM NaCl) and pH was lowered to 6.1 using 0.5M citric acid. The slurry was filtered through a large pore nylon filter to remove large debris and centrifuged 5000 g for 5 min at 4° C. The supernatant was collected and centrifuged again at 5000 g for 30 min (4° C.) to remove additional debris and passed through clarification filters. The supernatant was then loaded on a discontinuous iodixanol density gradient. Analytical density gradient centrifugation was performed as follows: 38 mL tubes containing discontinuous iodixanol density gradient in Tris buffer (3 ml at 35%, 3 ml at 30%, 3 ml at 25%, 3 ml at 15% and 5 ml at 10% of iodixanol) were prepared and overlaid with 22 ml of the extracts containing the virus-like particles. The gradients were centrifuged at 120 000 g for 2 hours (4° C.). After centrifugation, 1 mL fractions were collected from the bottom to the top and fractions were analyzed by SDS-PAGE combined with protein staining or Western blot. Fractions 6 to 9 were pooled and buffer-exchanged using Amicon centrifugation device. Protein content is determined by Bradford assay.
Immunoblotting was performed with a first incubation with a primary mAb, (anti-S1, Sino Biological, cat #40150-R007 or anti-S2, Novus biological, cat #NB100-56578) diluted in 2% skim milk in TBS-Tween 20 0.1%. Peroxydase-conjugated goat anti-rabbit (Jackson Immunoresearch, cat #115-035-144) was used as secondary antibody for chemiluminescence detection in 2% skim milk in TBS-Tween 20 0.1% Immunoreactive complexes were detected by chemiluminescence using luminol as the substrate (Roche Diagnostics Corporation). Horseradish peroxidase-enzyme conjugation of human IgG antibody was carried out by using the EZ-Link Plus® Activated Peroxidase conjugation kit (Pierce, Rockford, Ill.).
In planta yields were assessed on clarified crude extracts and analyzed using a capillary-based electrophoresis method (Protein Simple, BioTechne) technology and a WES analysis system. In brief, soluble proteins from crude extracts were separated by molecular weight in a capillary and fixed to the matrix. A standard curve using purified VLPs is used to determine S protein quantity and Anti-S2 antibody (Novus biological, cat #NB100-56578) is used for detection according to the manufacturer instructions. Yields are then normalized using a comparator construct which is set to 1.
The primary antibody for detection of SARS-CoV S protein was SARS-CoV Spike S1 subunit antibody from Sino Biologicals, 40150-MM08 (1/5000) and the secondary antibody used for detection was Goat anti-Mouse, JIR, 115-035-146 (1/10000). The primary antibody for detection of MERS CoV S protein was MERS-CoV spike protein S1 antibody (N-terminal) from Sino Biological, (100208-RP02, 1/5000). The secondary antibody used for detection was Goat anti-Mouse from JIR (115-035-144, 1/10000). The primary antibody used for detection was anti-coronavirus OC43 spike protein from Antibodies-online (ABIN2754654, 1/1000. The secondary antibody used for detection was Goat anti-Rabbit from JIR (111-035-144, 1/10000).
To determine whether expressed S protein assembled into VLPs, transmission electron microscopy (TEM) of immuno-trapped particles was performed on purified VLPs. Glow discharged carbon/copper grids (10 s, 0.3 mbar) were placed on 20 μL of purified VLPs (100 μg/mL) for 5 min and then washed 4 times with sterile distilled water. The grids were floated on 20 μL of 2% uranyl acetate for 1 min, excess solution is then removed by touching a moist filter paper and allowed to dry for 24 h on a filter paper before viewing under a TEM (Tecnai Microscope).
The following sequences were use in the examples described above.
All citations are hereby incorporated by reference.
The present invention has been described with regard to one or more embodiments. However, it will be apparent to persons skilled in the art that a number of variations and modifications can be made without departing from the scope of the invention as defined in the claims.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2021/051201 | 8/31/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63073327 | Sep 2020 | US | |
| 63211716 | Jun 2021 | US |
