SYNTHETIC MODIFIED VACCINIA ANKARA (sMVA) BASED CORONAVIRUS VACCINES

Abstract

Disclosed are synthetic MVA-based vaccines for preventing or treating infections caused by a coronavirus or variants thereof.

Description

SEQUENCE LISTING

This application contains an ST.26 compliant Sequence Listing, which is submitted concurrently in xml format via Patent Center and is hereby incorporated by reference in its entirety. The .xml copy, created on Apr. 14, 2023 is named 0544358219US02.xml and is 585,000 bytes in size.

BACKGROUND

Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China at the end of 2019, SARS-CoV-2 has spread rapidly worldwide, causing a global pandemic with millions of fatalities^1,2. Several SARS-CoV-2 vaccines were developed in response to the COVID-19 pandemic with unprecedented pace and showed 62-95% efficacy in Phase 3 clinical trials, leading to their emergency use authorization (EUA) in many countries by the end of 2020/beginning of 2021^3-8. This includes vaccines based on mRNA, adenovirus vectors, and nanoparticles that utilize different antigenic forms of the spike (S) protein to induce protective immunity against SARS-CoV-2 primarily through the function of neutralizing antibodies (NAb)^9-12. While the Phase 3 efficacy results provide hope for a rapid end of the COVID-19 pandemic, waning antibody responses and evasion of NAb by emerging variants of concern (VOC) pose imminent challenges for durable vaccine protection and herd immunity^13-19. Alternative vaccines based on different platforms or modified epitope or antigen design could therefore contribute to establish long-term and cross-reactive immunity against SARS-CoV-2 and its emerging VOC. Accordingly, this disclosure provides vaccines using a synthetic MVA platform to satisfy an urgent need in the field.

BRIEF DESCRIPTION OF THE DRAWINGS

This application contains at least one drawing executed in color. Copies of this application with color drawing(s) will be provided by the Office upon request and payment of the necessary fees.

FIGS. 1a-1h show COH04S1 immunogenicity in Syrian hamsters. FIG. 1a shows COH04S1 construct. COH04S1 is a sMVA vaccine vector that contains full-length SARS-CoV-2 N and S antigen and mH5 promoter sequences inserted into the Deletion 2 (Del2) and 3 (Del3) sites as indicated. ITR=inverted terminal repeat. FIG. 1b shows study design. Hamsters were immunized twice with COH04S1 by IM (COH04S1-IM) or IN (COH04S1-IN) route as indicated (black arrows). Unimmunized animals and hamsters immunized with empty sMVA vector by IM (sMVA-IM) or IN (sMVA-IN) route were used as controls. Blood samples were collected at 0, 28, and 42 day (red arrows). Hamsters were challenged IN at day 42 and body weight changes were recorded daily for 10 days. At endpoint, nasal wash, turbinates and lung tissue were collected for downstream analyses. FIGS. 1c and 1d show IgG endpoint titers. S, RBD, and N-specific binding antibody titers were measured in serum samples of vaccine and control groups at day 28 (d28) post prime and at day 42 (d42) post booster immunization via ELISA. Data are presented as geometric mean values+geometric SD. Dotted lines indicate lower limit of detection. Two-way ANOVA with Tukey's multiple comparison test was used. FIG. 1e shows IgG2-3/IgG1 ratios. S, RBD, and N-specific IgG2-3 and IgG1 endpoint titers were measured at day 42 (d42) in serum samples of vaccine and control groups and used to assess IgG2-3/IgG1 ratios. An IgG2-3/IgG1 ratio>1 is indicative of a Th1-biased response. Geometric means are indicated with a line. FIGS. 1f and 1g show NAb titers. NAb titers were measured in serum samples of vaccine and control groups post-first (d28) and post-second (d42) immunization via PRNT assay against SARS-CoV-2 infectious virus. Data are presented as geometric mean values+SD. Dotted lines indicate lower limit of detection. Values below the limit of detection (PRNT=20) are indicated as 10. One-way ANOVA with Holm-Sidak's multiple comparison test was used. FIG. 1h shows VOC-specific NAb titers. NAb were measured in pooled serum samples of vaccine and control groups collected at the time of challenge (d42) using pseudoviruses (pv) with S D614G mutation or S sequences based on several VOC, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). Titers are expressed as NT50. Fold NT50 reduction in comparison to D614G PV are shown. *0.05<p<0.01, **0.01<p<0.001, ***0.001<p<0.0001, ****p<0.0001.

FIGS. 2a-2n show COH04S1 immunogenicity in Syrian hamsters. FIGS. 2a-2f show binding antibody titers. Shown are the binding curves of S, RBD, and N antigen-specific binding antibody titers measured at day 28 (d28) or day 42 (d42) after the first and second immunization in serum samples of COH04S1-IM and COH04S1-IN-immunized hamsters and unimmunized and sMVA vector control animals. Two-way ANOVA with Tukey's multiple comparison test was used. FIGS. 2g-2i show IgG2-3/IgG1 antibody titers. Shown are the IgG endpoint titers of S, RBD, and N antigen-specific IgG2-3 and IgG1 binding antibodies measured in serum samples of day 42 (d42), and ratios are shown. Geometric means are indicated with a line. Dotted lines indicate lower limit of detection. FIGS. 2j-2n show VOC-specific NAb titers. Shown are NA titers measured at the indicated time points by PV variants with D614G mutation or based on several SARS-CoV-2 VOC in vaccine and control groups.

FIGS. 3a-3h show COH04S1-mediated vaccine protection in hamsters following sub-lethal SARS-CoV-2 challenge. FIG. 3a shows body weight change. Body weight of COH04S1-IM and COH04S1-IN-immunized animals as well as unimmunized and sMVA-IM and sMVA-IN vector control animals was measured daily for 10 days post-challenge. Weight loss is reported as mean±SD. Two-way ANOVA followed by Tukey's multiple comparison test was used to compare group mean values at each timepoint. FIG. 3b shows maximal weight loss. Percentage of maximal weight loss is shown in single animals of vaccine and control groups. Lines and bars represent median values and 95% Cl, respectively. Dotted line represents the maximum weight loss allowed before euthanasia. Peaks of weight loss in each group were compared using one-way ANOVA followed by Tukey's multiple comparison test. FIGS. 3c and 3d show Lung viral loads. SARS-CoV-2 genomic RNA (gRNA) and sub-genomic RNA (sgRNA) copies were quantified in lung tissue of vaccine and control groups at day 10 post-challenge by qPCR. Bars show RNA copies geometric mean±geometric SD. Dotted lines represent lower limit of detection. Kruskal-Wallis test followed by Dunn's multiple comparison test was used. FIGS. 3e-3h show histopathological findings. Hematoxylin/eosin-stained lung sections of COH04S1-immunized hamsters and control animals at day 10 post challenge were evaluated by a board-certified pathologist and microscopic findings were graded based on severity on a scale from 1 to 5 (Table 2). FIG. 3e shows the cumulative pathology score of all histopathologic findings in each group. FIG. 3f shows grading of bronchioalveolar hyperplasia disease severity in each group. One-way ANOVA followed by Holm-Sidak's multiple comparison test was used. FIG. 3g shows the severity of lung inflammatory microscopic findings based on 1-to-5 scaling of four inflammation types as indicated. Bars represent mean values±SD. One-way ANOVA followed by Tukey's multiple comparison test was used. In FIGS. 3b-3f *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0.0001. FIG. 3h shows representative images of histopathological findings in lung sections of COH04S1-immunized animals and control animals. Black arrows indicate moderate and mild bronchioalveolar hyperplasia in lung sections of sMVA-IM and sMVA-IN control animals and COH04S1-IN animals. Black arrows in lung sections of unimmunized control animals indicate hyperplastic alveolar cells. 10× magnification.

FIGS. 4a-4d show COH04S1-mediated protection of hamsters following sub-lethal SARS-CoV-2 challenge. Shown are SARS-CoV-2 genomic RNA (gRNA) and sub-genomic RNA (sgRNA) copies quantified by qPCR in nasal wash and turbinates of COH04S1-IM and COH04S1-IN-immunized hamsters and unimmunized and sMVA control animals at day 10 post-challenge. Bars show RNA copies geometric mean±geometric SD. Dotted lines represent lower limit of detection of the assay. Kruskal-Wallis test followed by Dunn's multiple comparison test was used. *=0.05<p<0.01, **=0.01<p<0.001.

FIGS. 5a-5b show correlative analysis of immunological and virological parameters in COH04S1-immunized hamsters challenged with SARS-CoV-2. A Spearman correlation analyses was performed between the indicated pre-challenge immune responses and post-challenge virological assessments of COH04S1-IM and COH04S1-IN-immunized hamsters and unimmunized and sMVA control animals. FIG. 5a show that Spearman correlation coefficients were calculated and plotted as a matrix. FIG. 5b show that two-tailed p values were calculated and indicated as: *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001. ns=not significant.

FIGS. 6a-6i show COH04S1 vaccine immunogenicity in NHP. FIG. 6a shows study design. African green monkey NHP were immunized with COH04S1 vaccine using two-dose (COH04S1-2D; N=6)) or single-dose (COH04S1-1D; N=6) immunization regimen as indicated. Mock-immunized NHP and NHP immunized with empty sMVA vector using the same dose immunization regimen were included as controls. Six weeks after immunization, NHP were IN/IT challenged with SARS-CoV-2 USA-WA1/2020 reference strain. Bronchoalveolar lavages (BAL) and oral and nasal swab samples for viral load analysis were collected at multiple time points post-challenge. A subset of animals in each group were necropsied at day 7 and 21 post-challenge for viral load and histopathology analysis. FIGS. 6b-6d show binding antibody titers. S, RBD, and N antigen-specific binding antibody titers were measured at the indicated time points in serum samples of COH04S1-2D and COH04S1-1D-immunized NHP via ELISA. Data is presented as geometric mean values±geometric SD. Two-way ANOVA followed by Sidak's multiple comparison test was used. FIG. 6e shows VOC-specific antibody titers. S-specific binding antibody titers were measured at day 62 by ELISA using S antigens based on the Wuhan-Hu-1 reference strain or several SARS-CoV-2 VOC, including Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). Endpoint titers are presented as geometric mean values±geometric SD. Two-way ANOVA with Sidak's multiple comparison test was used for statistical analysis. FIG. 6f shows BAL antibody titers. S, RBD, and N antigen-specific binding antibody titers were measured by ELISA at day 42 in BAL samples of COH04S1-IM and COH04S1-IN vaccine group. Endpoint titers are presented as geometric mean values±geometric SD. Two-way ANOVA with Sidak's multiple comparison test was used. FIG. 6g shows NAb titers. NAb titers were measured by PRNT assay against SARS-CoV-2 USA-WA1/2020 reference strain in serum samples of immunized NHP. Serum dilutions reducing the plaque number by 50% (ID50) are presented as geometric mean values±geometric SD. Two-way ANOVA followed by Sidak's multiple comparison test was used to compare ID50 values. PRNT-assayed NAb titers measured in serum samples of healthcare workers (N=14) vaccinated two times with Pfizer-BioNTech BNT162b2 mRNA vaccine were included. FIGS. 6h-6i show T cell responses. IFNγ, IL-2, and IL-4-expressing S and N-antigen-specific T cell responses were measured at two weeks post-challenge by ELISPOT. Bars represent mean values, lines represent ±SD. Two-way ANOVA followed by Tukey's multiple comparison test was used. Dotted lines indicate the arbitrary positive threshold of spots/10⁶ cells. *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001.

FIGS. 7a-7j show COH04S1-induced humoral immunity in NHP. FIGS. 7a-7f show binding antibody titers. Shown are S, RBD, and N antigen-specific IgG endpoint titers measured at the indicated time points in COH04S1-2D and COH04S1-1 D-immunized NHP and mock-immunized and sMVA vector control animals. Data are presented as geometric mean values±geometric SD. Two-way ANOVA followed by Sidak's multiple comparison test was used. FIGS. 7g and 7h show BAL binding antibodies. Shown are endpoint titers of IgG binding antibodies to S, RBD, and N measured in bronchoalveolar lavage (BAL) samples in vaccine and control groups at day 42. Endpoint titers are presented as geometric mean values±geometric SD. Two-way ANOVA with Sidak's multiple comparison test was used. FIGS. 7i and 7j show VOC-specific binding antibody titers. Shown are endpoint titers of S-specific IgG binding antibodies measured one week post challenge by ELISA with S antigens based on Wuhan-Hu-1 reference strain or several VOC, including Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). Endpoint titers are presented as geometric mean values±geometric SD. Two-way ANOVA with Sidak's multiple comparison test was used. *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001.

FIGS. 8a-8f show COH04S1-induced T cell responses in NHP. FIGS. 8a-8f show IFNγ, IL-2, and IL-4-expressing S and N-specific T cell responses measured two weeks pre-challenge by Fluorospot assay in COH04S1-2D and COH04S1-1 D-immunized NHP and mock-immunized and sMVA vector control animals. Bars represent mean values, lines represent ±SD. Two-way ANOVA followed by Tukey's multiple comparison test was used. Dotted lines indicate the arbitrary positive threshold of 30 spots/10⁶ cells. *=0.05<p<0.01.

FIGS. 9a-9i show BAL viral loads in COH04S1-immunized NHP following SARS-CoV-2 challenge. SARS-CoV-2 genomic RNA (gRNA; FIGS. 9a-9c) and subgenomic RNA (sgRNA; FIGS. 9d-9f) copies and TCID50 infectious virus titers (FIGS. 9g-9i) were measured at the indicated days post challenge in bronchoalveolar lavages (BAL) of COH04S1-2D and COH04S1-1D-immunized NHP and mock-immunized and sMVA vector control animals. Bars represent geometric means, lines represent ±geometric SD. Dotted lines represent lower limit of detection. Two-way ANOVA followed by Sidak's multiple comparison test was used. FIGS. 9c, 9f, and 9i show viral loads by area under the curve (AUC). Violin plots show values ranges with median values (dashed line) and quartiles (dotted line). AUC=0 was indicated as 1. One-way ANOVA followed by Tukey's multiple comparison test was used. *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001.

FIGS. 10a-10i show nasal swab viral loads in COH04S1-immunized NHP after SARS-CoV-2 challenge. SARS-CoV-2 genomic RNA (gRNA; FIGS. 10a-10c) and subgenomic RNA (sgRNA; FIGS. 10d-10f) copies and TCID50 infectious virus titers (FIGS. 10g-10i) were measured at the indicated days post challenge in nasal swab samples of COH04S1-2D and COH04S1-1D-immunized NHP and mock-immunized and sMVA vector-immunized control animals. Lines represent geometric means+geometric SD. Dotted lines represent lower limit of detection. Two-way ANOVA followed by Sidak's multiple comparison test was used. FIGS. 10c, 10f, and 10i show viral loads by area under the curve (AUC). Violin plots show values ranges with median values (dashed line) and quartiles (dotted line). AUC=C was indicated as 1. One-way ANOVA followed by Tukey's multiple comparison test was used. *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001.

FIGS. 11a-11f show oral swab viral loads in COH04S1-immunized NHP following SARS-CoV-2 challenge. SARS-CoV-2 genomic RNA (gRNA; FIGS. 11a-11c) and subgenomic RNA (sgRNA; FIGS. 11d-11f) copies were measured by qPCR at the indicated days post challenge in oral swab samples of COH04S1-2D and COH04S1-1D-immunized NHP and mock-immunized and sMVA vector control animals. Lines geometric means±geometric SD. Dotted lines represent assay lower limit of detection. Two-way ANOVA followed by Sidak's multiple comparison test was used. FIGS. 11c and 11f show viral loads by area under the curve (AUC). Violin plots show values ranges with median values (dashed line) and quartiles (dotted line). AUC=0 was indicated as 1. One-way ANOVA followed by Tukey's multiple comparison test was used. *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001.

FIGS. 12a-12l show SARS-CoV-2 viral loads in lungs and other organs of COH04S1 immunized NHP following challenge. Given are SARS-CoV-2 genomic RNA (gRNA; FIGS. 12a-12c) and subgenomic RNA (sgRNA; FIGS. 12d-12f) copies measured by qPCR at day 7 and 21 post challenge in the lungs and several other organs of necropsied COH04S1-2D and COH04S1-1D-immunized NHP and mock-immunized and sMVA vector control animals. Four lung samples were analyzed for each necropsied NHP (see Table 3 for necropsy schedule). Dotted lines represent assay lower limit of detection. Kruskal-Wallis test followed by Dunn's multiple comparison test was used. In FIGS. 12e-12l statistical evaluation was not performed because of the limited number of samples in the control groups. *=0.05<p<0.01, **=0.01<p<0.001.

FIGS. 13a-13b show correlative analysis of immunological and virological parameters in COH04S1-immunized NHP challenged with SARS-CoV-2. Spearman correlation analysis was performed between the indicated pre-challenge and post-challenge immune responses and post-challenge virological assessments of COH04S1-2D and COH04S1-1D-immunized NHP and mock-immunized and sMVA control animals. Post-challenge time-points are indicated with “+” before the day number. FIG. 13a shows that Spearman correlation coefficients were calculated and plotted as a matrix. FIG. 13b shows that two-tailed p values were calculated and indicated as: *=0.05<p<0.01, **=0.01<p<0.001, ***=0.001<p<0.0001, ****=p<0.0001. ns=not significant.

FIGS. 14a-141 show SARS-CoV-2-specific post-challenge immune responses in COH04S1-immunized NHP. SARS-CoV-2-specific humoral and cellular immune responses were measured at day 3, 7, 15 and 21 post-challenge in COH04S1-2D and COH04S1-1 D-immunized NHP and mock-immunized and sMVA vector control animals and compared to pre-challenge immunity assessed in these groups. FIGS. 14a-14f show S, RBD and N antigen specific binding antibody titers evaluated by ELISA. FIGS. 14g-14j show NAb titers measured by PRNT assay against SARS-CoV-2 USA-WA1/2020 reference strain. Lines represent geometric means±geometric SD. Dotted lines indicate lower limit of detection (LOD). Values below the LOD are indicated as ½ LOD. FIGS. 14h, 14i, 14k, and 141 show IFNγ-expressing S and N-specific T cell responses measured by Fluorospot assay. Bars represent mean values, lines represent ±SD. Dotted lines indicate the arbitrary positive threshold of 30 spots/10⁶ cells. Two-way ANOVA followed by Tukey's multiple comparison test was used. Time-points with <3 samples/group (d+15 and d+21) were excluded from the statistical evaluation. *0.05<p<0.01, **0.01<p<0.001, ***0.001<p<0.0001, ****p<0.0001.

FIGS. 15a-15d show SARS-CoV-2-specific post-challenge cellular IL-4-specific responses in COH04S1-immunized NHP. SARS-CoV-2-specific cellular immune responses were measured at day 3, 7, 15 and 21 post-challenge in COH04S1-2D and COH04S1-1 D-immunized NHP and mock-immunized and sMVA vector control animals and compared to pre-challenge immunity assessed in these groups. IL-4-expressing S and N-specific T cell responses were measured by Fluorospot assay. Bars represent mean values, lines represent ±SD. Dotted lines indicate the arbitrary positive threshold of 30 spots/10⁶ cells. Two-way ANOVA followed by Tukey's multiple comparison test was used. Time-points with <3 samples/group (d+15 and d+21) were excluded from the statistical evaluation. ****p<0.0001.

DETAILED DESCRIPTION

Disclosed herein is a vaccine composition and the use thereof in preventing or treating a coronavirus infection in a subject. The composition comprises a synthetic MVA vector comprising one or more DNA sequences encoding the Spike (S) protein and the Nucleocapsid (N) protein. In some embodiments, the composition is used for preventing or treating a coronavirus infection caused by a variant of concern such as VOC B.1.1.7 (alpha), VOC B.1.351 (beta), VOC P.1 (gamma), or VOC B.1.617.2 (delta). In some embodiments, the composition is administered to a subject by intramuscular injection. In some embodiments, the composition is administered to a subject by intranasal administration. In some embodiments, the composition is administered to a subject in a single dose. In some embodiments, the composition is administered to a subject in a prime dose followed by a booster dose. In some embodiments, the booster dose is the same as the prime dose. In some embodiments, the booster dose is lower than the prime dose. In some embodiments, one or more additional doses are administered to the subject after administration of the prime and booster doses. In some embodiments, the subject has previously received a different SARS-CoV-2 vaccine before administration of the vaccine composition disclosed herein.

Specifically, a fully synthetic Modified Vaccinia Ankara (sMVA)-based vaccine platform is used to develop COH04S1, a multi-antigenic poxvirus-vectored SARS-CoV-2 vaccine that co-expresses full-length spike (S) and nucleocapsid (N) antigens. As demonstrated in the working examples, protection against SARS-CoV-2 by COH04S1 in animal models was achieved. For example, intramuscular or intranasal vaccination of Syrian hamsters with COH04S1 stimulated robust Th1-biased S- and N-specific humoral immunity and cross-neutralizing antibodies (NAb) and protected against weight loss, lower respiratory tract infection, and lung injury following intranasal SARS-CoV-2 challenge. In addition, one- or two-dose vaccination of African Green Monkeys with COH04S1 induced robust antigen-specific binding antibodies, NAb, and Th1-biased T cells, protected against both upper and lower respiratory tract infection following intranasal/intratracheal SARS-CoV-2 challenge, and triggered potent post-challenge anamnestic antiviral recall responses. These results demonstrate that COH04S1 stimulates protective immunity against SARS-CoV-2 in animal models through different immunization routes and dose regimen, which complements ongoing investigation of this multiantigen sMVA-vectored SARS-CoV-2 vaccine in clinical trials.

While NAb blocking S-mediated entry are considered the principal SARS-CoV-2 immune correlate of protection, humoral and cellular immune responses to multiple antigens have been implicated in the protection against SARS-CoV-2^10,11,20. Besides the S protein, the nucleocapsid (N) protein is well-recognized as a dominant target of antibody and T cell responses in SARS-CoV-2-infected individuals and therefore suggested as an additional immunogen to augment vaccine-mediated protective immunity^21-24. Its high conservation and universal cytoplasmic expression makes the N protein an attractive complementary target antigen to elicit durable and broadly reactive T cells²³. Several recent studies highlight the benefits of N as a vaccine antigen in animal models^25-28.

Multi-antigenic SARS-CoV-2 vaccine candidates were previously constructed using a fully synthetic platform based on the well-characterized and clinically proven Modified Vaccinia Ankara (MVA) vector^29-32, which is marketed in the USA as Jynneos™ (Bavarian-Nordic)³³. Construction and sequences of SARS-CoV-2 vaccines discussed herein, including clinical vaccine candidate COH04S1, is disclosed in, for example, International Application Publication No. WO 2021/236550, the disclosure and sequence listing of which are hereby incorporated by reference in its entirety as if fully set forth herein, and which were included as part of the disclosure for U.S. Provisional Application No. 63/244,103 as Appendix A and the Sequence Listing submitted therewith.

MVA is a highly attenuated poxvirus vector that is widely used to develop vaccines for infectious diseases and cancer due to its excellent safety profile in animals and humans, versatile delivery and expression system, and ability to stimulate potent humoral and cellular immune responses to heterologous antigens^30-32. MVA has been used to develop vaccine candidates for preclinical testing in animal models of congenital cytomegalovirus disease while demonstrating vaccine efficacy in several clinical trials in solid tumor and stem cell transplant patients^34-39. Using the synthetic MVA (sMVA) platform, sMVA vectors co-expressing full-length S and N antigen sequences were constructed and demonstrated potent immunogenicity in mice to stimulate SARS-CoV-2 antigen-specific humoral and cellular immune responses, including NAb²⁹. One of these sMVA constructs forms the basis of clinical vaccine candidate COH04S1, which has shown to be safe and immunogenic in a randomized, double-blinded, placebo-controlled, single center Phase 1 trial in healthy adults (NCT04639466), and is currently evaluated in a randomized, double-blinded, single center Phase 2 trial in hematology patients who have received cellular therapy (NCT04977024).

As demonstrated herein, COH04S1 stimulates protective immunity against SARS-CoV-2 in Syrian hamsters by intramuscular (IM) and intranasal (IN) vaccination and in non-human primates (NHP) through two-dose (2D) and single-dose (11D) vaccination regimen. These results complement the clinical evaluation of this multiantigen sMVA-based SARS-CoV-2 vaccine.

Additionally, the emergence of several SARS-CoV-2 VOCs with the capacity to evade S-specific NAb threatens the efficacy of approved COVID-19 vaccines, which primarily utilize a single antigen design based solely on the S protein. One way to avoid or minimize the risk for SARS-CoV-2 evasion of vaccine-induced immunity could be the stimulation of broadly functional humoral and cellular immunity beyond the induction of S-specific NAb. Particularly the stimulation of T cells by a combination of multiple immunodominant antigens could act as an additional countermeasure to confer long-term and broadly effective immunity against SARS-CoV-2 and its emerging VOC^21-24. Several recent studies indicate that SARS-CoV-2 VOCs have the capacity to effectively escape humoral immunity, whereas they are unable to evade T cells elicited through natural infection and vaccination⁵⁷.

The multi-antigenic sMVA-vectored SARS-CoV-2 vaccine COH04S1 co-expressing full-length S and N antigens provides potent immunogenicity and protective efficacy in animal models. Using Syrian hamsters and NHP, it is shown that COH04S1 elicits robust antigen-specific humoral and cellular immune responses and protects against SARS-CoV-2 challenge through different immunization routes and dose regimen. While these animal studies were not designed to assess the contribution of N in COH04S1-mediated protective immunity, these results warrant further evaluation of COH04S1 in ongoing and future clinical trials. COH04S1 represents a second-generation COVID-19 vaccine candidate that could be used alone or in combination with other existing vaccines in parenteral or mucosal prime-boost or single-shot immunization strategies to augment vaccine-mediated protective immune responses against SARS-CoV-2.

Although several SARS-CoV-2 vaccines based on MVA have been developed and evaluated in animal models for immunogenicity and efficacy^29,58-61, there is currently no MVA-based SARS-CoV-2 vaccine approved for routine clinical use. COH04S1 and MVA-SARS-2-S, an MVA vector expressing S alone, are currently the only MVA-based SARS-CoV-2 vaccines that are clinically evaluated⁶¹. In addition, COH04S1 and a recently developed adenovirus vector approach are currently the only clinically evaluated SARS-CoV-2 vaccines that utilize an antigen combination composed of S and N⁶². These findings highlight the potential importance of COH04S1 as a second generation multiantigenic SARS-CoV-2 vaccine to contribute to the establishment of long-term protective immunity against COVID-19 disease. In addition, these findings highlight the potential of the sMVA platform and synthetic biology in poxvirus-vectored vaccine technology to rapidly generate protective and clinical-grade vaccine vectors for infectious disease prevention.

COH04S1 demonstrated potent immunogenicity in Syrian hamsters by IM and IN immunization and in NHP by 2D and 1D immunization regimen to elicit robust SARS-CoV-2-specific humoral and cellular immune responses to both S and N antigens. This included high-titer S and N-specific binding antibodies in addition to robust binding antibodies targeting the RBD, the primary target of NAb. Binding antibodies elicited by COH04S1 in hamsters as well as T cell responses induced by COH04S1 in NHP indicated Th1-biased immunity, which is thought to be the preferred antiviral adaptive immune response to avoid vaccine-associated enhanced respiratory disease^63,64. NAb elicited by COH04S1 in hamsters and NHP showed potent neutralizing activity against SARS-CoV-2 infectious virus, highlighting the potential of COH04S1 to induce antibody responses that are considered essential for protection against SARS-CoV-2. Notably, NAb titers stimulated by COH04S1 in NHP appeared similar to peak NAb titers stimulated in healthcare workers by two doses of the FDA approved Pfizer/BioNTech mRNA vaccine. In addition, NAb stimulated by COH04S1 in hamsters showed neutralizing activity against PV variants based on several SARS-CoV-2 VOC, including Alpha, Beta, Gamma, and the rapidly spreading Delta variant, indicating the capacity of COH04S1 to stimulate cross-protective NAb against SARS-CoV-2 VOC.

Both IM and IN immunization with COH04S1 provided potent efficacy to protect Syrian hamsters from progressive weight loss, lower respiratory tract infection, and lung injury upon IN challenge with SARS-CoV-2, highlighting the potential of COH04S1 to stimulate protective immunity against respiratory disease through parenteral and mucosal immunization routes. In contrast, IM or IN immunization of hamsters with COH04S1 appeared to provide only limited protection against upper respiratory tract infection following viral challenge, indicating that COH04S1-mediated parenteral or mucosal immune stimulation afforded only little protection in this small animal model at the site of viral inoculation, which may have been associated with the relatively aggressive sub-lethal viral challenge dose. While IM and IN immunization with COH04S1 provided overall similar immunogenicity and protective efficacy against SARS-CoV-2 in hamsters, IN immunization with COH04S1 appeared superior compared to IM immunization to protect against initial minor weight loss at the early phase after SARS-CoV-2 challenge. On the other hand, hamsters immunized IM with COH041S1 were completely protected from lung injury following challenge, while hamsters immunized IN with COH041S1 showed minor lung pathology and inflammation at day 10 post challenge, suggesting superior protection against viral- or immune-mediated lung pathology through IM immunization compared to IN immunization with COH04S1.

The immunogenicity and protective efficacy afforded by COH04S1 against SARS-CoV-2 in Syrian hamsters by IM and IN immunization appears consistent with known properties of MVA-vectored vaccines. While MVA is well-known to stimulate robust immunity by IM immunization, MVA has also been shown to elicit potent immunity through IN vaccination strategies at mucosal surfaces. A recombinant MVA vector expressing the S protein of Middle East Respiratory Syndrome coronavirus (MERS-CoV), a close relative of SARS-CoV-2, has recently been shown to be safe and immunogenic following IM administration in a Phase 1 clinical trial⁶⁵. This MVA vaccine has also been shown to protect dromedary camels against MERS-CoV challenge by co-immunization via IM and IN routes⁶⁶. In addition, several animal studies have shown that IN immunization with MVA vaccines is a potent stimulator of bronchus-associated lymphoid tissue (BALT), a tertiary lymphoid tissue structures within the lung that is frequently present in children and adolescents and that serves as a general priming site for T cells⁶⁷. While the precise mechanism and levels of protection afforded by COH04S1 against SARS-CoV-2 in the Syrian hamster model by IM and IN immunization remains unclear, especially at early phase after challenge, these findings support the use of COH04S1 to elicit SARS-CoV-2 protective immunity by mucosal vaccination.

In addition to the protection afforded by IM and IN immunization with COH04S1 in hamsters, 2D and 1D immunization with COH04S1 in NHP provided potent protection against lower and upper respiratory tract infection upon IN/IT challenge with SARS-CoV-2. These findings demonstrate protective efficacy of COH04S1 by different dose immunization regimen in a larger animal model that is thought to be critical to assess preclinical vaccine efficacy. While 2D and 1 D immunization of NHP with COH04S1 stimulated similar S and RBD-specific binding antibodies at the time of viral challenge, 2D immunization appeared to be overall more effective than 1 D immunization in stimulating humoral and cellular immune responses, including NAb. Despite these overall lower pre-challenge immune responses in 1 D-immunized animals compared to 2D-immunized NHP, 1 D and 2D immunization of NHP with COH04S1 afforded similar protection against lower and upper respiratory tract infection following viral challenge, suggesting that a single shot with COH04S1 is sufficient to induce protective immunity to SARS-CoV-2. In addition, while 2D immunization with COH04S1 appeared to elicit overall more potent pre-challenge responses than 1 D immunization, overall more potent post-challenge anamnestic antiviral immune responses were observed in 1 D-immunized NHP compared to 2D-immunized NHP, suggesting that a single shot with COH04S1 is sufficient to effectively prime vaccine-mediated protective re-call responses to SARS-CoV-2.

These results demonstrate that COH04S1 has the capacity to elicit potent and cross-reactive Th1-biased S and N-specific humoral and cellular responses that protect hamsters and NHP from SARS-CoV-2 by different immunization routes and dose regimen. This multi-antigen sMVA-vectored SARS-CoV-2 vaccine could be complementary to available vaccines to induce robust and long-lasting protective immunity against SARS-CoV-2 and its emerging VOC.

The following examples are intended to illustrate various embodiments of the invention. As such, the specific embodiments discussed are not to be constructed as limitations on the scope of the invention. It will be apparent to one skilled in the art that various equivalents, changes, and modifications may be made without departing from the scope of invention, and it is understood that such equivalent embodiments are to be included herein. Further, all references cited in the disclosure are hereby incorporated by reference in their entirety, as if fully set forth herein.

Examples

Materials and Methods

COH04S1 and sMVA vaccine stocks COH04S1 is a double-plaque purified virus isolate derived from the previously described sMVA-N/S vector (NCBI Accession #MW036243), which was generated using the three-plasmid system of the sMVA platform and fowlpox virus TROVAC as a helper virus for virus reconstitution²⁹. COH04S1 co-expresses full-length S and N antigen sequences based on the Wuhan-Hu-1 reference strain (NCBI Accession #NC_045512)²⁹. Sequence identity of COH04S1 seed stock virus was assessed by PaqBio long-read sequencing. COH04S1 and sMVA vaccine stocks for animal studies were produced using chicken embryo fibroblasts (CEF) and prepared by 36% sucrose cushion ultracentrifugation and virus resuspension in 1 mM Tris-HCl (pH 9). Virus stocks were stored at −80° C. and titrated on CEF by plaque immunostaining as described²⁹. Viral stocks were validated for antigen insertion and expression by PCR, sequencing, and Immunoblot.

Animals, study design and challenge: In life portion of hamsters and NHP studies were carried out at Bioqual Inc. (Rockville, Md.). Thirty female and male golden Syrian hamsters were randomly assigned to the groups, with 3 females and 3 males in each group. Hamsters were IM or IN immunized four weeks apart with 1×10⁸ PFU of COH04S1 or sMVA vaccine stocks diluted in phosphate-buffered saline (PBS). Two weeks post-booster immunization animals were challenged IN (50 μl/nare) with 3×10⁴ PFU (or 1.99×10⁴ Median Tissue Culture Infectious Dose, [TCID50]) of SARS-CoV-2 USA-WA1/2020 (BEI Resources; P4 animal challenge stock, NR-53780 lot no. 70038893). The stock was produced by infecting Vero E6-hACE2 cells (BEI Resources NR-53726) at low MOI with deposited passage 3 virus and resulted in a titer of 1.99×10⁶ TCID50/ml. Sequence identity was confirmed by next generation sequencing. Body weight and temperature were recorded daily for 10 days. Hamsters were humanely euthanized for lung samples collection. A total of 24 African green monkeys (Chlorocebus aethiops; 20 females and 4 males) from St. Kitts weighting 3-6 Kg were randomized by weight and sex to vaccine and control groups. For 2D immunization, NHP were either two times mock-immunized with PBS (N=3) in four weeks interval or immunized twice four weeks apart with 2.5×10⁸ PFU of COH04S1 (N=6) or sMVA control vector (N=3) diluted in PBS. For 1 D immunization, NHP were either one time mock-immunized (N=3) with PBS or immunized once with 5×10⁸ PFU of COH04S1 (N=6) or sMVA control vector (N=3) diluted in PBS. At six weeks post 2D or 1 D immunization (2D) NHP were challenged with 1×10⁵ TCID50 (Median Tissue Culture Infectious Dose) of SARS-CoV-2 USA-WA1/2020 strain diluted in PBS via combined IT (1 ml)/IN (0.5 ml/nare) route. Necropsy was performed 7 days and 21 days following challenge and organs were collected for gross pathology and histopathology. All animal studies were conducted in compliance with local, state, and federal regulations and were approved by Bioqual and City of Hope Institutional Animal Care and Use Committees (IACUC).

ELISA binding antibody detection: SARS-CoV-2-specific binding antibodies in hamsters and NHP samples were detected by indirect ELISA utilizing purified S, RBD, and N proteins (Sino Biological 40589-V08B11, 40592-V08H, 40588-V08B), or Beta, Gamma, and Delta VOC-specific S proteins (Acro Biosystems SPN-C52Hk, SPN-C52Hg, SPN-C52He). 96-well plates (Costar 3361) were coated with 100 ul/well of S, RBD, or N proteins at a concentration of 1 ug/ml in PBS and incubated overnight at 4° C. For binding antibody detection in hamsters serum, plates were washed 5× with wash buffer (0.05% Tween-20/PBS), then blocked with 250 ul/well of blocking buffer (0.5% casein/154 mM NaCl/10 mM Tris-HCl [pH 7.6]) for 2 hours at room temperature. After washing, 3-fold diluted heat-inactivated serum in blocking buffer was added to the plates and incubated 2 hours at room temperature. After washing, anti-Hamster IgG HRP secondary antibodies measuring total IgG(H+L), IgG₁, or IgG₂/IgG₃ (Southern Biotech 6061-05, 1940-05, 1935-05) were diluted 1:1000 in blocking buffer and added to the plates. After 1 hour incubation, plates were washed and developed with 1 Step TMB-Ultra (Thermo Fisher 34029). The reaction was stopped with 1 M H₂SO₄ and plates were immediately read on FilterMax F3 (Molecular Devices). For binding antibody detection in NHP serum, a similar protocol was used. Wash buffer was 0.1% Tween-20 in PBS, and blocking buffer was 1% casein/PBS for RBD and N antigen ELISA and 4% Normal Goat Serum/1% casein/PBS for S ELISA. For IgG quantification in NHP BAL samples 1% BSA/PBS was used as blocking and sample buffers. Goat anti-Monkey IgG (H+L) secondary antibody (ThermoFisher Cat #PA1-84631) was diluted 1:10,000. Endpoint titers were calculated as the highest dilution to have an absorbance>0.100.

PRNT assay: NAb were measured by PRNT assay using SARS-CoV-2 USA-WA1/2020 strain (Lot #080420-900). The stock was generated using Vero-E6 cells infected with seed stock virus obtained from Kenneth Plante at UTMB (lot #TVP 23156). Vero E6 cells (ATCC, CRL-1586) were seeded in 24-well plates at 175,000 cells/well in DMEM/10% FBS/Gentamicin. Serial 3-fold serum dilutions were incubated in 96-well plates with 30 PFU of SARS-CoV-2 USA-WA1/2020 strain (NR-53780 lot no. 70038893, BEI Resources) for 1 hour at 37° C. The serum/virus mixture was transferred to Vero-E6 cells and incubated for 1 hour at 37° C. After that, 1 ml of 0.5% methylcellulose media was added to each well and plates were incubated at 37° C. for three days. Plates were washed, and cells were fixed with methanol. Crystal violet staining was performed, and plaques were recorded. IC50 titers were calculated as the serum dilution that gave a 50% reduction in viral plaques in comparison to control wells. Serum samples collected from City of Hope healthcare workers (N=14) at day 60 post Pfizer/BioNTech BNT162b2 mRNA vaccination were part of an IRB-approved observational study to establish durability of immunogenic properties of EUA vaccines against COVID-19 (IRB20720).

Pseudovirus production: SARS-CoV-2 pseudovirus was produced using a plasmid lentiviral system based on pALD-gag-pol, pALD-rev, and pALD-GFP (Aldevron). Plasmid pALD-GFP was modified to express Firefly luciferase (pALD-Fluc). Plasmid pCMV3-S(Sino Biological VG40589-UT) was utilized and modified to express SARS-CoV-2 Wuhan-Hu-1 S with D614G modification. Customized gene sequences cloned into pTwist-CMV-BetaGlobin (Twist Biosciences) were used to express SARS-CoV-2 VOC-specific S variants (Table 1).

TABLE 1
SARS-CoV-2 VOC-specific S mutations
included in pseudoviral particles
	CDC
VOC	Classification	Substitutions/Deletions (Δ)
B.1.1.7	Alpha	Δ69/70, Δ144, N501Y, A570D, D614G,
		P681H, T716I, S9822A, D1118H
B.1351	Beta	L18F, D80A, D215G, Δ242-244, R246I,
		K417N, E484K, N501Y, D614G, A701V
P.1	Gamma	L18F, T20N, P26S, D138Y, R190S, K417T,
		E484K, N501Y, D614G, H655Y, T1027I,
		V1176F
B.1.617.2	Delta	T19R, G142D, Δ156-157, R158G, A222V,
		L452R, T478K, D614G, P681R, D950N

All S antigens were expressed with C-terminal 19 amino acids deletion. A transfection mixture was prepared with 1 ml OptiMEM that contained 30 μl of TransIT-LT1 transfection reagent (Mirus MIR2300) and 6 μg pALD-Fluc, 6 μg pALD-gag-pol, 2.4 μg pALD-rev, and 6.6 μg S expression plasmid. The transfection mix was added to 5×10⁶ HEK293T/17 cells (ATCC CRL11268) seeded the day before in 10 cm dishes and the cells were incubated for 72 h at 37° C. Supernatant containing pseudovirus was harvested and frozen in aliquots at −80° C. Lentivirus was titrated using the Lenti-XTM p24 Rapid Titer Kit (Takara) according to the manufacturer's instructions.

Pseudovirus neutralization assay: SARS-CoV-2 pseudoviruses were titrated in vitro to calculate the virus stock amount that equals 100,000-200,000 relative luciferase units. Flat-bottom 96-well plates were coated with 100 μL poly-L-lysine (0.01%). Serial 2-fold serum dilutions starting from 1:20 were prepared in 50 μL media and added to the plates in triplicates, followed by 50 μL of pseudovirus. Plates were incubated overnight at 4° C. The following day, 10,000 HEK293T-ACE2 cells⁶⁸ were added to each well in the presence of 3 μg/ml polybrene and plates were incubated at 37° C. After 48 hours of incubation, luciferase lysis buffer (Promega E1531) was added and luminescence was quantified using SpectraMax L (Molecular Devices, 100 μL One-Glo (Promega E6110) luciferin/well, 10 seconds integration time). For each plate, positive (pseudovirus only) and negative (cells only) controls were added. The neutralization titer for each dilution was calculated as follows: NT=[1-(mean luminescence with immune sera/mean luminescence without immune sera)]×100. The titers that gave 50% neutralization (NT50) were calculated by determining the linear slope of the graph plotting NT versus serum dilution by using the next higher and lower NT using Office Excel (v2019).

ELISPOT T cell detection: Peripheral blood mononuclear cells (PBMC) were isolated from fresh blood using Ficoll and counted using Luna-FL cell counter (Logos Biosystems). Pre-immune samples were evaluated using Human IFN-γ/IL-4 Double-Color FluoroSpot (ImmunoSpot); however, this kit only allowed to assess NHP IFN-γ but did not detect NHP IL-4. The remaining time-points were evaluated using Monkey IFNγ/IL-4 FluoroSpot FLEX kit and Monkey IL-2 FluoroSpot FLEX kit (Mabtech, X-21A16B and X-22B) following manufacturer instructions. Briefly, 200,000 cells/well in CTL-test serum free media (Immunospot CTLT-010) were added to duplicate wells and stimulated with peptide pools (15-mers, 11 aa overlap, >70% purity). Spike peptide library (GenScript) consisted of 316 peptides and was divided into 4 sub-pools spanning the S1 and S2 domains (1S1=1-86; 1S2=87-168; 2S1=169-242; 2S2=243-316; peptides 173 and 304-309 were not successfully synthesized therefore excluded from the pools). Nucleocapsid (GenScript) and Membrane (in house synthesized) libraries consisted of 102 and 53 peptides, respectively. Each peptide pool (2 μg/ml) and αCD28 (0.1 μg/ml, Mabtech) were added to the cells and plates were incubated for 48 hours at 37° C. Control cells (25,000/well) were stimulated with PHA (10 μg/ml). After incubation, plates were washed and primary and secondary antibodies were added according to manufacturer's protocol. Fluorescent spots were acquired using CTL S6 Fluorocore (Immunospot). For each sample, spots in unstimulated DMSO-only control wells were subtracted from spots in stimulated wells. Total spike response was calculated as the sum of the response to each spike sub-pool.

Quantification of SARS-CoV-2 gRNA: SARS-CoV-2 gRNA copies per ml nasal wash, BAL fluid or swab, or per gram of tissue were quantified by qRT-PCR assay (Bioqual, SOP BV-034) using primer/probe sequences binding to a conserved region of SARS-CoV-2 N gene. Viral RNA was isolated from BAL fluid or swabs using the Qiagen MinElute virus spin kit (57704). For tissues, viral RNA was extracted with RNA-STAT 60 (Tel-test B)/chloroform, precipitated and resuspended in RNAse-free water. To generate a control for the amplification, RNA was isolated from SARS-CoV-2 virus stocks. RNA copies were determined from an O.D. reading at 260, using the estimate that 1.0 OD at A260 equals 40 μg/ml of RNA. A final dilution of 10⁸ copies per 3 μl was then divided into single use aliquots of 10 μl. These were stored at −80° C. until needed. For the master mix preparation, 2.5 ml of 2× buffer containing Taq-polymerase, obtained from the TaqMan RT-PCR kit (Bioline BIO-78005), was added to a 15 ml tube. From the kit, 50 μl of the RT and 100 μl of RNAse inhibitor were also added. The primer pair at 2 μM concentration was then added in a volume of 1.5 ml. Lastly, 0.5 ml of water and 350 μl of the probe at a concentration of 2 μM were added and the tube vortexed. For the reactions, 45 μl of the master mix and 5 μl of the sample RNA were added to the wells of a 96-well plate. All samples were tested in triplicate. The plates were sealed with a plastic sheet. The control RNA was prepared to contain 10⁶ to 10⁷ copies per 3 μl. Eight 10-fold serial dilutions of control RNA were prepared using RNAse-free water by adding 5 μl of the control to 45 μl of water. Duplicate samples of each dilution were prepared as described. For amplification, the plate was placed in an Applied Biosystems 7500 Sequence detector and amplified using the following program: 48° C. for 30 minutes, 95° C. for 10 minutes followed by 40 cycles of 95° C. for 15 seconds, and 1 minute at 55° C. The number of copies of RNA per ml was calculated by extrapolation from the standard curve and multiplying by the reciprocal of 0.2 ml extraction volume. This gave a practical range of 50 to 5×10⁸ RNA copies per swabs or per ml BAL fluid. Primers/probe sequences: 5′-GAC CCC AAA ATC AGC GAA AT-3′ (SEQ ID NO: 91); 5′-TCT GGT TAC TGC CAG TTG AAT CTG-3′ (SEQ ID NO: 92); and 5′-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1-3′ (SEQ ID NO: 93).

Quantification of SARS-CoV-2 sgRNA: SARS-CoV-2 sgRNA copies were assessed through quantification of N gene mRNA by qRT-PCR using primer/probes specifically designed to amplify and bind to a region of the N gene mRNA that is not packaged into virions. SARS-CoV-2 RNA was extracted from samples as described above. The signal was compared to a known standard curve of plasmid containing a cDNA copy of the N gene mRNA target region to give copies per ml. For amplification, the plate was placed in an Applied Biosystems 7500 Sequence detector and amplified using the following program: 48° C. for 30 minutes, 95° C. for 10 minutes followed by 40 cycles of 95° C. for 15 seconds, and 1 minute at 55° C. The number of copies of RNA per ml was calculated by extrapolation from the standard curve and multiplying by the reciprocal of 0.2 ml extraction volume. This gave a practical range of 50 to 5×10⁷ RNA copies per swab or ml BAL fluid.

Primers/probe sequences:
(SEQ ID NO: 94)
5’-CGA TCT CTT GTA GAT CTG TTC TC-3’;
(SEQ ID NO: 95)
5’-GGT GAA CCA AGA CGC AGT AT-3’;
(SEQ ID NO: 96)
5’-FAM-TAA CCA GAA TGG AGA ACG CAG TGG G-BHQ-3’.

Quantification of SARS-CoV-2 infectious virus titers: Vero TMPRSS2 cells (Vaccine Research Center-NIAID) were plated at 25,000 cells/well in DMEM/10% FBS/Gentamicin. Ten-fold dilutions of the sample starting from 20 ul of material were added to the cells in quadruplicated and incubated at 37° C. for 4 days. The cell monolayers were visually inspected, and presence of CPE noted. TCID50 values were calculated using the Read-Muench formula.

Histopathology: Histopathological evaluation of hamsters and NHP lung sections were performed by Experimental Pathology Laboratories, Inc. (Sterling, Va.) and Charles River (Wilmington, Mass.) respectively. At necropsy organs were collected and placed in 10% neutral buffered formalin for histopathologic analysis. Tissues were processed through to paraffin blocks, sectioned once at approximately 5 microns thickness, and stained with H&E. Board certified pathologists were blinded to the vaccine groups and mock controls were used as a comparator.

Statistical analyses: Statistical analyses were performed using Prism 8 (GraphPad, v8.3.0). One-way ANOVA with Holm-Sidak's multiple comparison test, two-way ANOVA with Tukey's or Dunn's multiple comparison test, Kruskal-Wallis test followed by Dunn's multiple comparison test, and Spearman correlation analysis were used. All tests were two-sided. The test applied for each analysis and the significance level is indicated in each figure legend. Prism 8 was used to derive correlation matrices.

Additional materials and methods for construction of SARS-CoV-2 vaccines, including clinical vaccine candidate COH04S1, are disclosed in International Application Publication No. WO 2021/236550, the disclosure and sequence listing of which are hereby incorporated by reference in its entirety as if fully set forth herein, and which were included as part of the disclosure for U.S. Provisional Application No. 63/244,103 as Appendix A and the Sequence Listing submitted therewith.

Example 1. COH04S1 Induces Robust Th1-Biased S and N Antigen-Specific Antibodies and Cross-NAb Responses Against SARS-CoV-2 in Hamsters Through IM and IN Immunization

Syrian hamsters are widely used to evaluate vaccine protection against SARS-CoV-2 in a small animal model that mimics moderate-to-severe COVID-19 disease^40-45. Using this animal model, the efficacy of COH04S1 (FIG. 1a) to protect against SARS-CoV-2 challenge by either IM or IN vaccination was determined to assess vaccine protection via parenteral or mucosal immune stimulation. Hamsters were immunized twice in a four-week interval with 1×10⁸ plaque forming units (PFU) of COH04S1 by IM or IN route, referred to as COH04S1-IM or COH04S1-IN, respectively (FIG. 1b). Unimmunized animals and hamsters immunized IM or IN with empty sMVA vector were used as controls. COH04S1-IM and COH04S1-IN stimulated robust and comparable binding antibodies to both the S and N antigens, including antibodies to the S receptor binding domain (RBD), the primary target of NAb^46-48. Binding antibodies to S, RBD, and N were detected at high levels in both the COH04S1-IM and COH04S1-IN vaccine groups after the first immunization and boosted after the second immunization (FIGS. 1c-1d and 2), whereby a particularly strong booster effect was observed for RBD-specific antibodies. Antigen-specific binding antibodies stimulated by COH04S1-IM and COH04S1-IN in hamsters were mainly composed of IgG_2/3 isotypes and only to a minor extent of IgG₁ isotype (FIGS. 1e and 2), indicating Th1-biased immune responses.

Plaque reduction neutralization titer (PRNT) assay measuring neutralizing activity against SARS-CoV-2 infectious virus (USA-WA1/2020) demonstrated that potent and comparable NAb titers were stimulated by COH04S1-IM and COH04S1-IN after the booster immunizations (FIGS. 1f-1g). Furthermore, pooled post-boost immune sera from COH04S1-IM and COH04S1-IN-vaccinated animals demonstrated potent cross-reactive neutralizing activity against SARS-CoV-2 pseudoviruses (PV) with D614G S mutation or multiple S modifications based on several SARS-CoV-2 VOC (FIGS. 1h and 2 and Table 1), including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and the increasingly dominant Delta variant (B.1.617.2). Notably, while NAb titers measured with Alpha, Beta, and Gamma PV variants were generally similar to those determined with D614G PV, NAb titers measured with the Delta-matched PV variant were 2-8-fold reduced compared to those determined with D614G PV. In addition, NAb titers measured in COH04S1-IM immune sera using the different PV variants appeared overall lower than those measured in COH04S1-IN immune sera. These results demonstrate that IM and IN immunization of Syrian hamsters with COH04S1 elicits robust Th1-biased S and N antigen-specific binding antibodies as well as potent NAb responses with cross-reactivity to prevent PV infection by several SARS-CoV-2 VOC.

Example 2. IM and IN Immunization with COH04S1 Protect Hamsters from Progressive Weight Loss, Lower Respiratory Tract Infection, and Lung Pathology Following SARS-CoV-2 Challenge

Two weeks after the booster immunization, hamsters were challenged IN with 6×10⁴ PFU of SARS-CoV-2 reference strain USA-WA1/2020 and body weight changes were measured over a period of 10 days. While control animals showed rapid body weight loss post challenge, hamsters immunized IM or IN with COH04S1 were protected from severe weight loss following challenge (FIGS. 3a-3b). Control animals showed rapid body weight loss for 6-7 days post challenge, reaching maximum weight loss between 10-20%. In contrast, COH04S1-IM and COH04S1-IN-immunized animals showed no or only very minor body weight decline post challenge, with maximum body weight loss below 4% for all animals at any time point during the entire 10 day observation period (FIGS. 3a-3b). Notably, while minor weight loss was observed for COH04S1-IM-vaccinated animals at 1-2 days post challenge, COH04S1-IN-vaccinated animals did not show body weight decline at these early time points post challenge (FIG. 3a), suggesting improved protection from weight loss by COH04S1 through IN compared to IM immunization at an early phase post challenge.

At day 10 post challenge, hamsters were euthanized for viral load assessment and histopathology analysis. Viral load was measured in the lungs and nasal turbinates/wash by quantification of SARS-CoV-2 genomic RNA (gRNA) and sub-genomic RNA (sgRNA) to gauge the magnitude of total and replicating virus at lower and upper respiratory tracts. Compared to lung viral loads of control animals, markedly reduced gRNA and sgRNA copies were observed in the lungs of COH04S1-IM and COH04S1-IN-vaccinated animals (FIGS. 3c-3d), demonstrating potent vaccine protection against lower respiratory tract infection through IM and IN immunization. SARS-CoV-2 gRNA copies in the lungs of COH04S1-IM and COH04S1-IN-vaccinated animals were more than three to four orders of magnitude lower than in the lungs of control animals. Furthermore, while 103-10⁶ sgRNA copies were detected in the lungs of control animals, sgRNA was undetectable in the lungs of COH04S1-IM and COH04S1-IN-vaccinated animals, indicating complete absence of replicating virus in lung tissue of vaccinated hamsters. Compared to nasal viral loads of controls, gRNA and sgRNA viral loads in nasal turbinates and wash of COH04S1-IM and COH04S1-IN-immunized animals appeared only marginally reduced, indicating limited vaccine impact on upper respiratory tract infection by COH04S1 independent of immunization route (FIG. 4).

Histopathological findings in hematoxylin/eosin-stained lung sections of euthanized animals were assessed by a board-certified pathologist and scored in a blinded manner on a scale from 1 to 5 based on the severity and diffusion of the lesions (Table 2).

TABLE 2
Scoring parameters used to evaluate hamster lung histopathology
Grade	Severity	Findings
1	Minimal	Histopathologic change ranging from inconspicuous to barely noticeable but so minor, small, or
		infrequent as to warrant no more than the least assignable grade. For multifocal or diffusely-distributed
		lesions, this grade was used for processes where less than approximately 10% of the tissue in an
		average high-power field was involved. For focal or diffuse hyperplasitc/hypoplastic/atrophic lesions,
		this grade was used when the affected structure or tissue had undergone a less than approximately 10%
		increase or decrease in volume.
2	Mild	Histopathologic change that is a noticeable but not a prominent feature of the tissue. For multifocal or
		diffusely-distributed lesions, this grade was used for processes where between approximately 10% and
		25% of the tissue in an average high-power field was involved. For focal or diffuse hyperplasitc/
		hypoplastic/atrophic lesions, this grade was used when the affected structure or tissue had undergone
		between an approximately 10% to 25% increase or decrease in volume.
3	Moderate	Histopathologic change that is a prominent but not a dominant feature of the tissue. For multifocal or
		diffusely-distributed lesions, this grade was used for processes where between approximately 25% and
		50% of the tissue in an average high-power field was involved. For focal or diffuse hyperplasitc/
		hypoplastic/atrophic lesions, this grade was used when the affected structure or tissue had undergone
		between an approximately 25% to 50% increase or decrease in volume.
4	Marked	Histopathologic change that is a dominant but not an overwhelming feature of the tissue. For multifocal
		or diffusely-distributed lesions, this grade was used for processes where between approximately 50%
		and 95% of the tissue in an average high-power field was involved. For focal or diffuse hyperplasitc/
		hypoplastic/atrophic lesions, this grade was used when the affected structure or tissue had undergone
		between an approximately 50% to 95% increase or decrease in volume.
5	Severe	Histopathologic change that is a dominant but not an overwhelming feature of the tissue. For multifocal
		or diffusely-distributed lesions, this grade was used for processes where between approximately 95% of
		the tissue in an average high-power field was involved. For focal or diffuse hyperplasitc/hypoplastic/
		atrophic lesions, this grade was used when the affected structure or tissue had undergone a greater than
		approximately 95% increase or decrease in volume.

Control animals demonstrated compromised lung structure characterized by moderate bronchioloalveolar hyperplasia with consolidation of lung tissue, minimal to mild mononuclear or mixed cell inflammation, and syncytial formation (FIGS. 3e-3h). In contrast, COH04S1-IV-vaccinated animals did not show lung pathology of any type and grade in 6/6 hamsters, demonstrating potent vaccine protection against SARS-CoV-2-mediated lung injury in hamsters by IM vaccination with COH04S1. While COH04S1-IN-vaccinated animals presented no severe histopathological findings and significantly reduced lung pathology compared to controls, COH04S1-IN-immunized hamsters consistently showed a mild form of bronchioloalveolar hyperplasia and grade 1 interstitial inflammation in a subset of animals, indicating that IN immunization with COH04S1 mediated potent but incomplete vaccine protection against SARS-CoV-2-mediated lung damage in this model (FIGS. 3e-3h).

Correlative analysis of pre-challenge immunity and post-challenge outcome revealed that any of the evaluated COH04S1-induced responses, including S, RBD, and N-specific antibodies and NAb, correlated with protection from weight loss, lungs infection, and lung pathology (FIG. 5), confirming that the observed protection was vaccine-mediated. These results in sum demonstrate that hamsters immunized IM and IN with COH04S1 are protected from progressive weight loss, lower respiratory tract infection, and severe lung pathology following SARS-CoV-2 challenge.

Example 3. 2D and 1 D Immunization of NHP with COH04S1 Stimulates Robust Antigen-Specific Binding Antibodies, NAb Responses, and Antigen-Specific IFNγ and IL-2 Expressing T Cells

NHP represents a mild COVID-19 disease model that is widely used to bolster preclinical SARS-CoV-2 vaccine efficacy against upper and lower respiratory tract infection in an animal species that is more closely related to humans^49-56. The African green monkey NHP model was used to assess COH04S1 vaccine protection against SARS-CoV-2 by 2D and 1 D immunization regimen, referred to as COH04S1-2D and COH04S1-1 D, respectively. For 2D immunization, NHP were immunized twice in a four-week interval with 2.5×10⁸ PFU of COH04S1. For 1 D immunization, monkeys were immunized once with 5×10⁸ PFU of COH04S1 (FIG. 6). As controls, monkeys were either mock-immunized or immunized with empty sMVA vector via the same schedule and dose immunization regimen. Robust serum binding antibodies to S, RBD, and N were stimulated in NHP by both COH04S1-2D and COH04S1-1 D, whereas binding antibodies in the 2D vaccine group were strongly boosted after the second dose. At the time of challenge, S- and RBD-specific antibody titers measured in the 2D and 1 D vaccine groups were comparable (FIGS. 6b-6d, 7), while N-specific titers appeared higher in the 2D vaccine group than in the 1 D vaccine group. Notably, similar S-specific antibody titers were measured in 2D- and 1 D-immunized NHP by S antigens based on the original Wuhan-Hu-1 reference strain and various VOC (Beta, Gamma and Delta), whereas binding antibodies titers measured with VOC-specific S antigens tended to be lower than those measured with the Wuhan-Hu-1 S antigen (FIGS. 6e, 7). Antigen-specific binding antibodies of the IgG type were also measured in lung bronchoalveolar lavage (BAL) samples two weeks pre-challenge. BAL IgG binding antibodies to S, RBD, and N were detected in both COH04S1-2D and COH04S1-1 D-immunized NHP, although BAL IgG antibody titers measured at this time point pre-challenge were higher in the 2D vaccine group than in the 1 D vaccine group (FIGS. 6f, 7).

NAb measurements based on PRNT assay revealed that both COH04S1-2D and COH04S1-1 D elicited NAb responses with efficacy to neutralize SARS-CoV-2 infectious virus (USA-WA1/2020). NAb responses measured in COH04S1-2D-immunized animals were boosted after the second dose and exceeded those measured in COH04S1-1 D-immunized NHP at the time of challenge (FIG. 6g). Notably, NAb measured by PRNT assay in COH04S1-2D- and COH04S1-1D-immunized NHP were within the range of peak titers measured post-second dose in a cohort of healthcare workers that received the FDA-approved BNT162b2 mRNA vaccine from Pfizer/BioNTech.

At two weeks pre-challenge, SARS-CoV-2 antigen-specific T cell responses in COH04S1-immunized NHP were also assessed. Both 2D and 1D immunization with COH04S1 stimulated robust IFNγ and IL-2-expressing S and N antigen-specific T cells, whereas no or only very low levels of IL-4-expressing S and N-specific T cells were observed in COH04S1-2D or COH04S1-1 D-vaccinated animals, consistent with Th1-biased immunity (FIGS. 6h-6i, 8). S-specific T cells were generally detected at a higher frequency than N-specific T cells in both the COH04S1-2D and COH04S1-1 D vaccine groups. In addition, S-specific T cells measured at this time point pre-challenge were detected at a higher frequency in 2D-immunized NHP than in 1 D-immunized NHP. These results demonstrate that COH04S1 elicits robust antigen-specific binding antibodies, NAb, and antigen-specific IFNγ and IL-2-expressing T cells in NHP through 2D and 1D immunization regimen.

Example 4. 2D and 1 D Immunization with COH04S1 Protect NHP from Lower and Upper Respiratory Tract Infection Following SARS-CoV-2 Challenge

Six weeks after 2D or 1D vaccination with COH04S1, immunized NHP were challenged by IN/Intratracheal (IT) route with 1×10⁵ PFU of SARS-CoV-2 (USA-WA1/2020). SARS-CoV-2 viral loads in lower and upper respiratory tracts were assessed at several time points for 21 days post challenge in BAL and nasal/oral swabs by quantification of gRNA and sgRNA and infectious virus titers (FIGS. 9a-9i, 10a-10i and 11). Progressively declining viral loads were overall measured over the 21 days post challenge observation period in BAL and nasal/oral swabs of both COH04S1-immunized NHP and control animals. Compared to BAL viral loads of control animals, markedly reduced gRNA and sgRNA copies and infectious virus titers were measured in BAL of COH04S1-2D and COH04S1-1D-immunized NHP at almost all time points post challenge (FIGS. 9a-9b, 9d-9e, 9g-9h), indicating a potent vaccine impact on lower respiratory tract infection. Notably, BAL gRNA and sgRNA copies and infectious titers measured in COH04S1-2D and COH04S1-1D-immunized NHP at day 2 immediately after challenge were on average 2-3 orders of magnitude lower than those measured in controls, confirming rapid vaccine efficacy. The marked reduction in BAL viral loads of COH04S1-immunized NHP compared to controls was confirmed when combining viral loads measured at all timepoints post challenge by area under the curve (AUC; FIGS. 9c, 9f, 9i).

Similar to viral loads in BAL of COH04S1-immunized NHP, gRNA and sgRNA copies and infectious virus titers measured at the first 10 days post challenge in nasal swabs of COH04S1-2D or COH04S1-1D-immunzied NHP were consistently lower than those of control animals, demonstrating vaccine efficacy to prevent upper respiratory tract infection (FIGS. 10a-10i). In addition, gRNA and sgRNA in oral swabs of COH04S1-immunized NHP tended to be consistently lower than those in oral swabs of control animals (FIG. 11). Notably, nasal and oral swab gRNA and sgRNA copies and nasal swab infectious titers measured at 1-3 days immediately after challenge in COH04S1-immunized NHP were significantly reduced compared to those of controls, indicating immediate vaccine protection. Overall reduced nasal and oral swab viral loads in COH04S1-immunized NHP compared to control animals were confirmed when evaluating the nasal and oral swab viral loads over time by AUC (FIGS. 10c, 10f, 10i, 11). No significant differences in viral loads were observed between COH04S1-2D and COH04S1-1D-immunzied animals, indicating similar protection against lower and upper respiratory tract infection by COH04S1 through 2D and 1 D immunization. Viral loads measured at day 7 or 21 post challenge in lung tissue and several other organs of necropsied animals did not indicate evident differences between COH04S1-immunized NHP and control animals (FIG. 12). While gRNA and sgRNA copies measured at day 7 post challenge in lung samples of COH04S1-2D and COH04S1-1D-immunized NHP appeared reduced compared to those measured in lung samples of controls, these results were inconclusive due to low or undetectable gRNA and sgRNA levels in lung samples of the 1 D mock-immunized control monkey (FIG. 12). Histopathological findings assessed by a board-certified pathologist in a blinded manner at day 7 and 21 post challenge were generally only minor and comparable between in COH04S1 vaccine and control groups, and no increase in inflammation was observed for COH4S1-immunized NHP compared to control animals (Table 3).

TABLE 3
NHP vaccine groups, necropsy schedule, and gross pathological findings
Group	Study	Weight (kg)	Sex	Nx day +7	Nx day +21	Gross pathology findings at Nx
Mock	2D	4.76	F		X	All lobes normal
		3.02	F	X		Right caudal lung, remaining lobes normal. Overall
						hemorrhaging
		3.78	F		X	Left and Right caudal lung, remaining lobes normal
	1D	3.56	F	X		Pathology and congestion in all lobes
		3.45	F		X	Pathology and congestion in all lobes
		6.79	M		X	Left and Right caudal lung, remaining lobes normal
sMVA	2D	4.03	F	X		Right caudal lung, remaining lobes normal
		3.31	F	X		Gross congestion, possibly due to BALs. Lobes normal
		3.63	F		X	Right caudal lung, remaining lobes normal
sMVA	1D	3.41	F	X		Gross congestion, possibly due to BALs. Lobes normal
		3.73	F	X		Gross congestion, possibly due to BALs. Lobes normal
		6.05	M		X	All lobes normal
COG04S1	2D	4.02	F	X		Gross congestion, possibly due to BALs. Lobes normal
		2.91	F	X		Right caudal lung, remaining lobes normal
		3.69	F		X	Gross congestion, possibly due to BALs. Lobes normal
		3.68	F		X	Right caudal lung, remaining lobes normal
		3.37	F	X		Right caudal lung, remaining lobes normal
		7.23	M		X	Right caudal lung, remaining lobes normal
	1D	3.79	F	X		Gross congestion, possibly due to BALs. Lobes normal
		3.83	F		X	Right caudal lung, remaining lobes normal
		2.95	F	X		Gross congestion, possibly due to BALs. Lobes normal
		3.86	F		X	Gross congestion, possibly due to BALs. Lobes normal
		3.36	F	X		Right caudal lung, remaining lobes normal
		5.63	M		X	All lobes normal

A strong inverse correlation could be assessed between vaccine-induced humoral and cellular immune responses, including S, RBD, and N-specific binding antibodies in serum and BAL, NAb, and S- and N-specific T cells, and SARS-CoV-2 viral loads in BAL and nasal swab samples (FIG. 13). These results in sum demonstrate that 2D or 1 D immunization regimen of COH04S1 protect NHP from lower and upper respiratory tract infection following IN/IT challenge with SARS-CoV-2.

Example 5. NHP Immunized with 2D and 1 D Vaccination Regimen of COH04S1 Develop Robust Post-Challenge Anamnestic Immune Responses

To assess the vaccine impact on post-challenge viral immunity, humoral and cellular responses were evaluated in COH04S1-vaccinated NHP and control animals at 1, 2, and 3 weeks post-challenge (FIGS. 14, 15). This analysis revealed that control animals developed robust binding antibodies to S, RBD, and N at 15- or 21-days post challenge (FIGS. 14a-14f), which indicated stimulation of potent humoral responses by the SARS-CoV-2 challenge virus in naïve NHP. In contrast, NAb titers measured post challenge in control animals by PRNT assay against infectious virus were in general relatively low or at the limit of detection (FIGS. 14g, 14j), although elevated NAb responses were observed in 1D mock-vaccinated control animals at day 15 and 21 post challenge (FIG. 14j). In addition, no or only low level T cell responses were detected post-challenge in control animals, with the exception of elevated frequencies of S and N-specific IFNγ-expressing T cell responses in mock-immunized control animals at day 7 post challenge (FIGS. 14h, 14k, 14i).

Compared to antibodies measured pre-challenge in COH04S1-immunized NHP, boosted titers of S, RBD, and N antigen-specific binding antibodies and PRNT-assayed NAb were measured in COH04S1-immunized animals at day 15 and 21 post challenge (FIGS. 14a-14g, 14j), indicating induction of robust post-challenge anamnestic immune responses. This post-challenge booster effect on SARS-CoV-2-specific humoral immunity appeared more pronounced in COH04S1-1 D-vaccinated NHP than in COH04S1-2D-vaccinated NHP, which may be a result of the lower pre-challenge responses in the 1 D vaccine group compared to the 2D vaccine group. In addition, binding antibodies and NAb measured at day 15 and 21 post-challenge in COH04S1-vaccinated NHP generally exceeded those measured in control animals, indicating heightened vaccine-mediated humoral recall responses against SARS-CoV-2 through 2D or 1 D vaccination. While S and N antigen-specific IFNγ-expressing T cell levels measured in COH04S1-2D-vaccinated animals tended to increase only slightly after challenge, a marked increase in post-challenge S- and N-specific IFNγ-expressing T cells was observed in COH04S1-1 D-vaccinated NHP, indicating potent vaccine-mediated cellular recall responses following 1 D vaccination. S and N-specific IL-4-expressing T cells were either only very low or undetectable in COH04S1-vaccinated NHP and control animals at any time point post challenge, consistent with Th-1 biased immunity following challenge (FIG. 15). Correlation analysis did not unambiguously reveal a strong association between any of the post-challenge immunological parameters and post-challenge virological assessments (FIG. 13). These results demonstrate that NHP immunized with 2D or 1 D vaccination regimen of COH04S1 develop potent anamnestic antiviral post-challenge recall responses.

As demonstrated herein, intramuscular or intranasal vaccination of Syrian hamsters with COH04S1 stimulated robust Th1-biased S- and N-specific humoral immunity and cross-neutralizing antibodies (NAb) and protected against weight loss, lower respiratory tract infection, and lung injury following intranasal SARS-CoV-2 challenge. In addition, one- or two-dose vaccination of African Green Monkeys with COH04S1 induced robust antigen-specific binding antibodies, NAb, and Th1-biased T cells, protected against both upper and lower respiratory tract infection following intranasal/intratracheal SARS-CoV-2 challenge, and triggered potent post-challenge anamnestic antiviral recall responses. These results demonstrate that COH04S1 stimulates protective immunity against SARS-CoV-2 in animal models through different immunization routes and dose regimen, which complements ongoing investigation of this multiantigen sMVA-vectored SARS-CoV-2 vaccine in clinical trials.

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Claims

1. A vaccine composition for preventing or treating a coronavirus infection in a subject comprising: (i) a single synthetic DNA fragment comprising the entire genome of an MVA, or two or more synthetic DNA fragments each comprising a partial sequence of the genome of the MVA such that the two or more DNA fragments, when transferred into the host cell upon co-transfection, are assembled sequentially and comprise the full-length sequence of the MVA genome, and(ii) one or more DNA sequences encoding the S protein and the N protein of a coronavirus, subunits, or fragments thereof, inserted in one or more insertion sites of the MVA, wherein the S protein and the N protein are expressed in the host cell upon transfection of the one or more MVA DNA fragments.

2. The vaccine composition of claim 1, wherein the one or more DNA sequences encoding the S protein and the N protein are inserted into Del2/Del3 sites.

3. The vaccine composition of claim 2, wherein the one or more DNA sequences encoding the S protein and the N protein are under the control of an mH5 promoter.

4. The vaccine composition of any one of claims 1-3, further comprising a pharmaceutically acceptable carrier, adjuvant, additive or combination thereof.

5. The vaccine composition of any one of claims 1-4, wherein the composition is formulated for intramuscular administration.

6. The vaccine composition of any one of claims 1-4, wherein the composition is formulated for intranasal administration.

7. A method of preventing a coronavirus infection in a subject comprising administering a prophylactically or therapeutically effective amount of the vaccine composition of any one of claims 1-6 to the subject.

8. A method of eliciting an immune response in a subject comprising administering a prophylactically or therapeutically effective amount of the vaccine composition of any one of claims 1-6 to the subject, wherein the subject is infected with a coronavirus or at a risk of being infected with a coronavirus.

9. The method of claim 8, wherein the elicited immune response is a Th1-biased immune response.

10. The method of any one of claims 7-9, wherein the coronavirus infection is caused by a variant of concern (VOC) comprising a D614G mutation in the S protein.

11. The method of claim 10, wherein the VOC is selected from the group consisting of B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma), and B.1.617.2 (delta).

12. The method of claim 11, wherein VOC B.1.1.7 comprises deletion 69/70, deletion 144, N501Y, A570D, D614G, P681H, T7161, S982A, and D1118H in the S protein.

13. The method of claim 11, wherein VOC B.1.351 comprises L18F, D80A, D215G, deletion 242-244, R2461, K417N, E484K, N501Y, D614G, and A701V in the S protein.

14. The method of claim 11, wherein VOC P.1 comprises L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T10271, and V1176F in the S protein.

15. The method of claim 11, wherein VOC B.1.617.2 comprises T19R, G142D, deletion 156-157, R158G, A222V, L452R, T478K, D614G, P681R, and D950N in the S protein.

16. The method of any one of claims 7-15, wherein the vaccine composition is administered intramuscularly.

17. The method of any one of claims 7-15, wherein the vaccine composition is administered intranasally.

18. The method of any one of claims 7-17, wherein a single dose of the vaccine composition is administered.

19. The method of any one of claims 7-17, wherein two doses of the vaccine composition are administered.

20. The method of any one of claims 7-17, wherein three or more doses of the vaccine composition are administered.