VACCINES FOR VIRAL PATHOGENS CONFERRING UNIVERSAL PROTECTION IRRESPECTIVE OF VIRAL MUTATIONS

FIELD OF THE INVENTION

This invention pertains generally to vaccines and, more particularly multi-epitope vaccines for viral pathogens including SARS-CoV-2, the causative agent of COVID-19.

BACKGROUND OF THE INVENTION

An outbreak of pneumonia like disease termed COVID-19 caused by a novel coronavirus, SARS-CoV-2, has spread across the world and become a global pandemic. First generation vaccines targeting SARS-CoV-2 have been developed by BioNTech/Pfizer, Moderna, Oxford/Astra Zeneca and others. These first generation vaccines all target spike protein: the Oxford/Astra Zeneca vaccine uses an adenoviral vector; the vaccines by Moderna and Pfizer are RNA based; the vaccine by Imperial College London relies upon self-amplifying RNA.

The spike protein is a poor candidate choice for a vaccine. Spike is hypervariable and prone to mutations. A number of SARS-CoV-2 variants have been identified, and most of the sequence variant characterising them are usually located within Spike. Moreover, a low number of antibodies from survivors (10-30%) target spike protein. In addition, vaccines targeting spike protein will not immunise all individuals due to HLA variability.

To work, a vaccine must contain pathogen-derived molecules (typically proteins or glycans) processed first by the host cell into peptides and then presented (antigen presentation) at the host cell surface on its Human Leukocyte Antigens (HLA). HLAs are encoded within the highly polymorphic major histocompatibility complex (MHC) on Chromosome 6. This process leads to presentation of peptides originating from self and pathogen. HLA-peptide complexes are then specifically recognized by T-cells via the T-cell receptor (TCR); while self-peptide ligands do not typically elicit a response from the immune system, an immunogenic foreign peptide ligand-HLA complex will bind a TCR and trigger an immune response that leads to the development of cytotoxic and memory T- and B-cells. There are many components in the host immune system, but HLA molecules are the chief determinants of antigen presentation to the T- cells for subsequent activation of the immune response. The classical HLA genes are the most polymorphic genes in the human genome, with some having more than a thousand known alleles. Alleles are distributed unevenly around the world but typically clustered according to ethnicity. These genes are divided into two subgroups, mainly based on the source of the peptides they tend to present: HI_A I genes are expressed on all cells except red blood cells, and present peptides of intracellular origin (e.g. from self or viruses), whereas HLA-I I genes are expressed only on professional antigen presenting cells and present peptides that originate extracellularly (e.g. from bacteria). Thus, the response to a viral pathogen such as SARS-CoV-2 is mediated by HLA-I.

The HLA genes are co-dominantly expressed and encode HLA proteins that are referred to as HLA Class I (HLA-A, -B, -C,) and HLA Class II (HLA-D). They are critical in priming adaptive immune responses. CD4+ T helper/inducer cells recognize viral peptides bound to HLA-II encoded proteins and CD8+ Cytotoxic T cells recognize viral peptides bound to HLA-A, -B, -C, encoded proteins. The vast polymorphism in their extracellular peptide binding domains leads to the diversity of peptide antigens that can be bound and subsequently recognized by T-cell receptors. HLA class I molecules generally present short (8-12 amino acids) i ntracel I u I arly- derived peptides, such as viral antigens. HLA class II molecules are capable of presenting longer (i.e., generally more than 13 amino acids) extracellularly derived peptides, such as antigenic fragments generated from viral proteins. The HLA allele polymorphism renders each variant protein a distinct product with the main difference focused on the peptide-binding groove and the conformation of adjacent regions directly engaged with peptide binding and interaction with the TCR. A T-cell will recognize bound antigen as a complex with a restricted allelic variant of HLA molecule. Depending on the combinations of HLA-I and II alleles expressed, an individual may be differently equipped to resist certain viruses, including coronaviruses. Thus, individual genetic variation across HLA genes aids in understanding how variation in HLA may affect the course of COVID-19, and could help identify individuals at higher risk of succumbing to the disease.

Previous research on related virus strains (SARS-CoV-1 and MERS-Cov) demonstrated that viral antigen presentation of SARS-CoV-1 mainly depends on HLA-I and HLA-II molecules. Numerous HLA-I polymorphisms correlate to susceptibility of SARS-CoV-1, such as HLA- B*46:01 5, HLA-B*07:03, HLA-DR B1 *12:02, and HLA-Cw*08:01, whereas the HLA-DR*03:01, HLA-Cw15:02 and HLA-A*02:01 alleles are related to the protection from SARS-CoV-1 infection HLA-II molecules, such as HLA-DRB1 *11:01 and HLA-DQB1*02, are associated with the susceptibility to MERS-CoV infection. These data suggest that individual HLA genotypes may differentially control susceptibility or protection in T-cell mediated anti-SARS-CoV-2 responses. Thus, HLA polymorphism could potentially alter disease outcomes and SARS-CoV-2 transmission. The enormous diversity in HI_A genes means that some individuals can present an antigen and mount a strong immune response against it, while others cannot present it at all. This is especially relevant for vaccination strategies involving subunit vaccines, since the number of available antigens can be very small. In fact, HI_A polymorphism is a likely basis for the observed variations in vaccine efficacy.

Epitope-based or string of beads vaccines use concatemers of short immunogenic peptide sequences derived from antigens that are recognised by either CD4 or CD8 T-cells in the context of HLA-II or HLA-I respectively. They have several advantages over whole attenuated or subunit vaccines because they do not contain potentially infectious material. Furthermore, peptides can be chosen to take the genetic variation of pathogens and HLA-binding specificities into account. Development of such vaccines requires bioinformatics for prediction of HLA epitopes. Machine-learning methods, such as probabilistic models, neural networks, and support vectors machines, are routinely used with high accuracy for epitope prediction. Different algorithms have been used to create string of bead vaccines that generally concentrate on binding peptides for a small number of HLA-I epitopes.

A variety of platforms, including but not limited to nucleic acid, viral vectors, attenuated viruses and recombinant protein, are being examined for the development of the SARS-COV-2 vaccine. The use of nucleic acid-based vaccines allow for vaccines to be obtained in a short timeframe. Furthermore, nucleic acid-based vaccine manufacturing is safe and time-saving, and bypasses the need to grow highly pathogenic organisms at a large scale, resulting in a lower risk of contamination with live infectious reagents and release of dangerous pathogens.

The SAM vaccine platform is composed of one or more non-viral, typically virus-derived, engineered replicons that drive high levels of expression of encoding antigens. Very low doses are required (mgs) as tens of thousands of copies are made by transfected cells. They may be delivered via intramuscular (i.m.), in the same manner as earlier mRNA vaccines, and can be encapsulated within a lipid nanoparticle to further boost performance. This manufacturing process makes GMP grade SAM a promising vaccine approach for filling the gap between emerging infectious disease and the desperate need for effective COVID-19 vaccines. SAMs are an innovative platform for vaccine development. Within an alphavirus backbone, the mRNA replicates through a double stranded RNA intermediate, and the antigen of interest replaces structural proteins, so no infectious virus is made. Very low doses are required (pgs) as tens of thousands of copies are made by transfected cells. They are delivered via intramuscular (i.m.), in the same manner as earlier mRNA vaccines, and may be delivered as naked RNA or encapsulated within a lipid nanoparticle. Comparatively, mRNA vaccines confer several advantages over vaccines introduced by virus vectors and DNA vaccines: the production procedure to generate mRNA vaccines is cell-free, simple and rapid if compared to production of whole microbe, or live attenuated or subunit vaccines.

This background information is provided for the purpose of making known information believed by the applicant to be of possible relevance to the present invention. No admission is necessarily intended, nor should be construed, that any of the preceding information constitutes prior art against the present invention.

SUMMARY OF THE INVENTION

An object of the present invention is to provide a vaccine for viral pathogens conferring universal protection irrespective of viral mutations.

In accordance with an aspect of the present invention, there is provided a vaccine comprising or capable of expressing one or more concatemers of epitopes from a viral pathogen. In certain embodiments, the vaccine comprises or expresses epitopes for all MHC I and MHC II alleles with a frequency >1% in the target population. In certain embodiments, the target population is geographically restricted. In certain embodiments, the epitopes that bind MHC I or MHC II alleles associated with autoimmune disease are excluded. In certain embodiments, at least a portion of said epitopes are from conserved proteins from said viral pathogen. In certain embodiments, the epitopes are universal (common) epitopes of said viral pathogen. In certain embodiments, the epitopes are variant specific epitopes.

In certain embodiments, the viral pathogen is a sarbecovirus, including but not limited to SARS- CoV-2. In specific embodiments, the vaccine comprises or is capable of expressing expressing one or more concatemers of epitopes from one or more strains of sarbecovirus (e.g. SARS- CoV-2). Each concatemer of epitopes may include epitopes from a single strain or from multiple strains. For vaccines capable of expressing expressing one or more concatemers of epitopes from one or more strains, the one or more concatemers may be expressed by one or more expression vectors. In certain embodiments, each concatemer is expressed by a separate expression vector. In certain embodiments, one or more concatemers are expressed by a single expression vector.

In certain embodiments, a linker separates each of said epitopes. Exemplary linkers include RY, KRY, RYP, PRRARSV, PRRARSVKRY, PRRARSVRYP, ATLQA, QEAGAG and LALAA. The linkers may be the same or different between epitopes in a concatemer.

In certain embodiments, at least one of the one or more epitopes is as set forth in any one of the tables set forth below and/or as set forth in SEQ ID NOs 1-789.

In accordance with an aspect of the present invention, there is provided a vaccine comprising or capable of expressing one or more concatemers of epitopes set forth in any one of the tables set forth below and/or as set forth in SEQ ID NOs 1-789.

In accordance with an aspect of the present invention, there is provided a vaccine comprising or capable of expressing one or more concatemers set forth in SEQ ID NOs 798-851.

In certain embodiments, the vaccine is a viral vector-based vaccine, including but not limited to an adenoviral vector, a vesicular stomatitis virus vector or a vaccinia vector.

In certain embodiments, the vaccine is a nucleic acid-based vaccine.

In certain embodiments, the vaccine is a SAM RNA-based vaccine. In more specific embodiments, the SAM RNA-based vaccine is encapsulated in a lipid nanoparticle (LNP). In more specific embodiments, the LNP comprises a cationic lipid. In more specific embodiments, the LNP comprises phosphatidylcholine/cholesterol/PEG-lipid, C12-200, dimethyldioctadecylammonium (DDA), 1,2-dioleoyl-3-trimethylammonium propane (DOTAP) or 1,2-dilinoleyloxy-3-dimethylaminopropane (DLinDMA). In certain embodiments, the LNP comprises GEN-7036 (Lipid composition (ratio) =DOTAP:Chol:DOPE (1:0.75:0.5)).

In certain embodiments, the vaccine further comprises an adjuvant.

In certain embodiments, the vaccine further comprises a buffer.

In specific embodiments, the vaccine is a SAM RNA-based vaccine and comprises one or more SAM RNA vectors of the invention, cholesterol, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), ((4-hydroxybutyl)azanediyl)bis(hexane-6,1-diyl)bis(2- hexyldecanoate) (ALC-3015), 2- [(polyethylene glycol)-2000]-N,N-ditetradecylacetamide (ALC-0159), potassium chloride, monobasic potassium phosphate, sodium chloride, dibasic sodium phosphate dihydrate, water and sucrose.

In specific embodiments, the vaccine is a SAM RNA-based vaccine and comprises one or more SAM RNA vectors of the invention, cholesterol, 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), Lipid SM-102, 1,2-dimyristoyl-rac-glycero-3-methoxypolyethylene glycol-2000 (PEG2000-DMG), tromethamine tris(hydroxymethyl)aminomethane), tromethamine hydrochloride, acetic acid, sodium acetate, water, and sucrose.

In accordance with an aspect of the present invention, there is provided a method of treating, protecting against, and/or preventing infection by a target viral pathogen, including but not limited to a sarbecovirus such as SARS-CoV-2, in a subject in need thereof, the method comprising administering one or more of the vaccines of the invention to the subject.

In accordance with an aspect of the present invention, there is provided a method of generating an immune response against a target viral pathogen, including but not limited to sarbecovirus such as SARS-CoV-2, the method comprising administering one or more of the vaccines of the invention to the subject.

In certain embodiments, the one or more vaccines is administered more than once. In certain embodiments, a prime and boost strategy of vaccination is used. In more specific embodiments, a heterologous prime and boost strategy is utilized. Exemplary prime and boost strategies are known in the art (see for example Sapkota et al. J Travel Med. 2021 Dec 16; taab191. Doi: 10.1093/jtm/taab191; He et al, Emerg Microbes Infect. 2021; 10(1): 629-637; Kardani et al. Vaccine 2016, 34(4): 413-423).

In certain embodiments, wherein the subject is a mammal including but not limited to human, cat, dog, horse, sheep, goat, camel or cow.

In certain embodiments, the vaccines are formulated for parenteral administration, e.g., subcutaneous, intraperitoneal, intravenous, intradermal, and intramuscular. In certain embodiments, the vaccines are formulated for mucosal administration, e.g. oral administration, intranasal, and intravaginal routes. BRIEF DESCRIPTION OF THE DRAWINGS

These and other features of the invention will become more apparent in the following detailed description in which reference is made to the appended drawings.

Figure 1 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention.

Figure 2 provides the nucleic acid sequence of the vaccine from Figure 1. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 3 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention.

Figure 4 provides the nucleic acid sequence of the vaccine from Figure 3. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 5 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention.

Figure 6 provides the nucleic acid sequence of the vaccine from Figure 5. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 7 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention.

Figure 8 provides the nucleic acid sequence of vaccine from Figure 7. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 9 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention.

Figure 10 provides the nucleic acid sequence of vaccine from Figure 9. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 11 provides a map of a SAM based SARS-CoV-2 vaccine of an embodiment of the present invention. Figure 12 provides the nucleic acid sequence of the vaccine from Figure 11. Sequence represented as DNA for corresponding RNA sequence T is replaced with U.

Figure 13 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 14 provides the sequence of concatemers 1 to 6 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention..

Figure 15 provides the sequence of concatemers 1 to 6 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 16 provides the sequence of concatemers 1 to 6 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 17 provides the sequence of concatemers 1 to 6 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 18 provides the sequence of concatemers 1 to 6 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 19 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 20 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention. Figure 21 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 22 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

Figure 23 provides the sequence of concatemers 1 to 4 of SARS-CoV-2 epitopes separated by linking sequences expressed by an embodiment of the SARS-CoV-2 vaccine of the present invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides vaccines for viral pathogens which confer protection against a wide spectrum of strains of the target viral pathogen, including but not limited to a sarbecovirus. For example, in certain embodiments, by comprising or expressing multiple epitopes from a number of highly conserved genes of SARS-CoV-2, the vaccines confer protection against a wide spectrum of strains of SARS-CoV-2, therein including mutated strains arising in the future in the population and escape mutants generated in the future by other vaccines that only target a subset of the viral proteins (for instance, the spike protein alone). In addition, in certain embodiments, the vaccines are tailored to a majority of immunotypes present in the target population, the vaccines confer protection to a wide spectrum of individuals, irrespective of the make-up of their immune system in terms of MHC genes.

In certain embodiments, the invention provides vaccines against coronaviruses, including but not limited to a Sarbecovirus. In certain embodiments, the invention provides vaccines against SARS-associated coronaviruses (SARS-CoV). In specific embodiments, the invention provides vaccines against SARS-CoV-2. Also provided are pharmaceutical compositions comprising the vaccines and methods of generating a protective immune response against RNA viruses. In specific embodiments, there is provided pharmaceutical compositions comprising the vaccines and methods of generating a protective immune response against the SARS-CoV viral pathogens.

The vaccines may trigger a humoral (B-cell) and/or cellular (T-cell response). In certain embodiments, the vaccine comprises or expresses T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more RNA viral pathogens. In certain embodiments, the vaccine comprises or expresses T-cell MHC-I (e.g. H LA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more specific SARS-CoV pathogens. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more SARS-CoV-2 proteins.

In principle, a vaccine needs to comprise or express one epitope that binds an individual’s MHC alleles for the vaccine to have activity in the individual. Accordingly, in certain embodiments, the vaccine comprises or expresses epitopes for all MHC I and MHC II alleles with a frequency >1% (or another suitably selected frequency) in the target population, so as to achieve a vaccine capable of conferring protection to a wide spectrum of individuals irrespective of their MHC type. HLA types are distributed geographically, accordingly, in certain embodiments the target population is geographically limited.

In addition, it is known in the certain HLA types are associated with autoimmunity such as ankylosing spondylitis (HLA B27) or arthritis (HLA DR4). Accordingly toxicity related to autoimmunity may be reduced by omitting peptides that bind to these HLA types.

Vaccine Platforms

A variety of platforms may be used to generate the vaccines of the present invention. Exemplary vaccine platforms which may be used include but are not limited to protein-based platforms, virus-like particle-based vaccines, viral vector-based platforms and nucleic acid- based vaccine platforms.

In certain embodiments, the vaccine platform is a viral vector-based platform. The viral vectors may be attenuated viruses, may be replicating or non-replicating. Exemplary viral vectors include not are not limited to adenovirus, vaccinia or adeno associated virus, lentivirus or vesicular stomatitis virus (VSV). Accordingly, in certain embodiments the vaccine platform is an adenovirus, vaccinia or adeno associated virus, lentivirus or Vesicular stomatitis virus based vaccine.

In specific embodiments, the viral vector platform is an adenovirus vector platform. Various serotypes of adenoviruses have been used in vaccine development including Ad5, Ad26 and Ad35. In certain embodiments, the adenovirus vector is based on a simian adenovirus. Use of simian adenovirus vaccine vectors circumvent pre-existing human adenovirus immunity. Exemplary, simian adenovirus serotypes used in vaccine development include simian adenovirus type 23.

In certain embodiments, the vaccine platform is a nucleic acid-based platform. Nucleic acid- based vaccine platforms may be DNA or RNA-based. Optionally, the nucleic acids include one or more modified nucleosides.

In certain embodiments, the nucleic acid-based vaccine platform is a DNA-based vaccine platform. Appropriate DNA expression vectors for use as a DNA-based vaccine platform are known in the art. A worker skilled in the art would readily appreciate that such expression vectors include the necessary elements to allow for expression of the one or more immunogens. Such elements include a promoter, such as the CMV promoter which directs transcription of the mRNA encoded by the transgene, a polyadenylation signal which mediates mRNA cleavage and polyadenylation, and Kozak sequence which directs efficient transgene translation. In specific embodiments, the DNA-based vaccine is a plasmid-based vaccine. In certain embodiments the vaccine has been optimized for expression of the assembled epitopes. In certain embodiments, the vaccines comprise nucleic acid sequence expressing said concatemer of epitopes which is less than 20kb in length.

In certain embodiments, the vaccine comprises a sequence which has been codon optimized or deoptimized.

In certain embodiments, the nucleic acid-based vaccine is a RNA-based vaccine platform. In specific embodiments, a mRNA platform. The mRNA-based vaccine platform may be non replicating or self-amplifying. In certain embodiments, the nucleic acid-based vaccine platform is a self-amplifying (SAM) RNA platform. A variety of RNA based expression systems are known in the art, including but not limited to expression systems based on either positive-sense and negative-sense RNA viruses. Positive-strand RNA viruses used in the development expression system include but are not limited to alphaviruses and flaviviruses. Exemplary alphaviruses used for expression systems include but are not limited to Semliki Forest virus, Venezuelan equine encephalitis virus and Sindbis virus and poliovirus. Alphavirus replicon particle-based vaccine vectors derived from Sindbis virus (SIN), Semliki Forest virus (SFV), and Venezuelan equine encephalitis virus (VEE) have been shown to induce robust antigen-specific cellular, humoral, and mucosal immune responses in many animal models of infectious disease and cancer (Perri et al.; Journal of Virology Sep 2003, 77 (19) 10394-10403; DOI: 10.1128/JVI.77.19.10394-10403.2003; Karl Ljungberg & Peter Liljestrom (2015) Self-replicating alphavirus RNA vaccines, Expert Review of Vaccines, 14:2, 177-194, DOI:

10.1586/14760584.2015.965690). Exemplary flavivirus used for expression systems include Kunjin flavivirus. Negative sense RNA virus systems include measles and rhabdoviruses.

In specific embodiments, the SAM RNA vaccine platform is derived from an alphavirus. In such embodiments, the mRNA replicates through a double stranded RNA intermediate, and the antigen of interest replaces structural proteins, so no infectious virus is made.

Epitopes

The multi-epitope vaccines of the present invention comprise or expresses epitopes of one or more viral proteins.

In certain embodiments, the vaccine comprises or expresses one or more epitopes from conserved (such as structural proteins) viral proteins and one or more variable (hypervariable) viral proteins (such as spike protein from SARS-CoV2). By comprising or expressing both types of epitopes, the vaccine is likely to be much less prone to generate escape mutants and is more likely to confer sterilizing immunity while targeting a number of circulating variants. In addition, in certain embodiments, by comprising or expressing epitopes for all MHC I and MHC II alleles with a frequency >1% in the general human population are chosen, so as to be effective in a large portion of the population.

The vaccine may comprise or express MHC I epitopes and/or MHC II epitopes of one or more viral proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-I I) epitopes of one or more RNA viral proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-I I) epitopes of one or more coronavirus proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more sarbecovirus proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more SARS-CoV proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more SARS-CoV-2 proteins. In certain embodiments, the epitopes are T-cell MHC-I (e.g. HLA-I) and/or MHC-II (e.g. HLA-II) epitopes of one or more SARS-CoV-2 proteins. In specific embodiments, the vaccine comprises or expresses MHC-I and MHC-II epitopes. In certain embodiments, the vaccine comprises or expresses multiple epitopes from conserved (such as structural proteins) and variable (hypervariable) proteins (such as spike protein from SARS-CoV2).

In certain embodiments, each epitope comprises an amino acid sequence between 5 and 60 amino acids. In certain embodiments, the epitopes comprise a sequence comprising 8 to 44 amino acids. In certain embodiments, the epitopes comprise a sequence comprising 8 to 30 amino acids. In certain embodiments, the epitopes comprise a sequence comprising 8 to 22 amino acids. In certain embodiments, the vaccine comprises or expresses MHC I epitopes comprising a sequence comprising 8 to 15 amino acids. In certain embodiments, the vaccine comprises or expresses MHC II epitopes comprising a sequence comprising 9 to 22 amino acids. In certain embodiments, the vaccine comprises or expresses MHC II epitopes comprising a sequence comprising more than 13 amino acids.

In certain embodiments, the sequence of the epitope(s) the vaccine comprises or expresses is 100% identical to the sequence of the corresponding epitope(s) in the wild-type viral protein. In certain embodiments, the sequence of the epitope(s) the vaccine comprises or expresses comprises one or more substitutions, insertions and/or deletions of one or more amino acid residues as compared to the sequence of the epitope in the wild-type viral protein. In certain embodiments, the epitope(s) the vaccine comprises at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% sequence identity as compared to a reference epitope sequence. The reference sequence may be any of the viral epitope sequences disclosed herein or known in the art.

In certain embodiments, the sequence of the epitope(s) of the vaccine is derived from the consensus sequence of more than one viral sequence. In certain embodiments, such sequence is obtained by considering the consensus of the most frequent variants appearing in different viral strains or in any number of sequenced viruses that have been detected while circulating in the population. In certain embodiments, such a sequence is obtained by removing from the original sequence the positions at which variants occur with a frequency larger than a specified frequency threshold (i.e. , hypervariable positions in the sequence are removed, and only the positions in the sequence that are sufficiently constant are kept). In certain embodiments, additional sequences, encompassing the positions at which variants appear more frequently than some specified threshold, are added to the original sequence of the virus (i.e., one adds to the pool of potential peptides the ones generated by non-synonymous variants that occur with sufficient frequency). In certain embodiments, the variants which appear more frequently than some specific threshold are computed based on the strains circulating at some given time in some specific geographical region. In certain embodiments, In certain embodiments, the variants which appear more frequently than some specific threshold are computed based on viral lineages as defined by WHO, other public bodies, or research groups.

In certain embodiments, one or more epitopes are derived from one or more sarbecovirus proteins, including but not limited to SARS-CoV proteins including but not limited to SARS-CoV- 2 proteins.

The complete genome of SARs-CoV-2 is known in the art and is published under GenBank Accession NC_045512.2 (Nature 579 (7798), 265-269 (2020)). Variants of SARS-CoV-2 are known in the art. The targets of T cell responses to SARS-CoV-2 have been examined in exposed individuals. The targets were found to include but are not limited to M, Spike, N, nsp3, nsp4, ORF3a and ORF8 (Grifoni et al., Cell 181:1489-1501, 2020). Accordingly, in certain embodiments, the selection of epitopes is based on the clinical profile of convalescent COVD-19 patients. In specific embodiments, the selection of epitopes is based on the frequency of antigen specific T cell responses that convalescent patients make for both T helper (MHC II) and CTL (MHC I). In certain embodiments, eptiopes were selected based on antigenic score of the epitopes. In specific embodiments, the vaccine comprises MHC I and MHC II binding epitopes for different HI_A Alleles. In specific embodiments, the vaccine comprises MHC I and MHC II binding epitopes for all MHC I and MHC II alleles with a frequency >1% in the general human population are chosen.

In certain embodiments, the vaccine comprises or expresses one or more epitopes from one or more of the following SARS-CoV-2 proteins: spike, NSP1, NSP2, Proteinase 3CL-Pro, NSP7, NSP8, NSP9, NSP10, helicase, exonuclease, endonuclease, methyltransferase, ORF6, N protein, and ORF10.

In certain embodiments, the vaccine comprises or expresses one or more epitopes from one or more of the following SARS-CoV-2 proteins: spike, papain-like protease, NSP4, RNA dependent RNA polymerase, M protein, ORF7a, and ORF8.

In certain embodiments, the vaccine comprises or expresses one or more epitopes from one or more of the following SARS-CoV-2 proteins: 2’-0-ribose methyltransferase, 3C-like proteinase, 3’-to-5’ exonuclease, endoRNAse, envelope protein, helicase, leader protein, membrane glycoprotein, nsp10, nsp2, nsp3, nsp4, nsp6, nsp7, nsp8, nsp9, nucleocapsid phosphoprotein, ORF10 protein, ORF3a protein, ORF6 protein, ORF7a protein, ORF8 protein, RNA-dependent RNA polymerase, and surface glycoprotein.

In certain embodiments, the vaccine comprises or expresses one or more epitopes as set forth in any one of Tables below. In certain embodiments, the vaccine comprises or expresses one or more of the concatemer of epitopes (optionally the epitopes are separated by a linker sequence) as set forth in any one of Tables below.

In certain embodiments, the vaccine comprises or expresses one or more epitopes as set forth in any one of SEQ ID NOs 1-789. In certain embodiments, the vaccine comprises or expresses one or more of the concatemer of epitopes (optionally the epitopes are separated by a linker sequence) as set forth in any one of SEQ ID NOs 1-789. In specific embodiments, the linkers comprise the sequence as set forth in 790 or 791.

In certain embodiments, the vaccine comprises one or more nucleic acids capable of expressing one or more of the epitopes or concatemers of epitopes optionally separated by linker sequences described above. The one or more nucleic acids may be DNA or RNA. The vaccine comprising or capable of expressing the one or more epitopes may be virus-like particle-based vaccines, viral vector-based vaccines or nucleic acid-based vaccines. In nucleic acid-based vaccines, the nucleic acids may optionally include modifications including for example one or more modified nucleosides. In certain embodiments, the nucleic acid sequences are codon optimized. In certain embodiments, the nucleic acid sequences are codon optimized for expression in mammalian cells, optionally human cells. In certain embodiments, the nucleic acid sequences are deoptimized.

Linkers between Epitopes

In certain embodiments, the vaccines comprise or express one or more concatemer(s) of epitopes with intervening linker peptides. In certain embodiments, the linker peptides comprise a protease cleavage site(s). In certain embodiments, the insertion of protease cleavage sites enhances antigen processing. Exemplary cleavage sites include chymotryptic, tryptic and furin cleavage sties. In specific embodiments, the linker consists of other viral and cellular protease sites. In specific embodiments, the linker peptides comprise the following sequence: RY, KRY, RYP, PRRARSV, PRRARSVKRY or PRRARSVRYP. In certain embodiments, the linker can be any peptide consistent with the motif [AVTP][TKRV]LQ[AS]. In specific embodiments, the linker consists of the following sequence: ATLQA. In specific embodiments, the linker consists of the following sequence: QEAGAG. In specific embodiments, the linker consists of the following sequence: LALAA.

Exemplary Concatemers of Epitopes

In certain embodiments, the vaccine comprises or expresses at least one of concatemers of epitopes from SARS-CoV-2 with intervening linker sequences set forth in Table 1 below. In certain embodiments, the vaccine comprises or expresses at least two of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences set forth in Table 1 below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below in Table 1.

Table 1: concatemer P ^os _in_ ^conc atemer epitope gene pos_in_gene

1 1-12 LNVPLHGTILTR membrane_glycoprotein(26523-27191) 120-131

1 13-22 PRRARSVRYP linker 1-10

1 23-35 TVLKKCKSAFYIL nsp3(2720-8554) 526-538

1 36-45 PRRARSVRYP linker 1-10

1 46-53 IETISLAG nsp3(2720-8554) 684-691

1 54-63 PRRARSVRYP linker 1-10

1 64-73 NWNCVNCDTF nsp3(2720-8554) 1631-1640

1 74-83 PRRARSVRYP linker 1-10

1 84-97 DYDCVSFCYMHHME 3C-like_proteinase(10055-10972) 153-166

1 98-107 PRRARSVRYP linker 1-10

1 108-117 TPLIQPIGAL nsp4(8555-10054) 269-278

1 118-127 PRRARSVRYP linker 1-10

1 128-154 VTGLFKDCSKVITGLHPTQAPTHLSVD 3’-to-5’_exonuclease(18040-19620) 4-30

1 155-164 PRRARSVRYP linker 1-10

1 165-179 SDVLYQPPQTSITSA nsp4(8555-10054) 483-497

1 180-189 PRRARSVRYP linker 1-10

1 190-200 TKVDGVDVELF endoRNAse(19621 -20658) 33-43

1 201-210 PRRARSVRYP linker 1-10

1 211-221 ETICAPLTVFF endoRNAse(19621 -20658) 113-123

1 222-231 PRRARSVRYP linker 1-10

1 232-246 KETLYCIDGALLTKS nsp3(2720-8554) 1024-1038

1 247-256 PRRARSVRYP linker 1-10

1 257-270 QIELKFNPPALQDA nsp3(2720-8554) 867-880

1 271-280 PRRARSVRYP linker 1-10

1 281-298 HVQLSLPVLQVRDVLVRG leader_protein(266-805) 13-30

1 299-308 PRRARSVRYP linker 1-10

1 309-316 DHVISTSH helicase(16237-18039) 32-39

1 317-326 PRRARSVRYP linker 1-10

1 327-339 ANFCALILAYCNK nsp3(2720-8554) 890-902

1 340-349 PRRARSVRYP linker 1-10

1 350-357 LPINVIVFnsp3(2720-8554) 1718-1725

1 358-367 PRRARSVRYP linker 1-10

1 368-381 CATTRQVVNVVTTK nsp3(2720-8554) 1926-1939

1 382-391 PRRARSVRYP linker 1-10

1 392-399 YDKLVSSF nsp3(2720-8554) 365-372

1 400-409 PRRARSVRYP linker 1-10

1 410-418 KFPLKLRGT 2’-O-ribose_methyltransferase(20659-21552) 249-257

1 419-428 PRRARSVRYP linker 1-10

1 429-438 KSASVYYSQL nsp3(2720-8554) 1737-1746

1 439-448 PRRARSVRYP linker 1-10 449-463 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(18040-19620) 223-237

464-473 PRRARSVRYP linker 1-10

474-486 AIKCVPQADVEWK3’-to-5’_exonuclease(18040-19620) 337-349

487-496 PRRARSVRYP linker 1-10

497-510 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(18040-19620) 178-191

511-520 PRRARSVRYP linker 1-10

521-544 TYASALWEIQQVVDADSKIVQLSE nsp8(12092-12685) 148-171

545-554 PRRARSVRYP linker 1-10

555-562 YLKLRSDV nsp4(8555-10054) 427-434

563-572 PRRARSVRYP linker 1-10

573-586 DGCVPLNIIPLTTA nsp8(12092-12685) 112-125

587-596 PRRARSVRYP linker 1-10

597-609 KEILVTYNCCDDD RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 143-155

610-619 PRRARSVRYP linker 1-10

620-627 SDFVRATA ORF3a_protein(25393-26220) 26-33

628-637 PRRARSVRYP linker 1-10

638-650 GVVDYGARFYFYT nsp3(2720-8554) 596-608

651-660 PRRARSVRYP linker 1-10

661-674 QEHYVRITGLYPTLhelicase(16237-18039) 243-256

675-684 PRRARSVRYP linker 1-10

685-707 TFKVSIWNLDYIINLIIKNLSKSORF6_protein(27202-27387) 21-43 708-717 PRRARSVRYP linker 1-10

718-730 FVVEVVDKYFDCY RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 471-483

731-740 PRRARSVRYP linker 1-10

741-753 YTVSCLPFTINCQ ORF8_protein(27894-28259) 79-91

754-763 PRRARSVRYP linker 1-10

764-778 EILDITPCSFGGVSV surface_glycoprotein(21563-25384) 583-597

779-788 PRRARSVRYP linker 1-10

789-798 MPLGYVTHGL nsp3(2720-8554) 630-639

799-808 PRRARSVRYP linker 1-10 809-816 MADLVYAL RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 124-131 817-826 PRRARSVRYP linker 1-10

827-840 TSACVLAAECTI FK nsp4(8555-10054) 147-160 841-850 PRRARSVRYP linker 1-10

851-866 SAEVAVKMFDAYVNTF nsp3(2720-8554) 1765-1780

867-876 PRRARSVRYP linker 1-10 877-886 NEFYAYLRKH RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 743-752 887-896 PRRARSVRYP linker 1-10 897-906 LQYGSFCTQL surface_glycoprotein(21563-25384) 754-763 907-916 PRRARSVRYP linker 1-10 917-925 IQLSSYSLF 2’-O-ribose_methyltransferase(20659-21552) 237-245 926-935 PRRARSVRYP linker 1-10 936-946 CTLKSFTVEKG surface_glycoprotein(21563-25384) 301-311 947-956 PRRARSVRYP linker 1-10 957-964 PSFLGRYM nsp3(2720-8554) 822-829 965-974 PRRARSVRYP linker 1-10 975-989 ISNCVADYSVLYNSA surface_glycoprotein(21563-25384) 358-372 990-999 PRRARSVRYP linker 1-10

1000-1011 ISVTTEILPVSM surface_glycoprotein(21563-25384) 720-731

1012-1021 PRRARSVRYP linker 1-10

1022-1041 SEAVEAPLVGTPVCINGLML nsp2(806-2719) 591-610

1042-1051 PRRARSVRYP linker 1-10

1052-1061 FDVEGCHATR 3’-to-5’_exonuclease(18040-19620) 89-98

1062-1071 PRRARSVRYP linker 1-10

1072-1086 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(13442-13468+13468-16236)

857-871

1087-1096 PRRARSVRYP linker 1-10

1097-1113 DKYVRNLQHRLYECLYR RNA-dependent_RNA_polymerase(13442-13468+13468-16236)

717-733

1114-1123 PRRARSVRYP linker 1-10

1124-1160 FHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR ORF8_protein(27894-28259) 16-52

1161-1170 PRRARSVRYP linker 1-10

1171-1189 KLNVGDYFVLTSHTVMPLS helicase(16237-18039) 218-236

1190-1199 PRRARSVRYP linker 1-10

1200-1207 TSCCSCLK surface_glycoprotein(21563-25384) 1238-1245

1208-1217 PRRARSVRYP linker 1-10

1218-1225 AALQIPFA surface_glycoprotein(21563-25384) 892-899

1226-1235 PRRARSVRYP linker 1-10

1236-1243 NQMCLSTL nsp2(806-2719) 133-140

1244-1253 PRRARSVRYP linker 1-10 1 1254-1265 GSNVFQTRAGCL surface_glycoprotein(21563-25384) 639-650

1 1266-1275 PRRARSVRYP linker 1-10

1 1276-1285 KASCTLSEQL nsp2(806-2719) 30-39

1 1286-1295 PRRARSVRYP linker 1-10

1 1296-1323 IKDLPKEITVATSRTLSYYKLGASQRVA membrane_glycoprotein(26523-27191 ) 161-188

1 1324-1333 PRRARSVRYP linker 1-10

1 1334-1343 ARDLICAQKF surface_glycoprotein(21563-25384) 846-855

1 1344-1353 PRRARSVRYP linker 1-10

1 1354-1361 SQDLSVVS endoRNAse(19621 -20658) 308-315

1 1362-1371 PRRARSVRYP linker 1-10

1 1372-1379 DVVECLKL nsp3(2720-8554) 1832-1839

1 1380-1389 PRRARSVRYP linker 1-10

1 1390-1407 INVFAFPFTIYSLLLCRM ORF10_protein(29558-29674)4-21

2 1 -10 DKLQFTSLEI helicase(16237-18039) 583-592

2 11-20 PRRARSVRYP linker 1-10

2 21-33 SYELQTPFEIKLA nsp2(806-2719) 68-80

2 34-43 PRRARSVRYP linker 1-10

2 44-51 GYVMHANY 2’-O-ribose_methyltransferase(20659-21552) 221-228

2 52-61 PRRARSVRYP linker 1-10

2 62-94 YEPLTQDHVDILGPLSAQTGIAVLDMCASLKEL 3C-like_proteinase(10055-10972) 239-271

2 95-104 PRRARSVRYP linker 1-10

2 105-112 RVEAFEYY nsp3(2720-8554) 810-817

2 113-122 PRRARSVRYP linker 1-10

2 123-132 EGSVRVVTTF nsp4(8555-10054) 207-216

2 133-142 PRRARSVRYP linker 1-10

2 143-155 QCVQLHNDILLAK nsp7(11843-12091) 31-43

2 156-165 PRRARSVRYP linker 1-10

2 166-180 GETFVTHSKGLYRKC nsp2(806-2719) 526-540

2 181-190 PRRARSVRYP linker 1-10

2 191-205 FSGYLKLTDNVYIKN nsp3(2720-8554) 210-224

2 206-215 PRRARSVRYP linker 1-10

2 216-225 GEVPVSIINN endoRNAse(19621 -20658) 20-29

2 226-235 PRRARSVRYP linker 1-10

2 236-260 KVKPTVVVNAANVYLKHGGGVAGAL nsp3(2720-8554) 233-257

2 261 -270 PRRARSVRYP linker 1-10

2 271 -285 TKYLVQQESPFVMMS nsp3(2720-8554) 976-990

2 286-295 PRRARSVRYP linker 1-10

2 296-307 GDVVAIDYKHYT nsp3(2720-8554) 1147-1158

2 308-317 PRRARSVRYP linker 1-10

2 318-325 LMVVIPDY nsp8(12092-12685) 128-135

2 326-335 PRRARSVRYP linker 1-10

2 336-352 KHWPQIAQFAPSASAFF nucleocapsid_phosphoprotein(28274-29533) 299-315

2 353-362 PRRARSVRYP linker 1-10

2 363-376 SVGKFCLEASFNYL nsp3(2720-8554) 1387-1400

2 377-386 PRRARSVRYP linker 1-10

2 387-397 ITNCVKMLCTH nsp10(13025-13441) 38-48

2 398-407 PRRARSVRYP linker 1-10

2 408-418 ASCCLYCRCHI nsp10(13025-13441) 71-81

2 419-428 PRRARSVRYP linker 1-10

2 429-451 FGGCVFSYVGCHNKCAYWVPRAS nsp2(806-2719) 226-248

2 452-461 PRRARSVRYP linker 1-10

2 462-496 HEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFV RNA-dependent_RNA_polymerase(13442-

13468+13468-16236) 810-844

2 497-506 PRRARSVRYP linker 1-10

2 507-520 FGTVYEKLKPVLDW nsp2(806-2719) 437-450

2 521 -530 PRRARSVRYP linker 1-10

2 531-538 EHIVYGDF endoRNAse(19621 -20658) 233-240

2 539-548 PRRARSVRYP linker 1-10

2 549-566 KILNNLGVDIAANTVIWD endoRNAse(19621 -20658) 70-87

2 567-576 PRRARSVRYP linker 1-10

2 577-586 LAWPLIVTAL nsp8(12092-12685) 180-189

2 587-596 PRRARSVRYP linker 1-10

2 597-610 LSPVALRQMSCAAG nsp9(12686-13024) 4-17

2 611-620 PRRARSVRYP linker 1-10

2 621-632 YAKPFLNKVVST nsp3(2720-8554) 1323-1334

2 633-642 PRRARSVRYP linker 1-10

2 643-650 TFSVLACY 3C-like_proteinase(10055-10972) 111-118

2 651-660 PRRARSVRYP linker 1-10

2 661-668 VAFNVVNK endoRNAse(19621 -20658) 5-12

2 669-678 PRRARSVRYP linker 1-10 2 679-715 ARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYV RNA-dependent_RNA_polymerase(13442-

13468+13468-16236) 639-675

2 716-725 PRRARSVRYP linker MO

2 726-741 LVDFQVTIAEILLIIM ORF6_protein(27202-27387) 4-19

2 742-751 PRRARSVRYP linker 1-10

2 752-761 CPRHVICTSE 3C-like_proteinase(10055-10972) 38-47

2 762-771 PRRARSVRYP linker 1-10

2 772-787 LLKDCPAVAKHDFFKF RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 89-104

2 788-797 PRRARSVRYP linker 1-10

2 798-813 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 331-346

2 814-823 PRRARSVRYP linker 1-10

2 824-843 RAKHYVYIGDPAQLPAPRTL helicase(16237-18039) 392-411

2 844-853 PRRARSVRYP linker 1-10

2 854-863 TLPVNVAFEL endoRNAse(19621 -20658) 48-57

2 864-873 PRRARSVRYP linker 1-10

2 874-888 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 396-410

2 889-898 PRRARSVRYP linker 1-10

2 899-906 SVELKHFF RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 434-441

2 907-916 PRRARSVRYP linker 1-10

2 917-928 FNCYFPLQSYGF surface_glycoprotein(21563-25384) 486-497

2 929-938 PRRARSVRYP linker 1-10

2 939-952 FFSNVTWFHAIHVS surface_glycoprotein(21563-25384) 58-71

2 953-962 PRRARSVRYP linker 1-10

2 963-974 EVFAQVKQIYKT surface_glycoprotein(21563-25384) 780-791

2 975-984 PRRARSVRYP linker 1-10

2 985-994 YIAQVDVVNF 0RF10_protein(29558-29674) 26-35

2 995-1004 PRRARSVRYP linker 1-10

2 1005-1014 LLHKPIVWHV nsp3(2720-8554) 1167-1176

2 1015-1024 PRRARSVRYP linker 1-10

2 1025-1042 YQDVNCTEVPVAIHADQL surface_glycoprotein(21563-25384) 612-629

2 1043-1052 PRRARSVRYP linker 1-10

2 1053-1076 SELVIGAVILRGHLRIAGHHLGRC membrane_glycoprotein(26523-27191 ) 136-159

2 1077-1086 PRRARSVRYP linker 1-10

2 1087-1094 TDAVDCAL surface_glycoprotein(21563-25384) 286-293

2 1095-1104 PRRARSVRYP linker 1-10

1105-1112 SLIDLQEL surface_glycoprotein(21563-25384) 1196-1203

1113-1122 PRRARSVRYP linker 1-10

1123-1135 RTCCLCDRRATCF 3’-to-5’_exonuclease(18040-19620) 205-217

1136-1145 PRRARSVRYP linker 1-10

1146-1153 FVKATCEF nsp2(806-2719) 156-163

1154-1163 PRRARSVRYP linker 1-10

1164-1179 NFLVQAGNVQLRVIGH 3C-like_proteinase(10055-10972) 65-80

1180-1189 PRRARSVRYP linker 1-10

1190-1197 EVTPSGTW nucleocapsid_phosphoprotein(28274-29533) 323-330

1198-1207 PRRARSVRYP linker 1-10

1208-1217 FKHLIPLMYK 3’-to-5’_exonuclease(18040-19620) 146-155

1218-1227 PRRARSVRYP linker 1-10

1228-1255 SIPCSVCLSGLDSLDTYPSLETIQITIS nsp3(2720-8554) 1467-1494

1256-1265 PRRARSVRYP linker 1-10

1266-1273 ISDYDYYR RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 450-457

1274-1283 PRRARSVRYP linker 1-10

1284-1297 FQTLLALHRSYLTPsurface_glycoprotein(21563-25384) 238-251

1298-1307 PRRARSVRYP linker 1-10

1308-1315 NHTGVVGE nsp2(806-2719) 254-261

1316-1325 PRRARSVRYP linker 1-10

1326-1342 AAAYYVGYLQPRTFLLK surface_glycoprotein(21563-25384) 262-278

1343-1352 PRRARSVRYP linker 1-10

1353-1360 STFKCYGV surface_glycoprotein(21563-25384) 375-382

1361-1370 PRRARSVRYP linker 1-10

1371-1385 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(13442-13468+13468-16236)

368-382

1 -28 RLCAYCCNIVNVSLVKPSFYVYSRVKNL envelope_protein(26245-26472) 38-65

29-38 PRRARSVRYP linker 1-10

39-52 MPVCVETKAIVSTI nsp3(2720-8554) 571-584

53-62 PRRARSVRYP linker 1-10

63-74 KTTEVVGDIILK nsp3(2720-8554) 1249-1260

75-84 PRRARSVRYP linker 1-10

85-102 AFKLNIKLLGVGGKPCIK nsp6(10973-11842) 268-285 103-112 PRRARSVRYP linker 1-10

113-120 LLLDQALV nsp3(2720-8554) 1752-1759 121-130 PRRARSVRYP linker 1-10

131-150 ANSIVCRFDTRVLSNLNLPG 3’-to-5’_exonuclease(18040-19620) 394-413

151-160 PRRARSVRYP linker 1-10 161-172 LKKLKKSLNVAK nsp8(12092-12685) 35-46 173-182 PRRARSVRYP linker 1-10 183-192 KESVQTFFKL nsp2(806-2719) 492-501 193-202 PRRARSVRYP linker 1-10 203-225 GEAVKTQFNYYKKVDGVVQQLPE endoRNAse(19621 -20658) 169-191 226-235 PRRARSVRYP linker 1-10 236-245 IGDCATVHTA 2’-O-ribose_methyltransferase(20659-21552) 112-121 246-255 PRRARSVRYP linker 1-10 256-265 AQYELKHGTF nsp3(2720-8554) 994-1003 266-275 PRRARSVRYP linker 1-10

276-286 HNLAKHCLHVV nsp3(2720-8554) 290-300

287-296 PRRARSVRYP linker 1-10

297-333 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVF helicase(16237-18039) 54-90

334-343 PRRARSVRYP linker 1-10

344-370 NAACRKVQHMVVKAALLADKFPVLHDI3’-to-5’_exonuclease(18040-19 620) 306-332

371-380 PRRARSVRYP linker 1-10

381-391 VEEVLSEARQH leader_protein(266-805) 35-45

392-401 PRRARSVRYP linker 1-10

402-413 IEVQGYKSVNIT nsp3(2720-8554) 13-24

414-423 PRRARSVRYP linker 1-10

424-431 NYQCGHYK nsp3(2720-8554) 1012-1019

432-441 PRRARSVRYP linker 1-10

442-453 TVNVLAWLYAAV 3C-like_proteinase(10055-10972) 201-212

454-463 PRRARSVRYP linker 1-10

464-479 SEFSSLPSYAAFATAQ nsp8(12092-12685) 4-19 480-489 PRRARSVRYP linker 1-10 490-511 LPRVFSAVGNICYTPSKLIEYT nsp4(8555-10054) 122-143 512-521 PRRARSVRYP linker 1-10 522-536 SVLLSMQGAVDINKL nsp7(11843-12091) 57-71 537-546 PRRARSVRYP linker 1-10 547-560 CGACIRRPFLCCKC helicase(d16237-18039)) 16-29 561 -570 PRRARSVRYP linker 1-10

571-594 DPIHSLRVCVDTVRTNVYLAVFDK nsp3(2720-8554) 339-362

595-604 PRRARSVRYP linker 1-10

605-615 SEAFLIGCNYL 2’-O-ribose_methyltransferase(20659-21552) 202-212 616-625 PRRARSVRYP linker 1-10 626-641 DQVILLNKHIDAYKTF nucleocapsid_phosphoprotein(28274-29533) 348-363 642-651 PRRARSVRYP linker 1-10 652-659 E H VQ I H Tl OR F3a_prote in (25393-26220) 242-249 660-669 PRRARSVRYP linker 1-10

670-696 AKYTQLCQYLNTLTLAVPYNMRVIHFG 2’-O-ribose_methyltransferase(20659-21552) 45-71

697-706 PRRARSVRYP linker 1-10

707-726 GYLPQNAVVKIYCPACHNSE nsp2(806-2719) 178-197

727-736 PRRARSVRYP linker 1-10

737-753 IVKFISTCACEIVGGQI nsp2(806-2719) 468-484

754-763 PRRARSVRYP linker 1-10

764-775 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 231-242

776-785 PRRARSVRYP linker 1-10

786-810 DDRCILHCANFNVLFSTVFPPTSFG RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 303-327

811-820 PRRARSVRYP linker 1-10

821-846 QNSVRVLQKAAITILDGISQYSLRLI nsp2(806-2719) 376-401

847-856 PRRARSVRYP linker 1-10

857-876 VVIKVCEFQFCNDPFLGVYY surface_glycoprotein(21563-25384) 126-145 877-886 PRRARSVRYP linker 1-10

887-897 IEELFYSYATH 3’-to-5’_exonuclease(18040-19620) 363-373

898-907 PRRARSVRYP linker 1-10

908-939 VDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQ surface_glycoprotein(21563-25384) 1040-1071

940-949 PRRARSVRYP linker 1-10 950-967 PNFVFPLNSIIKTIQPRV nsp2(806-2719) 91-108 968-977 PRRARSVRYP linker 1-10 978-993 NDLCFTNVYADSFVIR surface_glycoprotein(21563-25384) 388-403 994-1003 PRRARSVRYP linker 1-10 1004-1012 VLGSLAATV nsp9(12686-13024) 102-110

1013-1022 PRRARSVRYP linker 1-10

1023-1032 FEYVSQPFLM surface_glycoprotein(21563-25384) 168-177

1033-1042 PRRARSVRYP linker 1-10 1043-1062 KGFCDLKGKYVQIPTTCAND nsp10(13025-13441) 87-106

1063-1072 PRRARSVRYP linker 1-10

1073-1092 INLVRDLPQGFSALEPLVDL surface_glycoprotein(21563-25384) 210-229

1093-1102 PRRARSVRYP linker 1-10

1103-1120 YADVFHLYLQYIRKLHDE RNA-dependent_RNA_polymerase(13442-13468+13468-16236)

877-894

1121-1130 PRRARSVRYP linker 1-10

1131-1140 KQYGDCLGDI surface_glycoprotein(21563-25384) 835-844

1141-1150 PRRARSVRYP linker 1-10

1151-1160 GVITHDVSSA helicase(16237-18039) 478-487

1161-1170 PRRARSVRYP linker 1-10

1171-1180 GPKVKYLYFI nsp9(12686-13024) 82-91

1181-1190 PRRARSVRYP linker 1-10

1191-1201 SPDAVTAYNGY nsp3(2720-8554) 661-671

1202-1211 PRRARSVRYP linker 1-10

1212-1225 ARSVASQSIIAYTM surface_glycoprotein(21563-25384) 684-697

1226-1235 PRRARSVRYP linker 1-10

1236-1246 VLPFNDGVYFA surface_glycoprotein(21563-25384) 83-93

1247-1256 PRRARSVRYP linker 1-10

1257-1271 AQSFLNRVCGVSAAR RNA-dependent_RNA_polymerase(13442-13468+13468-16236)

4-18

1272-1281 PRRARSVRYP linker 1-10 1282-1289 AEVQIDRL surface_glycoprotein(21563-25384) 989-996 1290-1299 PRRARSVRYP linker 1-10 1300-1307 DLSVVNAR helicase(16237-18039) 383-390 1308-1317 PRRARSVRYP linker 1-10 1318-1334 FRELGVVHNQDVNLHSS RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 348-364 1335-1344 PRRARSVRYP linker 1-10 1345-1356 NFRVQPTESIVR surface_glycoprotein(21563-25384) 317-328 1357-1366 PRRARSVRYP linker 1-10 1367-1387 CSARHINAQVAKSHNIALIWN nsp3(2720-8554) 1876-1896 1 -10 EQYVFCTVNA helicase(16237-18039) 353-362 11-20 PRRARSVRYP linker 1-10 21-32 TRAKVGILCIMS helicase(16237-18039) 566-577 33-42 PRRARSVRYP linker 1-10 43-54 FKLASHMYCSFY nsp3(2720-8554) 96-107 55-64 PRRARSVRYP linker 1-10 65-72 SRELKVTF nsp3(2720-8554) 1134-1141 73-82 PRRARSVRYP linker 1-10 83-100 DKACPLIAAVITREVGFV nsp4(8555-10054) 85-102

101-110 PRRARSVRYP linker 1-10 111-120 LEGSVAYESL nsp4(8555-10054) 176-185 121-130 PRRARSVRYP linker 1-10 131-140 GTNLPLQLGF 3’-to-5’_exonuclease(18040-19620) 102-111 141-150 PRRARSVRYP linker 1-10 151-158 ADAVIKTL nsp3(2720-8554) 58-65 159-168 PRRARSVRYP linker 1-10 169-177 RSVYPVASP nsp2(806-2719) 121-129 178-187 PRRARSVRYP linker 1-10

188-217 SDIDITFLKKDAPYIVGDVVQEGVLTAVVI nsp3(2720-8554) 454-483

218-227 PRRARSVRYP linker 1-10 228-238 TEISFMLWCKD endoRNAse(19621 -20658) 325-335 239-248 PRRARSVRYP linker 1-10 249-256 ARDLSLQF nsp3(2720-8554) 1652-1659 257-266 PRRARSVRYP linker 1-10

267-279 KLALGGSVAIKIT 2’-O-ribose_methyltransferase(20659-21552) 160-172

280-289 PRRARSVRYP linker 1-10

290-299 FDVVRQCSGV 3C-like_ pproteinased(10055-10972)) 294-303

300-309 PRRARSVRYP linker 1-10 310-319 RHSLSHFVNL nsp3(2720-8554) 1697-1706 320-329 PRRARSVRYP linker 1-10 330-337 KAVFISPY helicase(16237-18039) 508-515 338-347 PRRARSVRYP linker 1-10 348-368 LGVLVPHVGEIPVAYRKVLLR leader_protein(266-805) 104-124 369-378 PRRARSVRYP linker 1-10

379-394 IKPVTYKLDGVVCTEI nsp3(2720-8554) 1059-1074

395-404 PRRARSVRYP linker 1-10

405-412 SLWVYKQF 3’-to-5’_exonuclease(18040-19620) 507-514

413-422 PRRARSVRYP linker 1-10 4 423-436 RLTLGVYDYLVSTQ nsp6(10973-11842) 236-249

4 437-446 PRRARSVRYP linker 1-10

4 447-469 ELYHYQECVRGTTVLLKEPCSSG ORF7a_protein(27394-27759) 16-38

4 470-479 PRRARSVRYP linker 1-10

4 480-506 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(806-2719) 300-326

4 507-516 PRRARSVRYP linker 1-10

4 517-546 CQVHGNAHVASCDAIMTRCLAVHECFVKRV 3’-to-5’_exonuclease(18040-19620) 261-290

4 547-556 PRRARSVRYP linker 1-10

4 557-577 VKDCVVLHSYFTSDYYQLYST ORF3a_protein(25393-26220) 197-217

4 578-587 PRRARSVRYP linker 1-10

4 588-600 YTELEPPCRFVTD nsp9(12686-13024) 66-78

4 601-610 PRRARSVRYP linker 1-10

4 611-631 QPYRVVVLSFELLHAPATVCG surface_glycoprotein(21563-25384) 506-526

4 632-641 PRRARSVRYP linker 1-10

4 642-651 PRWYFYYLGT nucleocapsid_phosphoprotein(28274-29533) 106-115

4 652-661 PRRARSVRYP linker 1-10

4 662-698 ALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQE ORF7a_protein(27394-27759) 55-91

4 699-708 PRRARSVRYP linker 1-10

4 709-723 VEHVTFFIYNKIVDE ORF3a_protein(25393-26220)225-239

4 724-733 PRRARSVRYP linker 1-10

4 734-757 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(27894-28259) 95-118

4 758-767 PRRARSVRYP linker 1-10

4 768-779 ALGKLQDVVNQN surface_glycoprotein(21563-25384) 944-955

4 780-789 PRRARSVRYP linker 1-10

4 790-846 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKF helicase(16237-

18039) 290-346

4 847-856 PRRARSVRYP linker 1-10

4 857-874 ANSVFNICQAVTANVNAL RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 690-707

4 875-884 PRRARSVRYP linker 1-10

4 885-900 VREVLSDRELHLSWEV helicase(16237-18039) 154-169

4 901-910 PRRARSVRYP linker 1-10

4 911-918 FNSVCRLM helicase(16237-18039) 422-429

4 919-928 PRRARSVRYP linker 1-10

4 929-936 SAS Kl ITL O R F3a_prote in (25393-26220) 58-65

4 937-946 PRRARSVRYP linker 1-10

4 947-959 VEGCMVQVTCGTT 3C-like_proteinase(10055-10972) 13-25

4 960-969 PRRARSVRYP linker 1-10

4 970-1013 KSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(18040-19620) 433-476

4 1014-1023 PRRARSVRYP linker 1-10

4 1024-1038 EVPANSTVLSFCAFA nsp10(13025-13441) 6-20

4 1039-1048 PRRARSVRYP linker 1-10

4 1049-1065 LTQYNRYLALYNKYKYF nsp4(8555-10054) 438-454

4 1066-1075 PRRARSVRYP linker 1-10

4 1076-1083 NNLVVMAY nsp2(806-2719) 413-420

4 1084-1093 PRRARSVRYP linker 1-10

4 1094-1101 CSCGSCCK surface_glycoprotein(21563-25384) 1248-1255

4 1102-1111 PRRARSVRYP linker 1-10

4 1112-1119 DSYFVVKR RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 67-74

4 1120-1129 PRRARSVRYP linker 1-10

4 1130-1139 RQALLKTVQF RNA-dependent_RNA_polymerase(13442-13468+13468-16236) 183-192

4 1140-1149 PRRARSVRYP linker 1-10

4 1150-1160 AALALLLLDRL nucleocapsid_phosphoprotein(28274-29533) 217-227

4 1161-1170 PRRARSVRYP linker 1-10

4 1171-1180 SVLNDILSRL surface_glycoprotein(21563-25384) 975-984

4 1181-1190 PRRARSVRYP linker 1-10

4 1191-1210 YLFQHANLDSCKRVLNVVCKnsp3(2720-8554) 916-935

4 1211-1220 PRRARSVRYP linker 1-10

4 1221-1233 GVNLVAVPTGYVD 3’-to-5’_exonuclease(18040-19620) 114-126

4 1234-1243 PRRARSVRYP linker 1-10

4 1244-1251 I S E H DYQ I OR F3a_prote in (25393-26220) 179-186

4 1252-1261 PRRARSVRYP linker 1-10

4 1262-1282 KSILSPLYAFASEAARVVRSI nsp2(806-2719) 347-367

4 1283-1292 PRRARSVRYP linker 1-10

4 1293-1300 FTGCVIAW surface_glycoprotein(21563-25384) 429-436

4 1301-1310 PRRARSVRYP linker 1-10

4 1311-1322 MPLKAPKEIIFL nsp2(806-2719) 551-562

4 1323-1332 PRRARSVRYP linker 1-10

4 1333-1346 WNVVRIKIVQMLSD 3’-to-5’_exonuclease(18040-19620) 159-172

4 1347-1356 PRRARSVRYP linker 1-10 4 1357-1382 KNPLLYDANYFLCWHTNCYDYCIPYN ORF3a_protein(25393-26220) 136-161

4 1383-1392 PRRARSVRYP linker 1-10

4 1393-1408 LQSLQTYVTQQLIRAA surface_glycoprotein(21563-25384) 1001-1016

In certain embodiments, the vaccine comprises or expresses at least one of the contigs concatemers of epitopes from SARS-CoV-2 with intervening linker sequences set forth in Table 2 (also see Figure 13). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 2 concatemer P ^os J ⁿ _ ^conc atemer epitope gene P ^os J ⁿ _gene

1 1-24 TYASALWEIQQVVDADSKIVQLSE nsp8(12092-12685) 148-171

1 25-34 PRRARSVRYP linker 1-10

1 35-44 FDVVRQCSGV 3C-like_proteinase(10055-10972) 294-303

1 45-54 PRRARSVRYP linker 1-10

1 55-62 LMVVIPDY nsp8(12092-12685) 128-135

1 63-72 PRRARSVRYP linker 1-10

1 73-90 KILNNLGVDIAANTVIWD endoRNAse(19621 -20658) 70-87

1 91-100 PRRARSVRYP linker 1-10

1 101-111 TKVDGVDVELF endoRNAse(19621 -20658) 33-43

1 112-121 PRRARSVRYP linker 1-10

1 122-130 VLGSLAATV nsp9(12686-13024) 102-110

1 131-140 PRRARSVRYP linker 1-10

1 141-148 CSCGSCCK surface_glycoprotein(21563-25384) 1248-1255

1 149-158 PRRARSVRYP linker 1-10

1 159-169 VLPFNDGVYFA surface_glycoprotein(21563-25384) 83-93

1 170-179 PRRARSVRYP linker 1-10

1 180-193 FFSNVTWFHAIHVS surface_glycoprotein(21563-25384) 58-71

1 194-203 PRRARSVRYP linker 1-10

1 204-211 SQDLSVVS endoRNAse(19621 -20658) 308-315

1 212-221 PRRARSVRYP linker 1-10

1 222-232 SEAFLIGCNYL 2’-O-ribose_methyltransferase(20659-21552) 202-212

1 233-242 PRRARSVRYP linker 1-10

1 243-250 AEVQIDRL surface_glycoprotein(21563-25384) 989-996

1 251 -260 PRRARSVRYP linker 1-10

1 261-272 GSNVFQTRAGCL surface_glycoprotein(21563-25384) 639-650

1 273-282 PRRARSVRYP linker 1-10

1 283-310 IKDLPKEITVATSRTLSYYKLGASQRVA membrane_glycoprotein(26523-27191 ) 161-188

1 311-320 PRRARSVRYP linker 1-10

1 321-328 TDAVDCAL surface_glycoprotein(21563-25384) 286-293

1 329-338 PRRARSVRYP linker 1-10

1 339-350 FNCYFPLQSYGF surface_glycoprotein(21563-25384) 486-497

1 351 -360 PRRARSVRYP linker 1-10

1 361-370 GPKVKYLYFI nsp9(12686-13024) 82-91

1 371 -380 PRRARSVRYP linker 1-10

1 381-390 FEYVSQPFLM surface_glycoprotein(21563-25384) 168-177

1 391 -400 PRRARSVRYP linker 1-10

1 401-416 LQSLQTYVTQQLIRAA surface_glycoprotein(21563-25384) 1001-1016

1 417-426 PRRARSVRYP linker 1-10

1 427-440 TSACVLAAECTI FK nsp4(8555-10054) 147-160

1 441 -450 PRRARSVRYP linker 1-10

1 451-458 TSCCSCLK surface_glycoprotein(21563-25384) 1238-1245

1 459-468 PRRARSVRYP linker 1-10

1 469-496 RLCAYCCNIVNVSLVKPSFYVYSRVKNL envelope_protein(26245-26472) 38-65

1 497-506 PRRARSVRYP linker 1-10

1 507-516 TPLIQPIGAL nsp4(8555-10054) 269-278

1 517-526 PRRARSVRYP linker 1-10 527-538 ALGKLQDVVNQN surface_glycoprotein(21563-25384) 944-955

539-548 PRRARSVRYP linker 1-10

549-556 FTGCVIAW surface_glycoprotein(21563-25384) 429-436

557-566 PRRARSVRYP linker 1-10

567-579 YTELEPPCRFVTD nsp9(12686-13024) 66-78 580-589 PRRARSVRYP linker 1-10 590-603 LSPVALRQMSCAAG nsp9(12686-13024) 4-17 604-613 PRRARSVRYP linker 1-10

614-622 IQLSSYSLF 2’-O-ribose_methyltransferase(20659-21552) 237-245 1-10 EGSVRVVTTF nsp4(8555-10054) 207-216 11-20 PRRARSVRYP linker 1-10 21-36 SEFSSLPSYAAFATAQ nsp8(12092-12685) 4-19 37-46 PRRARSVRYP linker 1-10 47-54 VAFNVVNK endoRNAse(19621 -20658) 5-12 55-64 PRRARSVRYP linker 1-10 65-85 LGVLVPHVGEIPVAYRKVLLR leader_protein(266-805) 104-124 86-95 PRRARSVRYP linker 1-10 96-105 ARDLICAQKF surface_glycoprotein(21563-25384) 846-855

106-115 PRRARSVRYP linker 1-10 116-127 LNVPLHGTILTR membrane_glycoprotein(26523-27191) 120-131 128-137 PRRARSVRYP linker 1-10 138-147 SVLNDILSRL surface_glycoprotein(21563-25384) 975-984 148-157 PRRARSVRYP linker 1-10 158-168 AALALLLLDRL nucleocapsid_phosphoprotein(28274-29533) 217-227 169-178 PRRARSVRYP linker 1-10 179-186 EVTPSGTW nucleocapsid_phosphoprotein(28274-29533) 323-330 187-196 PRRARSVRYP linker 1-10 197-204 AALQIPFA surface_glycoprotein(21563-25384) 892-899 205-214 PRRARSVRYP linker 1-10 215-232 YQDVNCTEVPVAIHADQL surface_glycoprotein(21563-25384) 612-629 233-242 PRRARSVRYP linker 1-10 243-252 KQYGDCLGDI surface_glycoprotein(21563-25384) 835-844 253-262 PRRARSVRYP linker 1-10 263-275 QCVQLHNDILLAK nsp7(11843-12091) 31-43 276-285 PRRARSVRYP linker 1-10 286-295 LAWPLIVTAL nsp8(12092-12685) 180-189 296-305 PRRARSVRYP linker 1-10 306-323 HVQLSLPVLQVRDVLVRG leader_protein(266-805) 13-30 324-333 PRRARSVRYP linker 1-10 334-349 LVDFQVTIAEILLIIM ORF6_protein(27202-27387) 4-19 350-359 PRRARSVRYP linker 1-10 360-367 SLIDLQEL surface_glycoprotein(21563-25384) 1196-1203 368-377 PRRARSVRYP linker 1-10 378-409 VDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQ surface_glycoprotein(21563-25384) 1040-1071 410-419 PRRARSVRYP linker 1-10 420-429 LEGSVAYESL nsp4(8555-10054) 176-185 430-439 PRRARSVRYP linker 1-10 440-466 AKYTQLCQYLNTLTLAVPYNMRVIFIFG 2’-O-ribose_methyltransferase(20659-21552) 45-71 467-476 PRRARSVRYP linker 1-10 477-513 ALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQE ORF7a_protein(27394-27759) 55-91 514-523 PRRARSVRYP linker 1-10 524-534 ITNCVKMLCTH nsp10(13025-13441) 38-48 535-544 PRRARSVRYP linker 1-10 545-557 YTVSCLPFTINCQ ORF8_protein(27894-28259) 79-91

558-567 PRRARSVRYP linker 1-10

568-591 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(27894-28259) 95-118 592-601 PRRARSVRYP linker 1-10 602-614 KLALGGSVAIKIT 2’-O-ribose_methyltransferase(20659-21552) 160-172

615-624 PRRARSVRYP linker 1-10 625-636 LKKLKKSLNVAK nsp8(12092-12685) 35-46 1-15 SVLLSMQGAVDINKL nsp7(11843-12091 ) 57-71 16-25 PRRARSVRYP linker 1-10 26-58 YEPLTQDHVDILGPLSAQTGIAVLDMCASLKEL 3C-like_proteinase(10055-10972) 239-271 59-68 PRRARSVRYP linker 1-10 69-84 NDLCFTNVYADSFVIR surface_glycoprotein(21563-25384) 388-403 85-94 PRRARSVRYP linker 1-10 95-110 DQVILLNKHIDAYKTF nucleocapsid_phosphoprotein(28274-29533) 348-363 111-120 PRRARSVRYP linker 1-10 121-132 EVFAQVKQIYKT surface_glycoprotein(21563-25384) 780-791 133-142 PRRARSVRYP linker 1-10 143-162 VVIKVCEFQFCNDPFLGVYY surface_glycoprotein(21563-25384) 126-145 163-172 PRRARSVRYP linker 1-10 173-187 EILDITPCSFGGVSV surface_glycoprotein(21563-25384) 583-597 188-197 PRRARSVRYP linker 1-10 198-207 IGDCATVHTA 2’-O-ribose_methyltransferase(20659-21552) 112-121 208-217 PRRARSVRYP linker 1-10 218-232 SDVLYQPPQTSITSA nsp4(8555-10054) 483-497 233-242 PRRARSVRYP linker 1-10 243-250 YLKLRSDV nsp4(8555-10054) 427-434 251 -260 PRRARSVRYP linker 1-10

261-274 DYDCVSFCYMHHME 3C-like_proteinase(10055-10972) 153-166 275-284 PRRARSVRYP linker 1-10 285-292 GYVMHANY 2’-O-ribose_methyltransferase(20659-21552) 221-228 293-302 PRRARSVRYP linker 1-10 303-312 GEVPVSIINN endoRNAse(19621 -20658) 20-29

313-322 PRRARSVRYP linker 1-10

323-345 TFKVSIWNLDYIINLIIKNLSKSORF6_protein(27202-27387) 21-43

346-355 PRRARSVRYP linker 1-10 356-392 FHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR ORF8_protein(27894-28259) 16-52 393-402 PRRARSVRYP linker 1-10 403-413 ETICAPLTVFF endoRNAse(19621 -20658) 113-123 414-423 PRRARSVRYP linker 1-10 424-439 NFLVQAGNVQLRVIGH 3C-like_proteinase(10055-10972) 65-80 440-449 PRRARSVRYP linker 1-10 450-466 LTQYNRYLALYNKYKYF nsp4(8555-10054) 438-454 467-476 PRRARSVRYP linker 1-10 477-498 LPRVFSAVGNICYTPSKLIEYT nsp4(8555-10054) 122-143 499-508 PRRARSVRYP linker 1-10 509-520 NFRVQPTESIVR surface_glycoprotein(21563-25384) 317-328 521 -530 PRRARSVRYP linker 1-10 531 -545 EVPANSTVLSFCAFA nsp10(13025-13441) 6-20 546-555 PRRARSVRYP linker 1-10 556-569 FQTLLALHRSYLTPsurface_glycoprotein(21563-25384) 238-251 570-579 PRRARSVRYP linker 1-10 580-596 AAAYYVGYLQPRTFLLK surface_glycoprotein(21563-25384) 262-278 597-606 PRRARSVRYP linker 1-10 607-616 PRWYFYYLGT nucleocapsid_phosphoprotein(28274-29533) 106-115 617-626 PRRARSVRYP linker 1-10 627-640 RLTLGVYDYLVSTQ nsp6(10973-11842) 236-249 1-14 ARSVASQSIIAYTM surface_glycoprotein(21563-25384) 684-697 15-24 PRRARSVRYP linker 1-10 25-35 TEISFMLWCKD endoRNAse(19621 -20658) 325-335 36-45 PRRARSVRYP linker 1-10 46-66 QPYRVVVLSFELLHAPATVCG surface_glycoprotein(21563-25384) 506-526 67-76 PRRARSVRYP linker 1-10 77-99 GEAVKTQFNYYKKVDGVVQQLPE endoRNAse(19621 -20658) 169-191 100-109 PRRARSVRYP linker 1-10 110-126 KHWPQIAQFAPSASAFF nucleocapsid_phosphoprotein(28274-29533) 299-315 127-136 PRRARSVRYP linker 1-10 137-144 TFSVLACY 3C-like_proteinase(10055-10972) 111-118 145-154 PRRARSVRYP linker 1-10 155-162 EHIVYGDF endoRNAse(19621 -20658) 233-240 163-172 PRRARSVRYP linker 1-10 173-181 KFPLKLRGT 2’-O-ribose_methyltransferase(20659-21552) 249-257 182-191 PRRARSVRYP linker 1-10 192-199 STFKCYGV surface_glycoprotein(21563-25384) 375-382 200-209 PRRARSVRYP linker 1-10 210-219 LQYGSFCTQL surface_glycoprotein(21563-25384) 754-763 220-229 PRRARSVRYP linker 1-10 230-240 CTLKSFTVEKG surface_glycoprotein(21563-25384) 301-311 241 -250 PRRARSVRYP linker 1-10 251-261 VEEVLSEARQH leader_protein(266-805) 35-45

262-271 PRRARSVRYP linker 1-10 272-289 AFKLNIKLLGVGGKPCIK nsp6(10973-11842) 268-285 290-299 PRRARSVRYP linker 1-10 300-313 DGCVPLNIIPLTTA nsp8(12092-12685) 112-125

314-323 PRRARSVRYP linker 1-10

324-336 VEGCMVQVTCGTT 3C-like_proteinase(10055-10972) 13-25 337-346 PRRARSVRYP linker 1-10

347-366 KGFCDLKGKYVQIPTTCAND nsp10(13025-13441) 87-106 4 367-376 PRRARSVRYP linker 1-10

4 377-396 INLVRDLPQGFSALEPLVDL surface_glycoprotein(21563-25384) 210-229

4 397-406 PRRARSVRYP linker 1-10

4 407-416 CPRHVICTSE 3C-like_proteinase(10055-10972) 38-47

4 417-426 PRRARSVRYP linker 1-10

4 427-444 DKACPLIAAVITREVGFV nsp4(8555-10054) 85-102

4 445-454 PRRARSVRYP linker 1-10

4 455-466 TVNVLAWLYAAV 3C-like_proteinase(10055-10972) 201-212

4 467-476 PRRARSVRYP linker 1-10

4 477-500 SELVIGAVILRGHLRIAGHHLGRC membrane_glycoprotein(26523-27191 ) 136-159

4 501-510 PRRARSVRYP linker 1-10

4 511-533 ELYHYQECVRGTTVLLKEPCSSG ORF7a_protein(27394-27759) 16-38

4 534-543 PRRARSVRYP linker 1-10

4 544-553 TLPVNVAFEL endoRNAse(19621 -20658) 48-57

4 554-563 PRRARSVRYP linker 1-10

4 564-575 ISVTTEILPVSM surface_glycoprotein(21563-25384) 720-731

4 576-585 PRRARSVRYP linker 1-10

4 586-596 ASCCLYCRCHI nsp10(13025-13441) 71-81

4 597-606 PRRARSVRYP linker 1-10

4 607-621 ISNCVADYSVLYNSA surface_glycoprotein(21563-25384) 358-372

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences. In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemer set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 3 concatemer P ^os _i ⁿ _ ^conc atemer epitope gene P ^os J ⁿ _gene

1 1-24 TYASALWEIQQVVDADSKIVQLSE nsp8(12092-12685) 148-171

1 25-34 PRRARSVRYP linker 1-10

1 35-47 QCVQLHNDILLAK nsp7(11843-12091 ) 31 -43

1 48-57 PRRARSVRYP linker 1-10

1 58-70 VEGCMVQVTCGTT 3C-like_proteinase(10055-10972) 13-25

1 71-80 PRRARSVRYP linker 1-10

1 81-97 LTQYNRYLALYNKYKYF nsp4(8555-10054) 438-454

1 98-107 PRRARSVRYP linker 1-10

1 108-117 TPLIQPIGAL nsp4(8555-10054) 269-278

1 118-127 PRRARSVRYP linker 1-10

1 128-135 LMVVIPDY nsp8(12092-12685) 128-135

1 136-145 PRRARSVRYP linker 1-10

1 146-155 TLPVNVAFEL endoRNAse(19621 -20658) 48-57

1 156-165 PRRARSVRYP linker 1-10

1 166-181 DQVILLNKHIDAYKTF nucleocapsid_phosphoprotein(28274-29533) 348-363

1 182-191 PRRARSVRYP linker 1-10

1 192-203 LKKLKKSLNVAK nsp8(12092-12685) 35-46

1 204-213 PRRARSVRYP linker 1-10

1 214-221 EHIVYGDF endoRNAse(19621 -20658) 233-240

1 222-231 PRRARSVRYP linker 1-10

1 232-242 VEEVLSEARQH leader_protein(266-805) 35-45

1 243-252 PRRARSVRYP linker 1-10

1 253-266 DGCVPLNIIPLTTA nsp8(12092-12685) 112-125

1 267-276 PRRARSVRYP linker 1-10

1 277-299 ELYHYQECVRGTTVLLKEPCSSG ORF7a_protein(27394-27759) 16-38

1 300-309 PRRARSVRYP linker 1-10

1 310-319 PRWYFYYLGT nucleocapsid_phosphoprotein(28274-29533) 106-115

1 320-329 PRRARSVRYP linker 1-10

1 330-344 SDVLYQPPQTSITSA nsp4(8555-10054) 483-497

1 345-354 PRRARSVRYP linker 1-10

1 355-378 SELVIGAVILRGHLRIAGHHLGRC membrane_glycoprotein(26523-27191 ) 136-159

1 379-388 PRRARSVRYP linker 1-10

1 389-408 KGFCDLKGKYVQIPTTCAND nsp10(13025-13441) 87-106 409-418 PRRARSVRYP linker 1-10 419-436 AFKLNIKLLGVGGKPCIK nsp6(10973-11842) 268-285 1-10 EGSVRVVTTF nsp4(8555-10054) 207-216 11-20 PRRARSVRYP linker 1-10 21-29 KFPLKLRGT 2’-O-ribose_methyltransferase(20659-21552) 249-257 30-39 PRRARSVRYP linker 1-10 40-49 CPRHVICTSE 3C-like_proteinase(10055-10972) 38-47 50-59 PRRARSVRYP linker 1-10 60-77 DKACPLIAAVITREVGFV nsp4(8555-10054) 85-102 78-87 PRRARSVRYP linker 1-10 88-101 DYDCVSFCYMHHME 3C-like_proteinase(10055-10972) 153-166 102-111 PRRARSVRYP linker 1-10 112-127 NFLVQAGNVQLRVIGH 3C-like_proteinase(10055-10972) 65-80 128-137 PRRARSVRYP linker 1-10 138-146 IQLSSYSLF 2’-O-ribose_methyltransferase(20659-21552) 237-245 147-156 PRRARSVRYP linker 1-10

157-169 KLALGGSVAIKIT 2’-O-ribose_methyltransferase(20659-21552) 160-172 170-179 PRRARSVRYP linker 1-10

180-197 KILNNLGVDIAANTVIWD endoRNAse(19621 -20658) 70-87

198-207 PRRARSVRYP linker 1-10

208-235 IKDLPKEITVATSRTLSYYKLGASQRVA membrane_glycoprotein(26523-27191) 161-188 236-245 PRRARSVRYP linker 1-10 246-266 LGVLVPHVGEIPVAYRKVLLR leader_protein(266-805) 104-124 267-276 PRRARSVRYP linker 1-10 277-286 GEVPVSIINN endoRNAse(19621 -20658) 20-29 287-296 PRRARSVRYP linker 1-10 297-306 LAWPLIVTAL nsp8(12092-12685) 180-189 307-316 PRRARSVRYP linker 1-10 317-328 LNVPLHGTILTR membrane_glycoprotein(26523-27191) 120-131 329-338 PRRARSVRYP linker 1-10 339-346 EVTPSGTW nucleocapsid_phosphoprotein(28274-29533) 323-330 347-356 PRRARSVRYP linker 1-10 357-371 EVPANSTVLSFCAFA nsp10(13025-13441) 6-20 372-381 PRRARSVRYP linker 1-10 382-389 VAFNVVNK endoRNAse(19621 -20658) 5-12 390-399 PRRARSVRYP linker 1-10 400-422 GEAVKTQFNYYKKVDGVVQQLPE endoRNAse(19621 -20658) 169-191 423-432 PRRARSVRYP linker 1-10 433-443 ASCCLYCRCHI nsp10(13025-13441) 71-81 1-15 SVLLSMQGAVDINKL nsp7(11843-12091 ) 57-71 16-25 PRRARSVRYP linker 1-10 26-38 YTELEPPCRFVTD nsp9(12686-13024) 66-78 39-48 PRRARSVRYP linker 1-10 49-62 RLTLGVYDYLVSTQ nsp6(10973-11842) 236-249 63-72 PRRARSVRYP linker 1-10 73-86 LSPVALRQMSCAAG nsp9(12686-13024) 4-17 87-96 PRRARSVRYP linker 1-10 97-107 TEISFMLWCKD endoRNAse(19621 -20658) 325-335

108-117 PRRARSVRYP linker 1-10 118-129 TVNVLAWLYAAV 3C-like_proteinase(10055-10972) 201-212 130-139 PRRARSVRYP linker 1-10 140-157 HVQLSLPVLQVRDVLVRG leader_protein(266-805) 13-30

158-167 PRRARSVRYP linker 1-10 168-180 YTVSCLPFTINCQ ORF8_protein(27894-28259) 79-91

181-190 PRRARSVRYP linker 1-10 191-198 GYVMHANY 2’-O-ribose_methyltransferase(20659-21552) 221-228

199-208 PRRARSVRYP linker 1-10

209-232 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(27894-28259) 95-118 233-242 PRRARSVRYP linker 1-10 243-253 AALALLLLDRL nucleocapsid_phosphoprotein(28274-29533) 217-227 254-263 PRRARSVRYP linker 1-10 264-271 YLKLRSDV nsp4(8555-10054) 427-434 272-281 PRRARSVRYP linker 1-10 282-292 ITNCVKMLCTH nsp10(13025-13441) 38-48 293-302 PRRARSVRYP linker 1-10 303-316 TSACVLAAECTI FK nsp4(8555-10054) 147-160 317-326 PRRARSVRYP linker 1-10 327-335 VLGSLAATV nsp9(12686-13024) 102-110 336-345 PRRARSVRYP linker 1-10 346-353 TFSVLACY 3C-like_proteinase(10055-10972) 111-118 3 354-363 PRRARSVRYP linker 1-10

3 364-400 ALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQE O R F7a_prote in (27394-27759) 55-91

3 401 -410 PRRARSVRYP linker 1-10

3 411 -427 KHWPQIAQFAPSASAFF nucleocapsid_phosphoprotein(28274-29533) 299-315

4 1-10 FDVVRQCSGV 3C-like_proteinase(10055-10972) 294-303 4 11-20 PRRARSVRYP linker 1-10 4 21-47 AKYTQLCQYLNTLTLAVPYNMRVIHFG 2’-O-ribose_methyltransferase(20659-21552) 45-71 4 48-57 PRRARSVRYP linker 1-10 4 58-67 LEGSVAYESL nsp4(8555-10054) 176-185 4 68-77 PRRARSVRYP linker 1-10 4 78-85 SQDLSVVS endoRNAse(19621 -20658) 308-315 4 86-95 PRRARSVRYP linker 1-10 4 96-118 TFKVSIWNLDYIINLIIKNLSKSORF6_protein(27202-27387) 21-43 4 119-128 PRRARSVRYP linker 1-10 4 129-139 ETICAPLTVFF endoRNAse(19621 -20658) 113-123 4 140-149 PRRARSVRYP linker 1-10 4 150-186 FHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR ORF8_protein(27894-28259) 16-52 4 187-196 PRRARSVRYP linker 1-10 4 197-206 IGDCATVHTA 2’-O-ribose_methyltransferase(20659-21552) 112-121 4 207-216 PRRARSVRYP linker 1-10 4 217-227 SEAFLIGCNYL 2’-O-ribose_methyltransferase(20659-21552) 202-212 4 228-237 PRRARSVRYP linker 1-10 4 238-253 LVDFQVTIAEILLIIM ORF6_protein(27202-27387) 4-19 4 254-263 PRRARSVRYP linker 1-10 4 264-274 TKVDGVDVELF endoRNAse(19621 -20658) 33-43 4 275-284 PRRARSVRYP linker 1-10 4 285-317 YEPLTQDHVDILGPLSAQTGIAVLDMCASLKEL 3C-like_proteinase(10055-10972) 239-271 4 318-327 PRRARSVRYP linker 1-10 4 328-349 LPRVFSAVGNICYTPSKLIEYT nsp4(8555-10054) 122-143 4 350-359 PRRARSVRYP linker 1-10 4 360-375 SEFSSLPSYAAFATAQ nsp8(12092-12685) 4-19 4 376-385 PRRARSVRYP linker 1-10 4 386-395 GPKVKYLYFI nsp9(12686-13024) 82-91 4 396-405 PRRARSVRYP linker 1-10 4 406-433 RLCAYCCNIVNVSLVKPSFYVYSRVKNL envelope_protein(26245-26472) 38-65

Depending on the actual embodiment, the number of concatemers can be different. Depending on the actual embodiment, the sequence of the linker can be different. Depending on the actual embodiment, the concatemers can include epitopes derived from viral strains circulating in a specific geographical region or otherwise defined (it should be noted that the country names listed in the following sequences are actually placeholders for viral peptides circulating in more than one country).

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences (and as set forth in Figure 14). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses four of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses five of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below. Table 4 concatemer P ^os J ⁿ _ ^conc atemer epitope gene pos_in_gene

1 1-11 GPKVKYLYFIK nsp9(NC_045512:+:12686-13024) 82-92

1 12-16 ATLQA linker 1-5

1 17-39 TQLYLGGMSYYCKPHKPPISFPL helicase@lceland(NC_045512@lceland:+:16237-18039) 61-83

1 40-44 ATLQA linker 1-5

1 45-68 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-

25384) 205-228

1 69-73 ATLQA linker 1-5

1 74-89 NYTVSCLPFTINCQEP ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259)

78-93

1 90-94 ATLQA linker 1-5

1 95-109 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

1 110-114 ATLQA linker 1-5

1 115-128 TDTVVEHVTFFIYN ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 221-234

1 129-133 ATLQA linker 1-5

1 134-153 RLCAYCCNIVNVS LVKPSFY envelope_protein(NC_045512:+:26245-26472) 38-57

1 154-158 ATLQA linker 1-5

1 159-173 VEHVTFFIYNKIVDE QRF3a_protein(NC_045512:+:25393-26220) 225-239

1 174-178 ATLQA linker 1-5

1 179-187 VLGSLAATV nsp9(NC_045512:+:12686-13024) 102-110

1 188-192 ATLQA linker 1-5

1 193-202 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

1 203-207 ATLQA linker 1-5

1 208-215 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207

1 216-220 ATLQA linker 1-5

1 221-233 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480

1 234-238 ATLQA linker 1-5

1 239-257 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

1 258-262 ATLQA linker 1-5

1 263-278 VREVLSDRELHLSWEV helicase(NC_045512:+: 16237-18039) 154-169

1 279-283 ATLQA linker 1-5

1 284-308 KNPLLYDANYFLCWHTNCYDYCIPY QRF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

136-160

1 309-313 ATLQA linker 1-5

1 314-326 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

1 327-331 ATLQA linker 1-5

1 332-339 VQLRVIGH 3C-like_proteinase(NC_045512:+: 10055-10972) 73-80

1 340-344 ATLQA linker 1-5

1 345-368 TTVAAFHQECSLQLCTQHQPYVVD QRF8_protein@USA(NC_045512@USA:+:27894-28259) 11-34

1 369-373 ATLQA linker 1-5

1 374-385 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

1 386-390 ATLQA linker 1-5

1 391-400 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391-1400

1 401-405 ATLQA linker 1-5

1 406-423 QLALFKGVHFVCNLLLLF QRF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 70-87

1 424-428 ATLQA linker 1-5

1 429-442 APGCDVTDVTQLYL helicase@Aruba(NC_045512@Aruba:+:16237-18039) 52-65

1 443-447 ATLQA linker 1-5

1 448-459 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

1 460-464 ATLQA linker 1-5

1 465-481 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91-107

1 482-486 ATLQA linker 1-5

1 487-499 QCVQLHNDILLAK nsp7(NC_045512:+:11843-12091) 31-43

1 500-504 ATLQA linker 1-5

1 505-524 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

1 525-529 ATLQA linker 1-5

1 530-549 DANYFLCWHTNCYHYCIPYN QRF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220)

142-161

1 550-554 ATLQA linker 1-5

1 555-562 APLIELCV ORF8_protein(NC_045512:+:27894-28259) 55-62

1 563-567 ATLQA linker 1-5

1 568-575 TDVVYRAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 28-35

1 576-580 ATLQA linker 1-5

1 581-595 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

396-410 1 596-600 ATLQA linker 1-5

1 601-620 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942

1 621-625 ATLQA linker 1-5

1 626-648 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

1 649-653 ATLQA linker 1-5

1 654-661 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

1 662-666 ATLQA linker 1-5

1 667-674 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

1 675-679 ATLQA linker 1-5

1 680-693 ITTVAAFHQECSLQ ORF8_protein@Aruba(NC_045512@Aruba:+:27894-28259) 10-23

1 694-698 ATLQA linker 1-5

1 699-707 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129

1 708-712 ATLQA linker 1-5

1 713-727 ALLAVFHSASKIITL ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 51-65

1 728-732 ATLQA linker 1-5

1 733-740 TFSVLACY 3C-like_proteinase(NC_045512:+:10055-10972) 111-118

1 741-745 ATLQA linker 1-5

1 746-763 CANFNVLFSTVFPFTSFG RNA-dependent_RNA_polymerase@Nigeria(NC_045512@Nigeria:+:134 42-

13468+13468-16236) 310-327

1 764-768 ATLQA linker 1-5

1 769-776 YDFAVSKG RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

16236) 420-427

1 777-781 ATLQA linker 1-5

1 782-791 ISEHDYQIGG ORF3a_protein@FrenchGuiana(NC_045512@FrenchGuiana:+:25393-26 220) 179-188

1 792-796 ATLQA linker 1-5

1 797-810 IRNLQHRLYECLYR RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-

13468+13468-16236) 720-733 1 811-815 ATLQA linker 1-5 1 816-825 LAWPLIVTAL nsp8(NC_045512:+:12092-12685) 180-189 1 826-830 ATLQA linker 1-5 1 831-847 LTQYNRYLALYNKYKYF nsp4(NC_045512:+:8555-10054) 438-454 1 848-852 ATLQA linker 1-5 1 853-871 CYDYCIPYNSVTSLIVITS ORF3a_protein@Netherlands(NC_045512@Netherlands:+:25393-2622 0) 153-171

1 872-876 ATLQA linker 1-5 1 877-884 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 67-74 1 885-889 ATLQA linker 1-5 1 890-906 INFVRIIMRLWLCCKCR ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220) 118-134 1 907-911 ATLQA linker 1-5 1 912-926 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319 1 927-931 ATLQA linker 1-5 1 932-946 EVPANSTVLSFCAFA nsp10(NC_045512:+: 13025-13441 ) 6-20 1 947-951 ATLQA linker 1-5 1 952-971 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411 1 972-976 ATLQA linker 1-5 1 977-989 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335 1 990-994 ATLQA linker 1-5 1 995-1008 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608 1 1009-1013 ATLQA linker 1-5 1 1014-1035 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-

25384) 125-146

1 1036-1040 ATLQA linker 1-5 1 1041-1059 ANSVFNICQAVTANVNALL RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 690-708

1 1060-1064 ATLQA linker 1-5

1 1065-1073 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

1 1074-1078 ATLQA linker 1-5

1 1079-1086 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

1 1087-1091 ATLQA linker 1-5

1 1092-1107 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

1 1108-1112 ATLQA linker 1-5

1 1113-1120 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

1 1121-1125 ATLQA linker 1-5

1 1126-1136 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

1 1137-1141 ATLQA linker 1-5

1 1142-1161 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 826-845 1 1162-1166 ATLQA linker 1-5

1 1167-1186 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 209-228 1 1187-1191 ATLQA linker 1-5

1 1192-1206 IPIRASLPFGWLIVG ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220)

35-49

1 1207-1211 ATLQA linker 1-5

1 1212-1225 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

294-307

1 1226-1230 ATLQA linker 1-5

1 1231 -1240 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840

1 1241 -1245 ATLQA linker 1-5

1 1246-1254 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

1 1255-1259 ATLQA linker 1-5

1 1260-1269 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

1 1270-1274 ATLQA linker 1-5

1 1275-1284 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252

1 1285-1289 ATLQA linker 1-5

1 1290-1309 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-

1256

1 1310-1314 ATLQA linker 1-5

1 1315-1330 SLRCGACIRRPFLCCK helicase@Aruba(NC_045512@Aruba:+:16237-18039) 13-28

2 1-17 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

2 18-22 ATLQA linker 1-5

2 23-33 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

1088

2 34-38 ATLQA linker 1-5

2 39-46 WFTALTQH nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 52-59

2 47-51 ATLQA linker 1-5

2 52-79 FTSDYYQLYSTQLSTYTGVEHVTFFIYN ORF3a_protein@Latvia(NC_045512@Latvia:+:25393-

26220) 207-234

2 80-84 ATLQA linker 1-5

2 85-104 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

2 105-109 ATLQA linker 1-5

2 110-117 ISEHDYQI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 179-186

2 118-122 ATLQA linker 1-5

2 123-132 KNTVCTVCGM nsp10(NC_045512:+: 13025-13441 ) 113-122

2 133-137 ATLQA linker 1-5

2 138-158 KLSYGIAIVREVLSDRELHLS helicase@Colombia(NC_045512@Colombia:+:16237-18039) 146-166

2 159-163 ATLQA linker 1-5

2 164-183 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197

2 184-188 ATLQA linker 1-5

2 189-197 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11 -19

2 198-202 ATLQA linker 1-5

2 203-220 DKACPLIAAVITREVGFV nsp4(NC_045512:+:8555-10054) 85-102

2 221-225 ATLQA linker 1-5

2 226-237 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242

2 238-242 ATLQA linker 1-5

2 243-250 SSI VITSV ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 165-172

2 251-255 ATLQA linker 1-5

2 256-263 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

2 264-268 ATLQA linker 1-5

2 269-276 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

2 277-281 ATLQA linker 1-5

2 282-289 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191 ) 180-187

2 290-294 ATLQA linker 1-5

2 295-304 PFTINCQEPK ORF8_protein@lndia(NC_045512@lndia:+:27894-28259) 85-94

2 305-309 ATLQA linker 1-5

2 310-320 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973

2 321-325 ATLQA linker 1-5

2 326-337 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671

2 338-342 ATLQA linker 1-5

2 343-365 YLGGMSYYCKSHKLPISFPLCAN helicase@CostaRica(NC_045512@CostaRica:+:16237-18039)

64-86

2 366-370 ATLQA linker 1-5

2 371-378 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

2 379-383 ATLQA linker 1-5

2 384-434 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

2 435-439 ATLQA linker 1-5

2 440-457 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 470-487

2 458-462 ATLQA linker 1-5 2 463-478 ATVAYF N M VYM PASWV nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 76-91

2 479-483 ATLQA linker 1-5

2 484-498 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

2 499-503 ATLQA linker 1-5

2 504-511 TQALLQRQ nucleocapsid_phosphoprotein@CostaRica(NC_045512@CostaRica:+: 28274-29533) 379-386

2 512-516 ATLQA linker 1-5

2 517-526 LPFTINCQEL ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 84-93

2 527-531 ATLQA linker 1-5

2 532-541 YDANYFLCWH ORF3a_protein(NC_045512:+:25393-26220) 141-150

2 542-546 ATLQA linker 1-5

2 547-556 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

2 557-561 ATLQA linker 1-5

2 562-582 HPNCVNCSDDRCILHCANFNV RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 295-315

2 583-587 ATLQA linker 1-5

2 588-603 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

331-346

2 604-608 ATLQA linker 1-5

2 609-620 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

2 621-625 ATLQA linker 1-5

2 626-648 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

2 649-653 ATLQA linker 1-5

2 654-662 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390

2 663-667 ATLQA linker 1-5

2 668-681 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

2 682-686 ATLQA linker 1-5

2 687-715 FAFACPDGVKHVYQLRARSVSPKLFIRQE ORF7a_protein(NC_045512:+:27394-27759) 63-91

2 716-720 ATLQA linker 1-5

2 721-739 VKDCVVLHSYFTSDYYQLY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 197-215

2 740-744 ATLQA linker 1-5

2 745-756 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

2 757-761 ATLQA linker 1-5

2 762-793 MMFVKHKHAFLCLFLLPSFATVAYFNMVYMPA nsp6@lndonesia(NC_045512@lndonesia:+:10973-11842)

57-88

2 794-798 ATLQA linker 1-5

2 799-806 SDDAVVCF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

16236) 759-766

2 807-811 ATLQA linker 1-5

2 812-819 YLKLRSDV nsp4(NC_045512:+:8555-10054) 427-434

2 820-824 ATLQA linker 1-5

2 825-834 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

2 835-839 ATLQA linker 1-5

2 840-856 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

4-20

2 857-861 ATLQA linker 1-5

2 862-869 FNSVCRLM helicase@Aruba(NC_045512@Aruba:+:16237-18039) 422-429

2 870-874 ATLQA linker 1-5

2 875-888 KFIWPQIAQFAPSAS nucleocapsid_phosphoprotein@Australia(NC_045512@Australia:+: 28274-

29533) 299-312

2 889-893 ATLQA linker 1-5

2 894-906 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

2 907-911 ATLQA linker 1-5

2 912-933 GYQPYRVVVLSFELLHAPATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

2 934-938 ATLQA linker 1-5

2 939-957 QLSLSKGFHFVCNLLLLFV QRF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220) 70-88

2 958-962 ATLQA linker 1-5

2 963-979 INFVRIIMRLWLCLKCR ORF3a_protein@Mozambique(NC_045512@Mozambique:+:25393-26220)

118-134

2 980-984 ATLQA linker 1-5

2 985-993 KLMVVIPDY nsp8(NC_045512:+:12092-12685) 127-135

2 994-998 ATLQA linker 1-5

2 999-1009 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373

2 1010-1014 ATLQA linker 1-5

2 1015-1025 AALALLLLDRL nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533)

217-227

2 1026-1030 ATLQA linker 1-5

2 1031-1044 DYDCVSFCYMHHME 3C-like_proteinase(NC_045512:+:10055-10972) 153-166

2 1045-1049 ATLQA linker 1-5 1050-1057 AWLYAAVI 3C-like_proteinase(NC_045512:+: 10055-10972) 206-213 1058-1062 ATLQA linker 1-5 1063-1075 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329 1076-1080 ATLQA linker 1-5 1081-1103 YALVYFLQSINFVIIIMRLWLCW ORF3a_protein@Denmark(NC_045512@Denmark:+:25393- 26220) 109-131

2 1104-1108 ATLQA linker 1-5

2 1109-1120 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

2 1121-1125 ATLQA linker 1-5

2 1126-1134 IQLSSYSLF 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 237-245

2 1135-1139 ATLQA linker 1-5

2 1140-1149 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021

2 1150-1154 ATLQA linker 1-5

2 1155-1165 ETICAPLTVFF endoRNAse(NC_045512:+:19621 -20658) 113-123

2 1166-1170 ATLQA linker 1-5

2 1171-1184 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 721-734

2 1185-1189 ATLQA linker 1-5 2 1190-1197 FNSVCRFM helicase@Malaysia(NC_045512@Malaysia:+:16237-18039) 422-429 2 1198-1202 ATLQA linker 1-5 2 1203-1212 SSVLHSTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54 2 1213-1217 ATLQA linker 1-5 2 1218-1228 MMFVKHKHAFL nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 57-67 2 1229-1233 ATLQA linker 1-5 2 1234-1242 LKLKDCVMY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 105-113 2 1243-1247 ATLQA linker 1-5 2 1248-1262 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway :+:21563-25384) 129-143

2 1263-1267 ATLQA linker 1-5 2 1268-1279 TRAKVGILCITS helicase@SouthKorea(NC_045512@SouthKorea:+:16237-18039) 566-577 2 1280-1284 ATLQA linker 1-5 2 1285-1292 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293 2 1293-1297 ATLQA linker 1-5 2 1298-1311 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-

25384) 128-141

2 1312-1316 ATLQA linker 1-5

2 1317-1338 LLYDANYFLCWHINCYDYCIPY ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-

26220) 139-160

3 1-14 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

3 15-19 ATLQA linker 1-5

3 20-31 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639

3 32-36 ATLQA linker 1-5

3 37-48 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497

3 49-53 ATLQA linker 1-5

3 54-68 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 680-694

3 69-73 ATLQA linker 1-5

3 74-100 AKYTQLCQYLNTLTLAVPYNMRVIHFG 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 45-71

3 101-105 ATLQA linker 1-5

3 106-115 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895

3 116-120 ATLQA linker 1-5

3 121-133 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131

3 134-138 ATLQA linker 1-5

3 139-146 VVNPVMEP ORF3a_protein(NC_045512:+:25393-26220) 255-262

3 147-151 ATLQA linker 1-5

3 152-173 SQHTMLVKQFDDYVYLPYPDPS RNA- dependent_RNA_polymerase@Estonia(NC_045512@Estonia:+:13442-1 3468+13468-16236) 814-835

3 174-178 ATLQA linker 1-5

3 179-190 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

3 191-195 ATLQA linker 1-5

3 196-207 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24

3 208-212 ATLQA linker 1-5

3 213-223 YCPRHVICTSE 3C-like_proteinase(NC_045512:+: 10055-10972) 37-47

3 224-228 ATLQA linker 1-5

3 229-237 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266

3 238-242 ATLQA linker 1-5

3 243-250 YDFVVSKG RNA-dependent_RNA_polymerase@Japan(NC_045512@Japan:+:13442-1 3468+13468-

16236) 420-427 251-255 ATLQA linker 1-5 256-266 YDKLQFISLEI helicase@SouthAfrica(NC_045512@SouthAfrica:+: 16237-18039) 582-592 3 267-271 ATLQA linker 1-5

3 272-279 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

3 280-284 ATLQA linker 1-5

3 285-295 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006

3 296-300 ATLQA linker 1-5

3 301-316 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

3 317-321 ATLQA linker 1-5

3 322-335 LMNVLTLVYKVYYG nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 139-152

3 336-340 ATLQA linker 1-5

3 341-353 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42

3 354-358 ATLQA linker 1-5

3 359-371 YTELEPPCRFVTD nsp9(NC_045512:+:12686-13024) 66-78

3 372-376 ATLQA linker 1-5

3 377-387 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

3 388-392 ATLQA linker 1-5

3 393-419 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

3 420-424 ATLQA linker 1-5

3 425-432 DVLYQPPQ nsp4(NC_045512:+:8555-10054) 484-491

3 433-437 ATLQA linker 1-5

3 438-453 DKYVRNLQHRLYECLY RNA-dependent_RNA_polymerase@Aruba(NC 045512@Aruba:+:13442-

13468+13468-16236) 717-732

454-458 ATLQA linker 1-5

459-487 TLQCIMLVYCFLGYFCTCYFGLFCLLNRY nsp6@Aruba(NC_045512@Aruba:+: 10973-11842)

203-231

488-492 ATLQA linker 1-5

493-502 TLPVNVAFEL endoRNAse(NC_045512:+:19621 -20658) 48-57

503-507 ATLQA linker 1-5

508-517 ALLAVFHNAS ORF3a_protein@SmallSouthAmerica(NC_045512@SmallSouthAmerica: +:25393-26220)

51-60

518-522 ATLQA linker 1-5

523-536 TDTCVEHVTFFIYNQRF3a_protein@Luxembourg(NC_045512@Luxembourg: +:25393-26220) 221-234

537-541 ATLQA linker 1-5

542-550 APLIELCVD ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 55-63

551-555 ATLQA linker 1-5

556-566 RQALLKTVQFC RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

6236) 183-193

567-571 ATLQA linker 1-5

572-579 DMYSVMLT RNA-dependent_RNA_polymerase@Malaysia(NC_045512@Malaysia:+:1 3442-

13468+13468-16236) 901-908

3 580-584 ATLQA linker 1-5

3 585-599 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 368-382

3 600-604 ATLQA linker 1-5

3 605-617 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

3 618-622 ATLQA linker 1-5

3 623-637 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384) 496-510

3 638-642 ATLQA linker 1-5

3 643-659 GVHFVCNLLLLFVIVYS ORF3a_protein@Malaysia(NC_045512@Malaysia:+:25393-26220) 76-92

3 660-664 ATLQA linker 1-5

3 665-684 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

3 685-689 ATLQA linker 1-5

3 690-705 LMNVLTLFYKVYYGNA nsp6@Chile(NC_045512@Chile:+:10973-11842) 142-157

3 706-710 ATLQA linker 1-5

3 711-733 HQPYVVDDPCPIHFYSKWYIRVG ORF8_protein(NC_045512:+:27894-28259) 28-50

3 734-738 ATLQA linker 1-5

3 739-749 SAPLIELCLDE ORF8_protein@Russia(NC_045512@Russia:+:27894-28259) 54-64

3 750-754 ATLQA linker 1-5

3 755-777 QLALSKGVYFVCNLLLLFVTVYS QRF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 70-92

3 778-782 ATLQA linker 1-5

3 783-814 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

3 815-819 ATLQA linker 1-5

3 820-838 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236

3 839-843 ATLQA linker 1-5

3 844-860 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

877-893

3 861-865 ATLQA linker 1-5

3 866-876 CYTPSKLIEYT nsp4(NC_045512:+:8555-10054) 133-143 3 877-881 ATLQA linker 1-5

3 882-890 GVVQQLPET endoRNAse(NC_045512:+:19621 -20658) 184-192

3 891-895 ATLQA linker 1-5

3 896-915 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610

3 916-920 ATLQA linker 1-5

3 921 -936 SRIIPARARVDCFDKF helicase@Brazil(NC_045512@Brazil:+:16237-18039) 331-346

3 937-941 ATLQA linker 1-5

3 942-953 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

3 954-958 ATLQA linker 1-5

3 959-971 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

3 972-976 ATLQA linker 1-5

3 977-988 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

3 989-993 ATLQA linker 1-5

3 994-1001 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829

3 1002-1006 ATLQA linker 1-5

3 1007-1020 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450

3 1021 -1025 ATLQA linker 1-5

3 1026-1033 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691

3 1034-1038 ATLQA linker 1-5

3 1039-1047 DYYQLYSTQ ORF3a_protein(NC_045512:+:25393-26220) 210-218

3 1048-1052 ATLQA linker 1-5

3 1053-1062 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

743-752

3 1063-1067 ATLQA linker 1-5

3 1068-1078 GEVPVSIINNT endoRNAse(NC_045512:+:19621 -20658) 20-30

3 1079-1083 ATLQA linker 1-5

3 1084-1098 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

354-368

3 1099-1103 ATLQA linker 1-5

3 1104-1121 VTTVIFLARGIVFMCVEY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 179-196

3 1122-1126 ATLQA linker 1-5

3 1127-1146 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 )

205-224

3 1147-1151 ATLQA linker 1-5

3 1152-1159 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

3 1160-1164 ATLQA linker 1-5

3 1165-1175 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

3 1176-1180 ATLQA linker 1-5

3 1181 -1190 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

3 1191 -1195 ATLQA linker 1-5

3 1196-1204 FEHIVYGDF endoRNAse(NC_045512:+:19621 -20658) 232-240

3 1205-1209 ATLQA linker 1-5

3 1210-1224 ALLAVFQSASKIITLORF3a_protein@Bangladesh(NC_045512@Bangladesh :+:25393-26220)

51 -65

3 1225-1229 ATLQA linker 1-5

3 1230-1239 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

3 1240-1244 ATLQA linker 1-5

3 1245-1259 VDTSLSSLKLKDCVM nsp6@Latvia(NC_045512@Latvia:+:10973-11842) 101-115

3 1260-1264 ATLQA linker 1-5

3 1265-1283 ANSVFNICQSVTANVNALL RNA- dependent_RNA_polymerase@Croatia(NC_045512@Croatia:+:13442-1 3468+13468-16236) 690-708

3 1284-1288 ATLQA linker 1-5

3 1289-1296 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

3 1297-1301 ATLQA linker 1-5

3 1302-1311 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348

3 1312-1316 ATLQA linker 1-5

3 1317-1324 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349

3 1325-1329 ATLQA linker 1-5

3 1330-1338 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

4 1 -12 TEISFMLWCKDG endoRNAse(NC_045512:+:19621 -20658) 325-336 4 13-17 ATLQA linker 1-5 4 18-35 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404 4 36-40 ATLQA linker 1-5 4 41-50 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111 4 51 -55 ATLQA linker 1-5 4 56-76 QWNLVIGFLFLTWICLLQFAYmembrane_glycoprotein@Aruba(NC_045512@A ruba:+:26523-27191) 19-39 4 77-81 ATLQA linker 1-5 4 82-102 VMFLARGIVFMCVDYCPI FFI nsp6@Cyprus(NC_045512@Cyprus:+: 10973-11842) 179-199 4 103-107 ATLQA linker 1-5 4 108-115 ETQALPQR nucleocapsid_phosphoprotein@SmallNorthAmerica(NC_045512@Smal lNorthAmerica:+:28274-29533) 378-385

4 116-120 ATLQA linker 1-5

4 121-130 SPGVVNPVME ORF3a_protein@Brazil(NC_045512@Brazil:+:25393-26220) 252-261

4 131-135 ATLQA linker 1-5

4 136-146 ITNCVKMLCTH nsp10(NC_045512:+: 13025-13441 ) 38-48

4 147-151 ATLQA linker 1-5

4 152-171 HYQECVRGTTVLLKEPCSSG QRF7a_protein(NC_045512:+:27394-27759) 19-38

4 172-176 ATLQA linker 1-5

4 177-199 KNPLLYDANYFLCCHTNCYDYCI ORF3a_protein@Senegal(NC_045512@Senegal:+:25393-26220)

136-158

4 200-204 ATLQA linker 1-5

4 205-216 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

4 217-221 ATLQA linker 1-5

4 222-234 SMWALIISVTSNY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 160-172

4 235-239 ATLQA linker 1-5

4 240-247 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

4 248-252 ATLQA linker 1-5

4 253-281 FLYIIKLIFLWLLWPVTLACFVLAAVYRI membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191)

45-73

4 282-286 ATLQA linker 1-5

4 287-295 ASQGLLASI RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-13468+13468-

16236) 771-779

4 296-300 ATLQA linker 1-5

4 301-311 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

4 312-316 ATLQA linker 1-5

4 317-325 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

4 326-330 ATLQA linker 1-5

4 331 -342 SVFQSASKIITL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 54-65

4 343-347 ATLQA linker 1-5

4 348-357 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

4 358-362 ATLQA linker 1-5

4 363-383 HPNCVNCLDDRCILHCANFNV RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 295-315

4 384-388 ATLQA linker 1-5

4 389-398 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

4 399-403 ATLQA linker 1-5

4 404-418 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

4 419-423 ATLQA linker 1-5

4 424-437 TSACVLAAECTI FK nsp4(NC_045512:+:8555-10054) 147-160

4 438-442 ATLQA linker 1-5

4 443-450 SINVANYQ helicase@Mozambique(NC_045512@Mozambique:+:16237-18039) 263-270

4 451-455 ATLQA linker 1-5

4 456-465 EGSVRVVTTF nsp4(NC_045512:+:8555-10054) 207-216

4 466-470 ATLQA linker 1-5

4 471 -495 VLVQSTQWSLFFFFYENAFLPFAMG nsp6@lceland(NC_045512@lceland:+:10973-11842) 24-48

4 496-500 ATLQA linker 1-5

4 501 -533 YEPLTQDHVDILGPLSAQTGIAVLDMCASLKEL 3C-like_proteinase(NC_045512:+: 10055-10972) 239-271

4 534-538 ATLQA linker 1-5

4 539-547 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

4 548-552 ATLQA linker 1-5

4 553-570 YNLLKDCPAVAKHDFFKF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 87-104 4 571-575 ATLQA linker 1-5 4 576-597 TLGVLVPHVGEIPVAYRKVLLR leader_protein(NC_045512:+:266-805) 103-124 4 598-602 ATLQA linker 1-5 4 603-633 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1211-1241

4 634-638 ATLQA linker 1-5 4 639-654 LVDFQVTIAEILLIIM QRF6_protein(NC_045512:+:27202-27387) 4-19 4 655-659 ATLQA linker 1-5 4 660-671 TFKVSIWNLDYI ORF6_protein(NC_045512:+:27202-27387) 21 -32 4 672-676 ATLQA linker 1-5 4 677-686 GVGGKPCIKV nsp6@Aru ba (N C_045512@Aruba:+: 10973-11842) 274-283 4 687-691 ATLQA linker 1-5 4 692-716 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478 4 717-721 ATLQA linker 1-5 4 722-745 LGSLVVRCSFYEDFLEYHDVRVVL O R F8_protein(NC_045512:+: 27894-28259) 95-118 4 746-750 ATLQA linker 1-5 4 751-763 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902 4 764-768 ATLQA linker 1-5

4 769-794 YRLANECAQVLSEMVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 653-678

4 795-799 ATLQA linker 1-5

4 800-807 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

4 808-812 ATLQA linker 1-5

4 813-827 SYFAIGLALYYPSAR helicase@Austria(NC_045512@Austria:+:16237-18039) 289-303

4 828-832 ATLQA linker 1-5

4 833-842 SFKLKDCVMY nsp6@Malaysia(NC_045512@Malaysia:+: 10973-11842) 107-116

4 843-847 ATLQA linker 1-5

4 848-857 PRWYFYYLGT nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 106-115

4 858-862 ATLQA linker 1-5

4 863-899 VAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKC ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 97-133

4 900-904 ATLQA linker 1-5

4 905-916 SVLLSMQGAVDI nsp7(N C_045512 : + : 11843-12091) 57-68

4 917-921 ATLQA linker 1-5

4 922-932 ETTVDIVVFDE helicase@SmallAsia(NC_045512@SmallAsia:+:16237-18039) 365-375

4 933-937 ATLQA linker 1-5

4 938-961 TYASALWEIQQVVDADSKIVQLSE nsp8(NC_045512:+: 12092-12685) 148-171

4 962-966 ATLQA linker 1-5

4 967-977 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

4 978-982 ATLQA linker 1-5

4 983-1005 TTVMFLARGIVFMCVEYCPIFFI nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 177-199

4 1006-1010 ATLQA linker 1-5

4 1011-1018 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

4 1019-1023 ATLQA linker 1-5

4 1024-1031 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478

4 1032-1036 ATLQA linker 1-5

4 1037-1059 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

4 1060-1064 ATLQA linker 1-5

4 1065-1074 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

4 1075-1079 ATLQA linker 1-5

4 1080-1092 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

4 1093-1097 ATLQA linker 1-5

4 1098-1114 VPQEHYVRITGLYPTLN helicase@Aruba(NC_045512@Aruba:+:16237-18039) 241-257

4 1115-1119 ATLQA linker 1-5

4 1120-1144 VLVQSTQWSLFFFLYENAFLPFAMG nsp6@Aruba(NC_045512@Aruba:+:10973-11842)

24-48

4 1145-1149 ATLQA linker 1-5

4 1150-1161 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

810-821

4 1162-1166 ATLQA linker 1-5

4 1167-1185 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384)

607-625

4 1186-1190 ATLQA linker 1-5

4 1191-1210 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 303-322 4 1211-1215 ATLQA linker 1-5

4 1216-1225 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173

4 1226-1230 ATLQA linker 1-5

4 1231-1244 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

4 1245-1249 ATLQA linker 1-5

4 1250-1267 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

125-142

4 1268-1272 ATLQA linker 1-5

4 1273-1295 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278

4 1296-1300 ATLQA linker 1-5

4 1301-1323 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

4 1324-1328 ATLQA linker 1-5

4 1329-1349 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 605-625

5 1-16 YVRITGLYPTLNISYE helicase@SmallNorthAmerica(NC_045512@SmallNorthAmerica:+:162 37-18039)

246-261

5 17-21 ATLQA linker 1-5

5 22-35 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

142-155

5 36-40 ATLQA linker 1-5 5 41-50 LSVNPYVCNA helicase@Cyprus(NC_045512@Cyprus:+: 16237-18039) 43-52

5 51-55 ATLQA linker 1-5

5 56-65 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536

5 66-70 ATLQA linker 1-5

5 71-85 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

5 86-90 ATLQA linker 1-5

5 91-101 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291

5 102-106 ATLQA linker 1-5

5 107-116 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 434-443

5 117-121 ATLQA linker 1-5

5 122-135 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

5 136-140 ATLQA linker 1-5

5 141-148 EVTPSGTW nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 323-330

5 149-153 ATLQA linker 1-5

5 154-163 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

5 164-168 ATLQA linker 1-5

5 169-176 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

5 177-181 ATLQA linker 1-5

5 182-189 SSIVITSG ORF3a_protein@SouthKorea(NC_045512@SouthKorea:+:25393-26220) 165-172

5 190-194 ATLQA linker 1-5

5 195-233 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

5 234-238 ATLQA linker 1-5

5 239-246 DQDVLFAY RNA-dependent_RNA_polymerase@FrenchGuiana(NC_045512@FrenchGu iana:+: 13442-

13468+13468-16236) 523-530

5 247-251 ATLQA linker 1-5

5 252-261 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

5 262-266 ATLQA linker 1-5

5 267-274 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742

5 275-279 ATLQA linker 1-5

5 280-287 SDFVRATA ORF3a_protein(NC_045512:+:25393-26220) 26-33

5 288-292 ATLQA linker 1-5

5 293-304 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54

5 305-309 ATLQA linker 1-5

5 310-317 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

5 318-322 ATLQA linker 1-5

5 323-336 LSPVALRQMSCAAG nsp9(NC_045512:+:12686-13024) 4-17

5 337-341 ATLQA linker 1-5

5 342-360 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727

5 361-365 ATLQA linker 1-5

5 366-375 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980

5 376-380 ATLQA linker 1-5

5 381 -394 RLNVGDYFVLTSHT helicase@Austria(NC_045512@Austria:+:16237-18039) 218-231

5 395-399 ATLQA linker 1-5

5 400-408 ISEHDYHIG ORF3a_protein@NorthMacedonia(NC_045512@NorthMacedonia:+:2539 3-26220) 179-187

5 409-413 ATLQA linker 1-5

5 414-421 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

5 422-426 ATLQA linker 1-5

5 427-436 GLKLKDCVMY nsp6@Peru(NC_045512@Peru:+: 10973-11842) 107-116

5 437-441 ATLQA linker 1-5

5 442-449 SQDLSVVS endoRNAse(NC_045512:+:19621 -20658) 308-315

5 450-454 ATLQA linker 1-5

5 455-468 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498

5 469-473 ATLQA linker 1-5

5 474-489 AFKLNIKLLGVGGKPC nsp6(NC_045512:+:10973-11842) 268-283

5 490-494 ATLQA linker 1-5

5 495-502 DCATVHTA 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 114-121

5 503-507 ATLQA linker 1-5

5 508-518 SPGVFNPVMEP ORF3a_protein@Colombia(NC_045512@Colombia:+:25393-26220) 252-262

5 519-523 ATLQA linker 1-5

5 524-538 VCNLLLLFVTVYSHL QRF3a_protein@Croatia(NC_045512@Croatia:+:25393-26220) 80-94

5 539-543 ATLQA linker 1-5

5 544-585 TTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR

ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-2825 9) 11-52

5 586-590 ATLQA linker 1-5

5 591-600 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

5 601-605 ATLQA linker 1-5

5 606-626 ALCEKALKYFPIDKCSRIIPA helicase@Colombia(NC_045512@Colombia:+:16237-18039) 316-336

5 627-631 ATLQA linker 1-5 5 632-648 KDQVILLNKHIDAYKTF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533)

347-363

5 649-653 ATLQA linker 1-5

5 654-666 KLALGGSVAIKIT 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 160-172

5 667-671 ATLQA linker 1-5

5 672-681 NLIIKNLSKS ORF6_protein(NC_045512:+:27202-27387) 34-43

5 682-686 ATLQA linker 1-5

5 687-707 ELVIGAVILRGHLRIAGHHLG membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 137-157

5 708-712 ATLQA linker 1-5

5 713-726 TCFSVAALTNNVAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+ 13468-16236) 394-407

5 727-731 ATLQA linker 1-5

5 732-754 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481

5 755-759 ATLQA linker 1-5

5 760-773 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

5 774-778 ATLQA linker 1-5

5 779-796 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178

5 797-801 ATLQA linker 1-5

5 802-817 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31

5 818-822 ATLQA linker 1-5

5 823-851 SMWALIISVTSNYSGVVTIVMFLARGIVF nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+: 10973-11842) 160-188

5 852-856 ATLQA linker 1-5

5 857-864 IAANTVIW endoRNAse(NC_045512:+:19621 -20658) 79-86

5 865-869 ATLQA linker 1-5

5 870-878 SEAFLIGCN 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 202-210

5 879-883 ATLQA linker 1-5

5 884-892 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708

5 893-897 ATLQA linker 1-5

5 898-911 ESVVKDCVVLHSYF QRF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 194-207

5 912-916 ATLQA linker 1-5

5 917-929 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

5 930-934 ATLQA linker 1-5

5 935-945 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

5 946-950 ATLQA linker 1-5

5 951 -959 ASQGLVASI RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 771-779

5 960-964 ATLQA linker 1-5

5 965-980 QLALSKGFHFVCNLLL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 70-85

5 981-985 ATLQA linker 1-5

5 986-999 RLTLGVYDYLVSTQ nsp6(NC_045512:+:10973-11842) 236-249

5 1000-1004 ATLQA linker 1-5

5 1005-1015 KESVQTFFKLV nsp2(NC_045512: + :806-2719) 492-502

5 1016-1020 ATLQA linker 1-5

5 1021-1043 VAAGLEAPFFYLYALVYFLQSIN ORF3a_protein@Ecuador(NC_045512@Ecuador:+:25393-

26220) 97-119

5 1044-1048 ATLQA linker 1-5

5 1049-1070 SDFVRATATIPIRASLPFGWLI ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-

26220) 26-47

5 1071-1075 ATLQA linker 1-5

5 1076-1094 ECAQVLSETVMCGGSLYVK RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 658-676

5 1095-1099 ATLQA linker 1-5 5 1100-1111 LKKLKKSLNVAK nsp8(NC_045512:+: 12092-12685) 35-46 5 1112-1116 ATLQA linker 1-5 5 1117-1138 LGGMSYYCKSHKPSISFPLCAN helicase@NewZealand(NC_045512@NewZealand:+:16237-

18039) 65-86

5 1139-1143 ATLQA linker 1-5

5 1144-1156 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

5 1157-1161 ATLQA linker 1-5

5 1162-1177 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384)

59-74

5 1178-1182 ATLQA linker 1-5

5 1183-1199 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384)

258-274

5 1200-1204 ATLQA linker 1-5

5 1205-1220 NYTVSCSPFTINCQEP ORF8_protein@CostaRica(NC_045512@CostaRica:+:27894-28259)

78-93

5 1221-1225 ATLQA linker 1-5 5 1226-1240 YFTSDYYQLYSTQLI ORF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220) 206-220

5 1241-1245 ATLQA linker 1-5

5 1246-1260 RIIPARARVECFDKF helicase@Aruba(NC_045512@Aruba:+:16237-18039) 332-346

5 1261-1265 ATLQA linker 1-5

5 1266-1275 DGYVMHANYI 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 220-229

5 1276-1280 ATLQA linker 1-5

5 1281-1294 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

5 1295-1299 ATLQA linker 1-5

5 1300-1308 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788

5 1309-1313 ATLQA linker 1-5

5 1314-1329 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

5 1330-1334 ATLQA linker 1-5

5 1335-1349 YNLLKGCPAVAKHDF RNA- 87-101

6 1-11 GKPVPYCYDTN nsp4(NC_045512:+:8555-10054) 164-174 6 12-16 ATLQA linker 1-5 6 17-33 EVTPSGTWLTYTGAIKL nucleocapsid_phosphoprotein@Bulgaria(NC_045512@Bulgaria:+:28 274-29533)

323-339

6 34-38 ATLQA linker 1-5

6 39-60 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 206-227

6 61-65 ATLQA linker 1-5

6 66-76 YDNLQFISLEI helicase@Austria(NC_045512@Austria:+:16237-18039) 582-592

6 77-81 ATLQA linker 1-5

6 82-103 SDFVRATATIPIQASLPFGWLI QRF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 26-47

6 104-108 ATLQA linker 1-5

6 109-116 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

6 117-121 ATLQA linker 1-5

6 122-131 NVAFNVVNKG endoRNAse(NC_045512:+:19621 -20658) 4-13

6 132-136 ATLQA linker 1-5

6 137-153 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

6 154-158 ATLQA linker 1-5

6 159-167 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-1169

6 168-172 ATLQA linker 1-5

6 173-187 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

6 188-192 ATLQA linker 1-5

6 193-204 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

6 205-209 ATLQA linker 1-5

6 210-221 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362

6 222-226 ATLQA linker 1-5

6 227-242 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

6 243-247 ATLQA linker 1-5

6 248-260 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

6 261-265 ATLQA linker 1-5

6 266-287 QLALSKGVHFVCNLLLLFVTVY QRF3a_protein@Australia(NC_045512@Australia:+:25393-26220) 70-91

6 288-292 ATLQA linker 1-5

6 293-308 HWPQIAQFAPSASAFF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 300-315

6 309-313 ATLQA linker 1-5

6 314-321 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817

6 322-326 ATLQA linker 1-5

6 327-343 ILLNKHIDAYKTFPPIE nucleocapsid_phosphoprotein@Chile(NC_045512@Chile:+:28274-29 533) 351-367

6 344-348 ATLQA linker 1-5

6 349-357 KFPLKLRGT 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 249-257

6 358-362 ATLQA linker 1-5

6 363-372 NCYDYCIPYN ORF3a_protein(NC_045512:+:25393-26220) 152-161

6 373-377 ATLQA linker 1-5

6 378-391 GASCCLYCRCHIDH nsp10(NC_045512:+: 13025-13441 ) 70-83

6 392-396 ATLQA linker 1-5

6 397-406 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

6 407-411 ATLQA linker 1-5

6 412-422 CLPFTINCQKP ORF8_protein@Brazil(NC_045512@Brazil:+:27894-28259) 83-93

6 423-427 ATLQA linker 1-5

6 428-450 KEITVATSRTLSYYKLGASQRVA membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 166-188 451-455 ATLQA linker 1-5 456-466 VVNAANVYLKH nsp3(NC_045512 : + :2720-8554) 239-249 467-471 ATLQA linker 1-5 472-484 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349 485-489 ATLQA linker 1-5 490-506 LFFFLYENAFLPFVMGI nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+:10973-1 1842) 33-49 507-511 ATLQA linker 1-5 512-522 YDKLQFTSLEI helicase@Aruba(NC_045512@Aruba:+:16237-18039) 582-592 523-527 ATLQA linker 1-5 528-535 SSNVANYQ helicase@Austria(NC_045512@Austria:+:16237-18039) 263-270 536-540 ATLQA linker 1-5 541 -565 AAGLEAPFLYLYVLVYFLQSINFVR QRF3a_protein@Norway(NC_045512@Norway:+:25393-26220) 98-122 566-570 ATLQA linker 1-5 571-585 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219 586-590 ATLQA linker 1-5 591-605 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 857-871 606-610 ATLQA linker 1-5 611-618 VLSEARQH leader_protein(NC_045512:+:266-805) 38-45 619-623 ATLQA linker 1-5 624-637 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691 638-642 ATLQA linker 1-5 643-660 KGFCDLKGKYVQIPTTCA nsp10(NC_045512:+: 13025-13441) 87-104 661-665 ATLQA linker 1-5 666-675 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487 676-680 ATLQA linker 1-5 681-702 IAMACLVGLMWLSYFIASFRLF membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 82-103 703-707 ATLQA linker 1-5 708-717 TPLIQPIGAL nsp4(NC_045512:+:8555-10054) 269-278 718-722 ATLQA linker 1-5 723-736 IHFYSKWYIRVGAK ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 39-52 737-741 ATLQA linker 1-5 742-751 LPRVFSAVGN nsp4(NC_045512:+:8555-10054) 122-131 752-756 ATLQA linker 1-5 757-774 SQHTMLVKQGDDYVYLPY RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442- 13468+13468-16236) SI 4-831

6 775-779 ATLQA linker 1-5

6 780-805 YRLANECAQVLSEIVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Canada(NC_045512@Canada:+:13442-134 68+13468-16236) 653-678

806-810 ATLQA linker 1-5 811-828 CANFNVLFSTVFPPTSFG RNA-dependent_RNA_polymerase@China(NC_045512@China:+:13442- 13468+13468-16236) 310-327

6 829-833 ATLQA linker 1-5

6 834-845 DTSLKLKECVMY nsp6@SmallAsia(NC_045512@SmallAsia:+:10973-11842) 102-113

6 846-850 ATLQA linker 1-5

6 851-866 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

348-363

6 867-871 ATLQA linker 1-5

6 872-880 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579

6 881-885 ATLQA linker 1-5

6 886-901 SEFSSLPSYAAFATAQ nsp8(NC_045512:+:12092-12685) 4-19

6 902-906 ATLQA linker 1-5

6 907-922 EEIIYNLLKDCPAVAK RNA-dependent_RNA_polymerase@Senegal(NC_045512@Senegal:+: 13442-

13468+13468-16236) 83-98 6 923-927 ATLQA linker 1-5 6 928-940 VKGLQPSVGPKQA endoRNAse(NC_045512:+:19621 -20658) 148-160 6 941-945 ATLQA linker 1-5 6 946-961 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541 6 962-966 ATLQA linker 1-5 6 967-980 DGCVPLNIIPLTTA nsp8(NC_045512:+:12092-12685) 112-125 6 981-985 ATLQA linker 1-5 6 986-1003 FLYENAFLPFAMGVIAMS nsp6@Mexico(NC_045512@Mexico :+ : 10973-11842) 36-53 6 1004-1008 ATLQA linker 1-5 6 1009-1016 TQALPHRQ nucleocapsid_phosphoprotein@Mozambique(NC_045512@Mozambique: +:28274-29533) 379-386

6 1017-1021 ATLQA linker 1-5 6 1022-1040 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

6 1041-1045 ATLQA linker 1-5

6 1046-1061 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001-1016

6 1062-1066 ATLQA linker 1-5

6 1067-1086 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1048-1067

6 1087-1091 ATLQA linker 1-5

6 1092-1101 ISDYDYYRYN RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 450-459 6 1102-1106 ATLQA linker 1-5

6 1107-1114 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

6 1115-1119 ATLQA linker 1-5

6 1120-1130 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146

6 1131-1135 ATLQA linker 1-5

6 1136-1154 VKDCVLLHSYFTSDYYQLY ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220)

197-215

6 1155-1159 ATLQA linker 1-5

6 1160-1168 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474

6 1169-1173 ATLQA linker 1-5

6 1174-1188 HYVRITGLYPTLNIL helicase@lndonesia(NC_045512@lndonesia:+:16237-18039)

245-259

6 1189-1193 ATLQA linker 1-5

6 1194-1207 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

6 1208-1212 ATLQA linker 1-5

6 1213-1220 GSCGSVGF 3C-like_proteinase(NC_045512:+: 10055-10972) 143-150

6 1221-1225 ATLQA linker 1-5

6 1226-1234 KHWPQIAQF nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 299-307

6 1235-1239 ATLQA linker 1-5

6 1240-1254 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

6 1255-1259 ATLQA linker 1-5

6 1260-1268 YGIIWVATE nucleocapsid phosphoprotein@SmallSouthAmerica(NC_045512@SmallSouthAmerica :+:28274-29533) 128-136

6 1269-1273 ATLQA linker 1-5

6 1274-1281 EHVQIHTI ORF3a_protein(NC_045512:+:25393-26220) 242-249

6 1282-1286 ATLQA linker 1-5

6 1287-1301 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384)

132-146

6 1302-1306 ATLQA linker 1-5

6 1307-1320 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384)

5-18

6 1321-1325 ATLQA linker 1-5

6 1326-1335 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences (and as set forth in Figure 15). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses four of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses five of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 5 concatemers pos_in_concatemer epitope gene pos_in_gene 1 1-12 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261 13 17 ATLQA linker 1-5

18-34 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765 35-39 ATLQA linker 1-5 40-52 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126 53-57 ATLQA linker 1-5 58-69 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731 70-74 ATLQA linker 1-5 75-89 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319 90-94 ATLQA linker 1-5 95-104 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855 105-109 ATLQA linker 1-5 110-119 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424 120-124 ATLQA linker 1-5 125-140 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 331-346

141-145 ATLQA linker 1-5 146-161 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 348-363 162-166 ATLQA linker 1-5 167-177 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191 ) 136-146 178-182 ATLQA linker 1-5 183-194 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362 195-199 ATLQA linker 1-5 200-218 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236 219-223 ATLQA linker 1-5 224-236 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42 237-241 ATLQA linker 1-5 242-249 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691 250-254 ATLQA linker 1-5 255-268 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928 269-273 ATLQA linker 1-5 274-287 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450 288-292 ATLQA linker 1-5 293-308 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016 309-313 ATLQA linker 1-5 314-325 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671 326-330 ATLQA linker 1-5 331-342 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639 343-347 ATLQA linker 1-5 348-356 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440 357-361 ATLQA linker 1-5 362-373 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242 374-378 ATLQA linker 1-5 379-386 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207 387-391 ATLQA linker 1-5 392-401 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021 402-406 ATLQA linker 1-5 407-425 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450 426-430 ATLQA linker 1-5 431-448 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 470-487 1 -13 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

14 18 ATLQA linker 1-5

19-32 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191 33-37 ATLQA linker 1-5 38-45 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131 46-50 ATLQA linker 1-5 51 -60 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844 61 -65 ATLQA linker 1-5 66-73 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436 74-78 ATLQA linker 1-5 79-86 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145 87-91 ATLQA linker 1-5 92-111 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 303-322 112-116 ATLQA linker 1-5 117-136 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197 137-141 ATLQA linker 1-5

142-153 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821 154-158 ATLQA linker 1-5 159-172 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608 173-177 ATLQA linker 1-5 178-189 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24 190-194 ATLQA linker 1-5 195-207 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349 208-212 ATLQA linker 1-5 213-235 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476 236-240 ATLQA linker 1-5 241-253 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902 254-258 ATLQA linker 1-5

259-268 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 434-443 269-273 ATLQA linker 1-5

274-284 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973 285-289 ATLQA linker 1-5 290-307 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161 -178 308-312 ATLQA linker 1-5 313-327 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82 328-332 ATLQA linker 1-5 333-346 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843 347-351 ATLQA linker 1-5 352-359 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365 360-364 ATLQA linker 1-5 365-379 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219 380-384 ATLQA linker 1-5 385-393 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788 394-398 ATLQA linker 1-5 399-409 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291 410-414 ATLQA linker 1-5 415-423 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579 424-428 ATLQA linker 1-5 429-436 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742 437-441 ATLQA linker 1-5 442-449 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899 1-10 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536 11 -15 ATLQA linker 1-5 16-32 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 4-20 33-37 ATLQA linker 1-5 38-53 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654 54-58 ATLQA linker 1-5 59-67 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512 68-72 ATLQA linker 1-5 73-81 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390 82-86 ATLQA linker 1-5 87-101 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 396-410 102-106 ATLQA linker 1-5 107-114 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829 115-119 ATLQA linker 1-5 120-139 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610 140-144 ATLQA linker 1-5 145-157 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480 158-162 ATLQA linker 1-5 163-177 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 857-871 178-182 ATLQA linker 1-5 183-192 NEFYAYLRKH RNA-deppendent__RNA__ppolyymerase((NC__045512:+:13442-13468+ 13468-16236)) 743-752 193-197 ATLQA linker 1-5 198-209 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176 210-214 ATLQA linker 1-5 215-237 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481 238-242 ATLQA linker 1-5 243-259 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 877-893

260-264 ATLQA linker 1-5 265-274 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

275-279 ATLQA linker 1-5 280-294 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881 295-299 ATLQA linker 1-5 300-319 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 826-845

320-324 ATLQA linker 1-5

325-347 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061 348-352 ATLQA linker 1-5

353-362 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348

363-367 ATLQA linker 1-5

368-379 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

380-384 ATLQA linker 1-5 385-392 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203 393-397 ATLQA linker 1-5 398-406 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66 407-411 ATLQA linker 1-5 412-450 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92 1-10 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

11-15 ATLQA linker 1-5

16-38 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278 39-43 ATLQA linker 1-5

44-58 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

59-63 ATLQA linker 1-5

64-114 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

115-119 ATLQA linker 1-5 120-134 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 368-382 135-139 ATLQA linker 1-5 140-147 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817 148-152 ATLQA linker 1-5 153-168 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31 169-173 ATLQA linker 1-5 174-186 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131 187-191 ATLQA linker 1-5 192-201 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13 202-206 ATLQA linker 1-5 207-214 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293 215-219 ATLQA linker 1-5 220-230 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819 231-235 ATLQA linker 1-5 236-245 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400 246-250 ATLQA linker 1-5 251 -260 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248 261-265 ATLQA linker 1-5 266-281 VREVLSDRELHLSWEV helicase(NC_045512:+: 16237-18039) 154-169 282-286 ATLQA linker 1-5 287-306 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942 307-311 ATLQA linker 1-5 312-322 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006 323-327 ATLQA linker 1-5 328-338 VVNAANVYLKH nsp3(NC_045512:+:2720-8554) 239-249 339-343 ATLQA linker 1-5 344-362 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600 363-367 ATLQA linker 1-5 368-387 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39 388-392 ATLQA linker 1-5 393-405 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171 406-410 ATLQA linker 1-5 411-423 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93 424-428 ATLQA linker 1-5 429-438 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746 1-9 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129 10-14 ATLQA linker 1-5 15-28 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 142-155 29-33 ATLQA linker 1-5 34-45 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497 46-50 ATLQA linker 1-5 51-58 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996 59-63 ATLQA linker 1-5 64-74 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363 75-79 ATLQA linker 1-5 5 80-89 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111

5 90-94 ATLQA linker 1-5

5 95-102 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

5 103-107 ATLQA linker 1-5

5 108-115 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349

5 116-120 ATLQA linker 1-5

5 121-128 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

5 129-133 ATLQA linker 1-5

5 134-141 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

5 142-146 ATLQA linker 1-5

5 147-178 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

5 179-183 ATLQA linker 1-5

5 184-192 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708

5 193-197 ATLQA linker 1-5

5 198-208 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

5 209-213 ATLQA linker 1-5

5 214-221 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

5 222-226 ATLQA linker 1-5

5 227-234 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

5 235-239 ATLQA linker 1-5

5 240-247 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

5 248-252 ATLQA linker 1-5

5 253-265 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

5 266-270 ATLQA linker 1-5

5 271-278 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 67-74

5 279-283 ATLQA linker 1-5

5 284-296 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

5 297-301 ATLQA linker 1-5

5 302-311 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252

5 312-316 ATLQA linker 1-5

5 317-326 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

5 327-331 ATLQA linker 1-5

5 332-341 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487

5 342-346 ATLQA linker 1-5

5 347-356 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

5 357-361 ATLQA linker 1-5

5 362-373 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

5 374-378 ATLQA linker 1-5

5 379-398 MTSCCSCLKGCCSCGSCCKF su rfa ce_g ly co p ro te i n ( N C_045512:+:21563-25384) 1237-1256

5 399-403 ATLQA linker 1-5

5 404-413 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

5 414-418 ATLQA linker 1-5

5 419-430 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

5 431-435 ATLQA linker 1-5

5 436-455 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

6 1-18 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404 6 19-23 ATLQA linker 1-5 6 24-37 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 721-734

6 38-42 ATLQA linker 1-5

6 43-51 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

6 52-56 ATLQA linker 1-5

6 57-78 GYQPYRVVVLSFELLHAPATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

6 79-83 ATLQA linker 1-5

6 84-92 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

6 93-97 ATLQA linker 1-5

6 98-105 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

6 106-110 ATLQA linker 1-5

6 111-137 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

6 138-142 ATLQA linker 1-5

6 143-150 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

6 151-155 ATLQA linker 1-5

6 156-163 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

6 164-168 ATLQA linker 1-5

6 169-183 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

6 184-188 ATLQA linker 1-5

6 189-208 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

6 209-213 ATLQA linker 1-5

6 214-223 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157 6 224-228 ATLQA linker 1-5

6 229-245 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91-107

6 246-250 ATLQA linker 1-5

6 251-261 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373

6 262-266 ATLQA linker 1-5

6 267-276 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

6 277-281 ATLQA linker 1-5

6 282-297 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

6 298-302 ATLQA linker 1-5

6 303-312 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

6 313-317 ATLQA linker 1-5

6 318-342 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

6 343-347 ATLQA linker 1-5

6 348-358 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

6 359-363 ATLQA linker 1-5

6 364-383 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

6 384-388 ATLQA linker 1-5

6 389-405 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-126

6 406-410 ATLQA linker 1-5

6 411-423 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

6 424-428 ATLQA linker 1-5

6 429-444 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences (and as set forth in Figure 16). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses four of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses five of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 6 concatemers P ^os J ⁿ _ ^conc atemer epitope gene pos_in_gene

1 1-12 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

1 13-17 ATLQA linker 1-5

1 18-32 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368

1 33-37 ATLQA linker 1-5

1 38-45 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

1 46-50 ATLQA linker 1-5

1 51-58 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

1 59-63 ATLQA linker 1-5

1 64-114 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

1 115-119 ATLQA linker 1-5

1 120-136 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 877-893

1 137-141 ATLQA linker 1-5

1 142-154 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480

1 155-159 ATLQA linker 1-5

1 160-167 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817

1 168-172 ATLQA linker 1-5

1 173-180 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

1 181-185 ATLQA linker 1-5

1 186-205 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

1 206-210 ATLQA linker 1-5 1 211-218 EIYQAGSK surfface_g glyycopprotein@@Mexico((NC_045512@@Mexico:+:21563-25384)) 471-478

1 219-223 ATLQA linker 1-5

1 224-235 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

1 236-240 ATLQA linker 1-5

1 241 -250 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

1 251-255 ATLQA linker 1-5

1 256-270 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

1 271-275 ATLQA linker 1-5

1 276-291 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31

1 292-296 ATLQA linker 1-5

1 297-309 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

1 310-314 ATLQA linker 1-5

1 315-331 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

1 332-336 ATLQA linker 1-5

1 337-351 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 368-382

1 352-356 ATLQA linker 1-5

1 357-367 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

1 368-372 ATLQA linker 1-5

1 373-381 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708

1 382-386 ATLQA linker 1-5

1 387-401 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319

1 402-406 ATLQA linker 1-5

1 407-418 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

1 419-423 ATLQA linker 1-5

1 424-435 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671

1 436-440 ATLQA linker 1-5

1 441 -460 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197

1 461-465 ATLQA linker 1-5

1 466-475 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

1 476-480 ATLQA linker 1-5

1 481-492 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

1 493-497 ATLQA linker 1-5

1 498-513 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001-1016

1 514-518 ATLQA linker 1-5

1 519-541 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

1 542-546 ATLQA linker 1-5

1 547-560 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18

1 561-565 ATLQA linker 1-5

1 566-575 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

1 576-580 ATLQA linker 1-5

1 581-591 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

1 592-596 ATLQA linker 1-5

1 597-628 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

2 1-13 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

2 14-18 ATLQA linker 1-5

2 19-32 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

2 33-37 ATLQA linker 1-5

2 38-47 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980

2 48-52 ATLQA linker 1-5

2 53-66 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

2 67-71 ATLQA linker 1-5

2 72-91 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224

2 92-96 ATLQA linker 1-5

2 97-109 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

2 110-114 ATLQA linker 1-5

2 115-125 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973

2 126-130 ATLQA linker 1-5

2 131-140 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

2 141-145 ATLQA linker 1-5

2 146-155 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

2 156-160 ATLQA linker 1-5

2 161-172 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639

2 173-177 ATLQA linker 1-5

2 178-187 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 743-752

2 188-192 ATLQA linker 1-5

2 193-207 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

2 208-212 ATLQA linker 1-5

2 213-235 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481 236-240 ATLQA linker 1-5

241-257 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

258-262 ATLQA linker 1-5

263-272 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021

273-277 ATLQA linker 1-5

278-293 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

294-298 ATLQA linker 1-5

299-307 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142 308-312 ATLQA linker 1-5

313-323 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006 324-328 ATLQA linker 1-5

329-337 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19 338-342 ATLQA linker 1-5

343-364 GYQPYRVVVLSFELLHAPATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525 365-369 ATLQA linker 1-5

370-389 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1048-1067 390-394 ATLQA linker 1-5

395-406 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54 407-411 ATLQA linker 1-5

412-425 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608

426-430 ATLQA linker 1-5 431-440 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133 441-445 ATLQA linker 1-5 446-453 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899 454-458 ATLQA linker 1-5

459-474 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

475-479 ATLQA linker 1-5

480-487 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349 488-492 ATLQA linker 1-5 493-507 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway :+:21563-25384) 129-143 508-512 ATLQA linker 1-5 513-527 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384) 496-510 528-532 ATLQA linker 1-5 533-546 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 294-307 547-551 ATLQA linker 1-5 552-564 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349 565-569 ATLQA linker 1-5 570-589 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39 590-594 ATLQA linker 1-5 595-614 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 209-228 615-619 ATLQA linker 1-5 620-638 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236 1-10 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536 11 -15 ATLQA linker 1-5 16-38 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278 39-43 ATLQA linker 1-5 44-52 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474 53-57 ATLQA linker 1-5 58-66 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512 67-71 ATLQA linker 1-5 72-84 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246 85-89 ATLQA linker 1-5 90-103 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843 104-108 ATLQA linker 1-5 109-116 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372 117-121 ATLQA linker 1-5 122-129 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725 130-134 ATLQA linker 1-5 135-145 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146 146-150 ATLQA linker 1-5 151-163 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42 164-168 ATLQA linker 1-5 169-183 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 396-410 184-188 ATLQA linker 1-5 189-197 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266 3 198-202 ATLQA linker 1-5

3 203-241 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

3 242-246 ATLQA linker 1-5

3 247-256 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391-1400

3 257-261 ATLQA linker 1-5

3 262-272 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

3 273-277 ATLQA linker 1-5

3 278-289 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

3 290-294 ATLQA linker 1-5

3 295-302 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691

3 303-307 ATLQA linker 1-5

3 308-319 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497

3 320-324 ATLQA linker 1-5

3 325-339 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384)

680-694

3 340-344 ATLQA linker 1-5

3 345-354 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 434-443

3 355-359 ATLQA linker 1-5

3 360-372 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

3 373-377 ATLQA linker 1-5

3 378-389 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362

3 390-394 ATLQA linker 1-5

3 395-407 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

3 408-412 ATLQA linker 1-5

3 413-420 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

3 421-425 ATLQA linker 1-5

3 426-444 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

3 445-449 ATLQA linker 1-5

3 450-465 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

3 466-470 ATLQA linker 1-5

3 471 -482 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

3 483-487 ATLQA linker 1-5

3 488-501 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384)

58-71

3 502-506 ATLQA linker 1-5

3 507-517 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

1088

3 518-522 ATLQA linker 1-5

3 523-534 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821

3 535-539 ATLQA linker 1-5

3 540-547 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

3 548-552 ATLQA linker 1-5

3 553-568 VREVLSDRELHLSWEV helicase(NC_045512:+: 16237-18039) 154-169

3 569-573 ATLQA linker 1-5

3 574-589 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 59-74

3 590-594 ATLQA linker 1-5

3 595-602 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

3 603-607 ATLQA linker 1-5

3 608-615 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

3 616-620 ATLQA linker 1-5

3 621 -630 SSVLHSTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

4 1-10 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881 4 11 -15 ATLQA linker 1-5 4 16-32 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 4-20

4 33-37 ATLQA linker 1-5

4 38-50 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

4 51-55 ATLQA linker 1-5

4 56-67 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

4 68-72 ATLQA linker 1-5

4 73-86 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

4 87-91 ATLQA linker 1-5

4 92-111 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 826-845

4 112-116 ATLQA linker 1-5

4 117-136 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

4 137-141 ATLQA linker 1-5

4 142-153 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242

4 154-158 ATLQA linker 1-5 159-176 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 470-487 177-181 ATLQA linker 1-5 182-192 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291 193-197 ATLQA linker 1-5 198-207 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487 208-212 ATLQA linker 1-5 213-224 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24 225-229 ATLQA linker 1-5 230-243 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-2 5384) 128-141 244-248 ATLQA linker 1-5 249-258 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989 259-263 ATLQA linker 1-5 264-278 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733 279-283 ATLQA linker 1-5 284-295 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176 296-300 ATLQA linker 1-5 301-317 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91-107 318-322 ATLQA linker 1-5 323-331 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579 332-336 ATLQA linker 1-5 337-344 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207 345-349 ATLQA linker 1-5 350-369 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942 370-374 ATLQA linker 1-5 375-384 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855 385-389 ATLQA linker 1-5 390-408 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727 409-413 ATLQA linker 1-5 414-422 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390 423-427 ATLQA linker 1-5 428-441 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498 442-446 ATLQA linker 1-5 447-456 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895 457-461 ATLQA linker 1-5 462-480 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384) 607-625 481-485 ATLQA linker 1-5 486-495 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252 496-500 ATLQA linker 1-5 501-514 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450 515-519 ATLQA linker 1-5 520-529 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65 530-534 ATLQA linker 1-5 535-542 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365 543-547 ATLQA linker 1-5 548-556 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788 557-561 ATLQA linker 1-5 562-574 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335 575-579 ATLQA linker 1-5 580-587 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293 588-592 ATLQA linker 1-5 593-604 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731 605-609 ATLQA linker 1-5 610-617 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436 618-622 ATLQA linker 1-5 623-640 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142 1-9 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129 10-14 ATLQA linker 1-5 15-28 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 142-155 29-33 ATLQA linker 1-5 34-48 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274 49-53 ATLQA linker 1-5 54-84 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563- 1211-1241

85-89 ATLQA linker 1-5

90-104 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 857-871

105-109 ATLQA linker 1-5 5 110-117 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829

5 118-122 ATLQA linker 1-5

5 123-142 DDRCILHCAN FNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 303-322

5 143-147 ATLQA linker 1-5

5 148-155 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

5 156-160 ATLQA linker 1-5

5 161-176 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

348-363

5 177-181 ATLQA linker 1-5

5 182-191 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173

5 192-196 ATLQA linker 1-5

5 197-218 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384)

125-146

5 219-223 ATLQA linker 1-5

5 224-231 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

5 232-236 ATLQA linker 1-5

5 237-254 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

5 255-259 ATLQA linker 1-5

5 260-269 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348

5 270-274 ATLQA linker 1-5

5 275-297 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

5 298-302 ATLQA linker 1-5

5 303-322 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610

5 323-327 ATLQA linker 1-5

5 328-342 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219

5 343-347 ATLQA linker 1-5

5 348-370 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

5 371-375 ATLQA linker 1-5

5 376-391 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

5 392-396 ATLQA linker 1-5

5 397-404 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

5 405-409 ATLQA linker 1-5

5 410-419 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111

5 420-424 ATLQA linker 1-5

5 425-439 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

5 440-444 ATLQA linker 1-5

5 445-455 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

5 456-460 ATLQA linker 1-5

5 461 -475 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

5 476-480 ATLQA linker 1-5

5 481-500 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

5 501-505 ATLQA linker 1-5

5 506-520 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

5 521-525 ATLQA linker 1-5

5 526-533 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

5 534-538 ATLQA linker 1-5

5 539-563 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

5 564-568 ATLQA linker 1-5

5 569-592 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-

25384) 205-228

5 593-597 ATLQA linker 1-5

5 598-607 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

5 608-612 ATLQA linker 1-5

5 613-625 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131

5 626-630 ATLQA linker 1-5

5 631-638 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

6 1 -22 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

206-227

6 23-27 ATLQA linker 1-5

6 28-41 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 721-734

6 42-46 ATLQA linker 1-5

6 47-62 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

6 63-67 ATLQA linker 1-5

6 68-78 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

6 79-83 ATLQA linker 1-5

6 84-95 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

6 96-100 ATLQA linker 1-5 6 101-110 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

6 111-115 ATLQA linker 1-5

6 116-123 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

6 124-128 ATLQA linker 1-5

6 129-137 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

6 138-142 ATLQA linker 1-5

6 143-153 KESVQTFFKLV nsp2(NC_045512: + :806-2719) 492-502

6 154-158 ATLQA linker 1-5

6 159-174 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 331-346

6 175-179 ATLQA linker 1-5

6 180-197 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178

6 198-202 ATLQA linker 1-5

6 203-211 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-1169

6 212-216 ATLQA linker 1-5

6 217-226 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840

6 227-231 ATLQA linker 1-5

6 232-245 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

6 246-250 ATLQA linker 1-5

6 251-270 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-1256

6 271-275 ATLQA linker 1-5

6 276-292 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384) 258-274

6 293-297 ATLQA linker 1-5

6 298-305 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

6 306-310 ATLQA linker 1-5

6 311-333 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

6 334-338 ATLQA linker 1-5

6 339-349 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373

6 350-354 ATLQA linker 1-5

6 355-373 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

6 374-378 ATLQA linker 1-5

6 379-386 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742

6 387-391 ATLQA linker 1-5

6 392-404 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

6 405-409 ATLQA linker 1-5

6 410-418 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

6 419-423 ATLQA linker 1-5

6 424-450 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

6 451-455 ATLQA linker 1-5

6 456-466 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

6 467-471 ATLQA linker 1-5

6 472-484 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902

6 485-489 ATLQA linker 1-5

6 490-502 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

6 503-507 ATLQA linker 1-5

6 508-521 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

6 522-526 ATLQA linker 1-5

6 527-540 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

6 541-545 ATLQA linker 1-5

6 546-553 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 67-74

6 554-558 ATLQA linker 1-5

6 559-567 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

6 568-572 ATLQA linker 1-5

6 573-582 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

6 583-587 ATLQA linker 1-5

6 588-597 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

6 598-602 ATLQA linker 1-5

6 603-623 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 605-625

6 624-628 ATLQA linker 1-5

6 629-639 VVNAANVYLKH nsp3(NC_045512:+:2720-8554) 239-249

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences (and as set forth in Figure 17). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses four of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses five of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 7 concat pos_in_concat epitope gene pos_in_gene

1 1-20 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

1 21-25 ATLQA linker 1-5

1 26-39 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

1 40-44 ATLQA linker 1-5

1 45-63 ANSVFNICQSVTANVNALL RNA-dependent_RNA_polymerase@Croatia(NC_045512@Croatia:+:134 42-

13468+13468-16236) 690-708

1 64-68 ATLQA linker 1-5 1 69-83 SYFAIGLALYYPSAR helicase@Austria(NC_045512@Austria:+:16237-18039) 289-303 1 84-88 ATLQA linker 1-5 1 89-98 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65 1 99-103 ATLQA linker 1-5 1 104-115 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671 1 116-120 ATLQA linker 1-5 1 121-131 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006 1 132-136 ATLQA linker 1-5 1 137-147 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363 1 148-152 ATLQA linker 1-5 1 153-172 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610 1 173-177 ATLQA linker 1-5 1 178-185 FNSVCRLM helicase@Aruba(NC_045512@Aruba:+:16237-18039) 422-429 1 186-190 ATLQA linker 1-5 1 191-206 SLRCGACIRRPFLCCK helicase@Aruba(NC_045512@Aruba:+:16237-18039) 13-28 1 207-211 ATLQA linker 1-5 1 212-232 KLSYGIAIVREVLSDRELHLS helicase@Colombia(NC_045512@Colombia:+:16237-18039) 146-166 1 233-237 ATLQA linker 1-5 1 238-250 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902 1 251-255 ATLQA linker 1-5 1 256-267 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261 1 268-272 ATLQA linker 1-5 1 273-280 YDFVVSKG RNA-dependent_RNA_polymerase@Japan(NC_045512@Japan:+:13442-1 3468+13468-

16236) 420-427

1 281-285 ATLQA linker 1-5

1 286-295 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

1 296-300 ATLQA linker 1-5

1 301 -351 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

1 352-356 ATLQA linker 1-5

1 357-364 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349

1 365-369 ATLQA linker 1-5

1 370-396 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

1 397-401 ATLQA linker 1-5

1 402-411 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173

1 412-416 ATLQA linker 1-5

1 417-428 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

1 429-433 ATLQA linker 1-5

1 434-446 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

1 447-451 ATLQA linker 1-5

1 452-471 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224

1 472-476 ATLQA linker 1-5

1 477-495 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384) 607-625

1 496-500 ATLQA linker 1-5 1 501-515 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

1 516-520 ATLQA linker 1-5

1 521-531 YDNLQFISLEI helicase@Austria(NC_045512@Austria:+:16237-18039) 582-592

1 532-536 ATLQA linker 1-5

1 537-555 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236

1 556-560 ATLQA linker 1-5

1 561-568 SSNVANYQ helicase@Austria(NC_045512@Austria:+:16237-18039) 263-270

1 569-573 ATLQA linker 1-5

1 574-588 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384) 496-510

1 589-593 ATLQA linker 1-5

1 594-601 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

1 602-606 ATLQA linker 1-5

1 607-629 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

1 630-634 ATLQA linker 1-5

1 635-643 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161 -1169

1 644-648 ATLQA linker 1-5

1 649-656 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

1 657-661 ATLQA linker 1-5

1 662-669 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

1 670-674 ATLQA linker 1-5

1 675-685 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

1088

1 686-690 ATLQA linker 1-5

1 691-702 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54

1 703-707 ATLQA linker 1-5

1 708-724 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 877-893

1 725-729 ATLQA linker 1-5

1 730-739 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

1 740-744 ATLQA linker 1-5

1 745-760 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

1 761-765 ATLQA linker 1-5

1 766-776 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

1 777-781 ATLQA linker 1-5

1 782-791 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

2 1 -8 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

2 9-13 ATLQA linker 1-5

2 14-24 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973

2 25-29 ATLQA linker 1-5

2 30-38 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

2 39-43 ATLQA linker 1-5

2 44-56 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

2 57-61 ATLQA linker 1-5

2 62-70 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

2 71-75 ATLQA linker 1-5

2 76-107 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

2 108-112 ATLQA linker 1-5

2 113-120 SINVANYQ helicase@Mozambique(NC_045512@Mozambique:+:16237-18039) 263-270

2 121-125 ATLQA linker 1-5

2 126-135 LSVNPYVCNA helicase@Cyprus(NC_045512@Cyprus:+: 16237-18039) 43-52

2 136-140 ATLQA linker 1-5

2 141-148 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

2 149-153 ATLQA linker 1-5

2 154-163 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021

2 164-168 ATLQA linker 1-5

2 169-179 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291

2 180-184 ATLQA linker 1-5

2 185-200 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 331-346

2 201-205 ATLQA linker 1-5

2 206-220 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

2 221-225 ATLQA linker 1-5

2 226-233 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

2 234-238 ATLQA linker 1-5

2 239-256 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142

2 257-261 ATLQA linker 1-5 262-276 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 857-871 277-281 ATLQA linker 1-5 282-301 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 826-845 302-306 ATLQA linker 1-5 307-314 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207 315-319 ATLQA linker 1-5 320-330 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159 331-335 ATLQA linker 1-5 336-355 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645 356-360 ATLQA linker 1-5 361-368 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691 369-373 ATLQA linker 1-5 374-384 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146 385-389 ATLQA linker 1-5 390-405 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016 406-410 ATLQA linker 1-5 411 -423 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693 424-428 ATLQA linker 1-5 429-437 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474 438-442 ATLQA linker 1-5 443-456 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608 457-461 ATLQA linker 1-5 462-475 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18 476-480 ATLQA linker 1-5 481 -489 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270 490-494 ATLQA linker 1-5 495-503 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19 504-508 ATLQA linker 1-5 509-520 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497 521-525 ATLQA linker 1-5 526-533 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203 534-538 ATLQA linker 1-5 539-553 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319 554-558 ATLQA linker 1-5 559-568 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980 569-573 ATLQA linker 1-5 574-581 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817 582-586 ATLQA linker 1-5 587-604 CANFNVLFSTVFPPTSFG RNA-dependent_RNA_polymerase@China(NC_045512@China:+:13442- 310-327 605-609 ATLQA linker 1-5

610-623 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498 624-628 ATLQA linker 1-5 629-646 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 470-487 647-651 ATLQA linker 1-5 652-661 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133 662-666 ATLQA linker 1-5 667-674 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742 675-679 ATLQA linker 1-5 680-687 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420 688-692 ATLQA linker 1-5 693-715 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481 716-720 ATLQA linker 1-5 721 -735 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 680-694 736-740 ATLQA linker 1-5 741-751 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373 752-756 ATLQA linker 1-5 757-765 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788 766-770 ATLQA linker 1-5 771-778 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478 779-783 ATLQA linker 1-5 784-797 APGCDVTDVTQLYL helicase@Aruba(NC_045512@Aruba:+:16237-18039) 52-65 1-12 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362 13-17 ATLQA linker 1-5 18-40 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278 41 -45 ATLQA linker 1-5 3 46-55 ISDYDYYRYN RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 450-459

3 56-60 ATLQA linker 1-5

3 61-86 YRLANECAQVLSEMVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 653-678

3 87-91 ATLQA linker 1-5

3 92-99 SDDAVVCF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

16236) 759-766

3 100-104 ATLQA linker 1-5

3 105-112 FNSVCRFM helicase@Malaysia(NC_045512@Malaysia:+:16237-18039) 422-429

3 113-117 ATLQA linker 1-5

3 118-128 VVNAANVYLKH nsp3(NC_045512 : + :2720-8554) 239-249

3 129-133 ATLQA linker 1-5

3 134-145 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

3 146-150 ATLQA linker 1-5

3 151-160 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

3 161-165 ATLQA linker 1-5

3 166-188 YLGGMSYYCKSHKLPISFPLCAN helicase@CostaRica(NC_045512@CostaRica:+:16237-18039)

64-86

3 189-193 ATLQA linker 1-5

3 194-205 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242

3 206-210 ATLQA linker 1-5

3 211-220 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

3 221-225 ATLQA linker 1-5

3 226-247 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

206-227 3 248-252 ATLQA linker 1-5

3 253-268 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

3 269-273 ATLQA linker 1-5

3 274-283 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252

3 284-288 ATLQA linker 1-5

3 289-296 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 67-74

3 297-301 ATLQA linker 1-5

3 302-313 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639

3 314-318 ATLQA linker 1-5

3 319-357 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

3 358-362 ATLQA linker 1-5

3 363-374 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

3 375-379 ATLQA linker 1-5

3 380-398 ANSVFNICQAVTANVNALL RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 690-708

3 399-403 ATLQA linker 1-5

3 404-413 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840

3 414-418 ATLQA linker 1-5

3 419-439 HPNCVNCLDDRCILHCANFNV RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 295-315

3 440-444 ATLQA linker 1-5

3 445-456 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

3 457-461 ATLQA linker 1-5

3 462-472 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

3 473-477 ATLQA linker 1-5

3 478-487 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895

3 488-492 ATLQA linker 1-5

3 493-509 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

3 510-514 ATLQA linker 1-5

3 515-532 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

3 533-537 ATLQA linker 1-5

3 538-550 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

3 551-555 ATLQA linker 1-5

3 556-569 RLNVGDYFVLTSHT helicase@Austria(NC_045512@Austria:+:16237-18039) 218-231

3 570-574 ATLQA linker 1-5

3 575-599 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

3 600-604 ATLQA linker 1-5

3 605-620 DKYVRNLQHRLYECLY RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 717-732

621-625 ATLQA linker 1-5

626-639 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

640-644 ATLQA linker 1-5

645-661 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384) 258-274 3 662-666 ATLQA linker 1-5

3 667-687 ALCEKALKYFPIDKCSRIIPA helicase@Colombia(NC_045512@Colombia:+:16237-18039) 316-336

3 688-692 ATLQA linker 1-5

3 693-706 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-2 5384)

128-141

3 707-711 ATLQA linker 1-5

3 712-731 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197

3 732-736 ATLQA linker 1-5

3 737-744 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

3 745-749 ATLQA linker 1-5

3 750-760 YDKLQFTSLEI helicase@Aruba(NC_045512@Aruba:+:16237-18039) 582-592

3 761-765 ATLQA linker 1-5

3 766-784 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

3 785-789 ATLQA linker 1-5

3 790-804 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

4 1 -11 YDKLQFISLEI helicase@SouthAfrica(NC_045512@SouthAfrica:+:16237-18039) 582-592 4 12-16 ATLQA linker 1-5 4 17-24 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725 4 25-29 ATLQA linker 1-5 4 30-47 SQHTMLVKQGDDYVYLPY RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442- 13468+13468-16236) SI 4-831

4 48-52 ATLQA linker 1-5

4 53-66 IRNLQHRLYECLYR RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-

13468+13468-16236) 720-733

4 67-71 ATLQA linker 1-5

4 72-82 RQALLKTVQFC RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 183-193

4 83-87 ATLQA linker 1-5

4 88-95 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

4 96-100 ATLQA linker 1-5

4 101 -112 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

4 113-117 ATLQA linker 1-5

4 118-131 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

4 132-136 ATLQA linker 1-5

4 137-145 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390

4 146-150 ATLQA linker 1-5

4 151-158 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

4 159-163 ATLQA linker 1-5

4 164-181 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178

4 182-186 ATLQA linker 1-5

4 187-201 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 368-382

4 202-206 ATLQA linker 1-5

4 207-219 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42

4 220-224 ATLQA linker 1-5

4 225-232 DMYSVMLT RNA-dependent_RNA_polymerase@Malaysia(NC_045512@Malaysia:+:1 3442-

13468+13468-16236) 901-908

4 233-237 ATLQA linker 1-5

4 238-252 YNLLKGCPAVAKHDF RNA-dependent_RNA_polymerase@Poland(NC_045512@Poland:+:13442 -

13468+13468-16236) 87-101

4 253-257 ATLQA linker 1-5

4 258-273 VREVLSDRELHLSWEV helicase(NC_045512:+: 16237-18039) 154-169

4 274-278 ATLQA linker 1-5

4 279-286 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

4 287-291 ATLQA linker 1-5

4 292-305 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

4 306-310 ATLQA linker 1-5

4 311-326 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

348-363

4 327-331 ATLQA linker 1-5

4 332-354 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

4 355-359 ATLQA linker 1-5

4 360-372 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

4 373-377 ATLQA linker 1-5

4 378-396 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

4 397-401 ATLQA linker 1-5

4 402-418 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91 -107

4 419-423 ATLQA linker 1-5

4 424-431 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

4 432-436 ATLQA linker 1-5 4 437-446 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111

4 447-451 ATLQA linker 1-5

4 452-473 GY Q PYR VVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

4 474-478 ATLQA linker 1-5

4 479-501 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

4 502-506 ATLQA linker 1-5

4 507-518 TRAKVGILCITS helicase@SouthKorea(NC_045512@SouthKorea:+:16237-18039) 566-577

4 519-523 ATLQA linker 1-5

4 524-531 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829

4 532-536 ATLQA linker 1-5

4 537-544 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

4 545-549 ATLQA linker 1-5

4 550-565 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

4 566-570 ATLQA linker 1-5

4 571-579 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266

4 580-584 ATLQA linker 1-5

4 585-594 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

4 595-599 ATLQA linker 1-5

4 600-613 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 294-307

4 614-618 ATLQA linker 1-5

4 619-634 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

4 635-639 ATLQA linker 1-5

4 640-651 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

4 652-656 ATLQA linker 1-5

4 657-676 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-1256

4 677-681 ATLQA linker 1-5

4 682-691 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 743-752

4 692-696 ATLQA linker 1-5

4 697-706 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

4 707-711 ATLQA linker 1-5

4 712-723 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

4 724-728 ATLQA linker 1-5

4 729-738 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

4 739-743 ATLQA linker 1-5

4 744-757 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

4 758-762 ATLQA linker 1-5

4 763-777 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219

4 778-782 ATLQA linker 1-5

4 783-793 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

5 1 -22 LGGMSYYCKSHKPSISFPLCAN helicase@NewZealand(NC_045512@NewZealand:+:16237-18039) 65-86 23-27 ATLQA linker 1-5 28-37 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348 38-42 ATLQA linker 1-5 43-50 YDFAVSKG RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

6236) 420-427 51-55 ATLQA linker 1-5 56-63 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103 64-68 ATLQA linker 1-5 69-76 DQDVLFAY RNA-dependent_RNA_polymerase@FrenchGuiana(NC_045512@FrenchGu iana:+: 13442-

13468+13468-16236) 523-530

77-81 ATLQA linker 1-5 82-90 ASQGLVASI RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 771-779

5 91-95 ATLQA linker 1-5

5 96-115 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942

5 116-120 ATLQA linker 1-5

5 121-129 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

5 130-134 ATLQA linker 1-5

5 135-144 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

5 145-149 ATLQA linker 1-5

5 150-159 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

5 160-164 ATLQA linker 1-5

5 165-174 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

5 175-179 ATLQA linker 1-5

5 180-193 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 721-734

5 194-198 ATLQA linker 1-5 5 199-208 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 434-443

5 209-213 ATLQA linker 1-5

5 214-230 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

4-20

5 231-235 ATLQA linker 1-5

5 236-250 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

5 251-255 ATLQA linker 1-5

5 256-270 HYVRITGLYPTLNIL helicase@lndonesia(NC_045512@lndonesia:+:16237-18039) 245-259

5 271-275 ATLQA linker 1-5

5 276-288 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480

5 289-293 ATLQA linker 1-5

5 294-313 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

303-322

5 314-318 ATLQA linker 1-5

5 319-338 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

5 339-343 ATLQA linker 1-5

5 344-374 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1211-1241

5 375-379 ATLQA linker 1-5

5 380-398 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727

5 399-403 ATLQA linker 1-5

5 404-412 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

5 413-417 ATLQA linker 1-5

5 418-432 RIIPARARVECFDKF helicase@Aruba(NC_045512@Aruba:+:16237-18039) 332-346

5 433-437 ATLQA linker 1-5

5 438-448 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

5 449-453 ATLQA linker 1-5

5 454-477 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-

25384) 205-228

5 478-482 ATLQA linker 1-5

5 483-498 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 59-74

5 499-503 ATLQA linker 1-5

5 504-511 TDVVYRAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 28-35

5 512-516 ATLQA linker 1-5

5 517-529 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

5 530-534 ATLQA linker 1-5

5 535-547 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349

5 548-552 ATLQA linker 1-5

5 553-565 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

5 566-570 ATLQA linker 1-5

5 571 -593 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

5 594-598 ATLQA linker 1-5

5 599-613 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 129-143

5 614-618 ATLQA linker 1-5

5 619-639 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 605-625

5 640-644 ATLQA linker 1-5

5 645-656 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821

5 657-661 ATLQA linker 1-5

5 662-677 EEIIYNLLKDCPAVAK RNA-dependent_RNA_polymerase@Senegal(NC_045512@Senegal:+:134 42-

13468+13468-16236) 83-98

5 678-682 ATLQA linker 1-5

5 683-694 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

5 695-699 ATLQA linker 1-5

5 700-722 TQLYLGGMSYYCKPHKPPISFPL helicase@lceland(NC_045512@lceland:+:16237-18039) 61-83

5 723-727 ATLQA linker 1-5

5 728-738 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

5 739-743 ATLQA linker 1-5

5 744-753 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400

5 754-758 ATLQA linker 1-5

5 759-766 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

5 767-771 ATLQA linker 1-5

5 772-779 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

5 780-784 ATLQA linker 1-5

5 785-794 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

6 1-18 YNLLKDCPAVAKHDFFKF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 87-104

6 19-23 ATLQA linker 1-5 6 24-44 HPNCVNCSDDRCILHCANFNV RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 295-315

6 45-49 ATLQA linker 1-5

6 50-58 ASQGLLASI RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-13468+13468-

16236) 771-779

6 59-63 ATLQA linker 1-5

6 64-80 VPQEHYVRITGLYPTLN helicase@Aruba(NC_045512@Aruba:+:16237-18039) 241-257

6 81-85 ATLQA linker 1-5

6 86-95 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536

6 96-100 ATLQA linker 1-5

6 101-117 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

6 118-122 ATLQA linker 1-5

6 123-136 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

6 137-141 ATLQA linker 1-5

6 142-151 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487

6 152-156 ATLQA linker 1-5

6 157-165 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579

6 166-170 ATLQA linker 1-5

6 171-184 TCFSVAALTNNVAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba :+: 13442- 13468+ 13468-16236) 394-407

6 185-189 ATLQA linker 1-5

6 190-205 SRIIPARARVDCFDKF helicase@Brazil(NC_045512@Brazil:+:16237-18039) 331-346

6 206-210 ATLQA linker 1-5

6 211-219 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129

6 220-224 ATLQA linker 1-5

6 225-242 CANFNVLFSTVFPFTSFG RNA-dependent_RNA_polymerase@Nigeria(NC_045512@Nigeria:+: 13442-

13468+13468-16236) 310-327

6 243-247 ATLQA linker 1-5

6 248-261 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

142-155

6 262-266 ATLQA linker 1-5

6 267-288 SQHTMLVKQFDDYVYLPYPDPS RNA- dependent_RNA_polymerase@Estonia(NC_045512@Estonia:+:13442-1 3468+13468-16236) 814-835

6 289-293 ATLQA linker 1-5

6 294-301 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

6 302-306 ATLQA linker 1-5

6 307-315 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708

6 316-320 ATLQA linker 1-5

6 321-340 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

6 341-345 ATLQA linker 1-5

6 346-358 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

6 359-363 ATLQA linker 1-5

6 364-383 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

1048-1067

6 384-388 ATLQA linker 1-5

6 389-403 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368

6 404-408 ATLQA linker 1-5

6 409-424 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31

6 425-429 ATLQA linker 1-5

6 430-443 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

6 444-448 ATLQA linker 1-5

6 449-461 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

6 462-466 ATLQA linker 1-5

6 467-481 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

6 482-486 ATLQA linker 1-5

6 487-501 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 396-410 502-506 ATLQA linker 1-5 507-519 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191) 119-131 520-524 ATLQA linker 1-5 525-543 ECAQVLSETVMCGGSLYVK RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442- 3468+13468-162: 3) 658-676

544-548 ATLQA linker 1-5

549-564 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654 565-569 ATLQA linker 1-5

570-579 SSVLHSTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

580-584 ATLQA linker 1-5

585-610 YRLANECAQVLSEIVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Canada(NC_045512@Canada:+:13442-134 68+13468-16236) 653-678 6 611-615 ATLQA linker 1-5

6 616-637 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384)

125-146

6 638-642 ATLQA linker 1-5

6 643-654 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

6 655-659 ATLQA linker 1-5

6 660-673 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

6 674-678 ATLQA linker 1-5

6 679-693 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

6 694-698 ATLQA linker 1-5

6 699-706 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

6 707-711 ATLQA linker 1-5

6 712-723 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24

6 724-728 ATLQA linker 1-5

6 729-742 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450

6 743-747 ATLQA linker 1-5

6 748-762 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

6 763-767 ATLQA linker 1-5

6 768-787 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 209-228

6 788-792 ATLQA linker 1-5

6 793-805 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes from SARS-CoV-2 with intervening linker sequences (and as set forth in Figure 18). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses four of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses five of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 8 concatemer P ^os J ⁿ _ ^conc atemer epitope gene pos_in_gene 1 1 -8 TQALLQRQ nucleocapsid_phosphoprotein@CostaRica(NC_045512@CostaRica:+: 28274-29533)

379-386 1 9-13 ATLQA linker 1-5

1 14-28 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

1 29-33 ATLQA linker 1-5

1 34-45 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

1 46-50 ATLQA linker 1-5

1 51-58 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

1 59-63 ATLQA linker 1-5

1 64-76 SMWALIISVTSNY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 160-172

1 77-81 ATLQA linker 1-5

1 82-100 QLSLSKGFHFVCNLLLLFV ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220) 70-88

1 101-105 ATLQA linker 1-5

1 106-114 ISEHDYHIG ORF3a_protein@NorthMacedonia(NC_045512@NorthMacedonia:+:2539 3-26220)

179-187 1 115-119 ATLQA linker 1-5

1 120-129 PFTINCQEPK ORF8_protein@lndia(NC_045512@lndia:+:27894-28259) 85-94

1 130-134 ATLQA linker 1-5

1 135-142 WFTALTQH nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 52-59

1 143-147 ATLQA linker 1-5

1 148-156 YGIIWVATE nucleocapsid_phosphoprotein@SmallSouthAmerica(NC_045512@Smal lSouthAmerica:+:28274-29533) 128-136 1 157-161 ATLQA linker 1-5

1 162-203 TTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 11-52

1 204-208 ATLQA linker 1-5

1 209-222 RLTLGVYDYLVSTQ nsp6(NC_045512:+:10973-11842) 236-249

1 223-227 ATLQA linker 1-5

1 228-242 VCNLLLLFVTVYSHL ORF3a_protein@Croatia(NC_045512@Croatia:+:25393-26220) 80-94

1 243-247 ATLQA linker 1-5

1 248-255 ISEHDYQI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 179-186

1 256-260 ATLQA linker 1-5

1 261-275 YFTSDYYQLYSTQLI QRF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220) 206-220

1 276-280 ATLQA linker 1-5

1 281-289 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

1 290-294 ATLQA linker 1-5

1 295-304 GLKLKDCVMY nsp6@Peru(NC_045512@Peru:+: 10973-11842) 107-116

1 305-309 ATLQA linker 1-5

1 310-318 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19

1 319-323 ATLQA linker 1-5

1 324-344 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 605-625

1 345-349 ATLQA linker 1-5

1 350-372 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

1 373-377 ATLQA linker 1-5

1 378-395 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142

1 396-400 ATLQA linker 1-5

1 401-408 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

1 409-413 ATLQA linker 1-5

1 414-421 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

1 422-426 ATLQA linker 1-5

1 427-438 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54

1 439-443 ATLQA linker 1-5

1 444-460 EVTPSGTWLTYTGAIKL nucleocapsid_phosphoprotein@Bulgaria(NC_045512@Bulgaria:+:28 274-29533)

323-339

1 461-465 ATLQA linker 1-5

1 466-476 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

1 477-481 ATLQA linker 1-5

1 482-491 SSVLFISTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

1 492-496 ATLQA linker 1-5

1 497-513 ILLNKHIDAYKTFPPIE nucleocapsid_phosphoprotein@Chile(NC_045512@Chile:+:28274-29 533)

351-367

1 514-518 ATLQA linker 1-5

1 519-529 SPGVFNPVMEP ORF3a_protein@Colombia(NC_045512@Colombia:+:25393-26220) 252-262

1 530-534 ATLQA linker 1-5

1 535-542 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

1 543-547 ATLQA linker 1-5

1 548-569 IAMACLVGLMWLSYFIASFRLF membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191)

82-103

1 570-574 ATLQA linker 1-5

1 575-589 IPIRASLPFGWLIVG ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 35-49

1 590-594 ATLQA linker 1-5

1 595-606 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

1 607-611 ATLQA linker 1-5

1 612-632 ELVIGAVILRGHLRIAGHHLG membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 137-157

1 633-637 ATLQA linker 1-5

1 638-652 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

2 1-37 VAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKC

QRF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 97-133

2 38-42 ATLQA linker 1-5

2 43-53 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

2 54-58 ATLQA linker 1-5

2 59-72 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

2 73-77 ATLQA linker 1-5

2 78-86 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-1169

2 87-91 ATLQA linker 1-5

2 92-111 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

1048-1067

2 112-116 ATLQA linker 1-5

2 117-127 CLPFTINCQKP QRF8_protein@Brazil(NC_045512@Brazil:+:27894-28259) 83-93 2 128-132 ATLQA linker 1-5

2 133-161 SMWALIISVTSNYSGVVTIVMFLARGIVF nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+: 10973-11842) 160-188

2 162-166 ATLQA linker 1-5

2 167-197 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

2538· 1211-1241

2 198-202 ATLQA linker 1-5

2 203-234 MMFVKHKHAFLCLFLLPSFATVAYFNMVYMPA nsp6@lndonesia(NC_045512@lndonesia:+:10973-11842) 57-88

2 235-239 ATLQA linker 1-5

2 240-255 QLALSKGFHFVCNLLL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 70-85

2 256-260 ATLQA linker 1-5

2 261-272 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

2 273-277 ATLQA linker 1-5

2 278-290 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

2 291-295 ATLQA linker 1-5

2 296-306 AALALLLLDRL nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 217-227

2 307-311 ATLQA linker 1-5

2 312-319 SSIVITSV ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 165-172

2 320-324 ATLQA linker 1-5

2 325-338 ESVVKDCVVLHSYF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 194-207

2 339-343 ATLQA linker 1-5

2 344-355 SVFQSASKIITL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 54-65

2 356-360 ATLQA linker 1-5

2 361-379 CYDYCIPYNSVTSLIVITS QRF3a_protein@Netherlands(NC_045512@Netherlands:+:25393-2622 0) 153-171

2 380-384 ATLQA linker 1-5

2 385-395 MMFVKHKHAFL nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 57-67

2 396-400 ATLQA linker 1-5

2 401-408 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

2 409-413 ATLQA linker 1-5

2 414-435 QLALSKGVHFVCNLLLLFVTVY ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220) 70-91

2 436-440 ATLQA linker 1-5

2 441-454 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 294-307

2 455-459 ATLQA linker 1-5

2 460-467 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

2 468-472 ATLQA linker 1-5

2 473-488 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

2 489-493 ATLQA linker 1-5

2 494-507 ITTVAAFHQECSLQ ORF8_protein@Aruba(NC_045512@Aruba:+:27894-28259) 10-23

2 508-512 ATLQA linker 1-5

2 513-527 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384)

680-694

2 528-532 ATLQA linker 1-5

2 533-555 KNPLLYDANYFLCCHTNCYDYCI ORF3a_protein@Senegal(NC_045512@Senegal:+:25393-26220) 136-158

2 556-560 ATLQA linker 1-5

2 561-579 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727

2 580-584 ATLQA linker 1-5

2 585-595 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

1088

2 596-600 ATLQA linker 1-5

2 601-617 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384) 258-274

2 618-622 ATLQA linker 1-5

2 623-641 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384) 607-625

3 1 -10 YDANYFLCWH ORF3a_protein(NC_045512:+:25393-26220) 141-150

3 11 -15 ATLQA linker 1-5

3 16-26 SAPLIELCLDE ORF8_protein@Russia(NC_045512@Russia:+:27894-28259) 54-64

3 27-31 ATLQA linker 1-5

3 32-55 TTVAAFHQECSLQLCTQHQPYVVD ORF8_protein@USA(NC_045512@USA:+:27894-28259) 11-34

3 56-60 ATLQA linker 1-5

3 61-74 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

3 75-79 ATLQA linker 1-5

3 80-88 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266

3 89-93 ATLQA linker 1-5

3 94-109 NYTVSCSPFTINCQEP ORF8_protein@CostaRica(NC_045512@CostaRica:+:27894-28259) 78-93

3 110-114 ATLQA linker 1-5

3 115-124 PRWYFYYLGT nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 106-115 125-129 ATLQA linker 1-5

130-137 SSIVITSG ORF3a_protein@SouthKorea(NC_045512@SouthKorea:+:25393-26220) 165-172 138-142 ATLQA linker 1-5

143-150 ETQALPQR nucleocapsid_phosphoprotein@SmallNorthAmerica(NC_045512@Smal lNorthAmerica:+:28274-29533) 378-385 151-155 ATLQA linker 1-5

156-179 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(NC_045512:+:27894-28259) 95-118

180-184 ATLQA linker 1-5

185-197 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

198-202 ATLQA linker 1-5

203-210 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478

211-215 ATLQA linker 1-5

216-225 GVGGKPCIKV nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 274-283

226-230 ATLQA linker 1-5

231 -252 LLYDANYFLCWHINCYDYCIPY QRF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220)

139-160

253-257 ATLQA linker 1-5

258-273 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

274-278 ATLQA linker 1-5

279-291 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

292-296 ATLQA linker 1-5

297-309 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

310-314 ATLQA linker 1-5

315-324 ISEHDYQIGG ORF3a_protein@FrenchGuiana(NC_045512@FrenchGuiana:+:25393-26 220) 179-188

325-329 ATLQA linker 1-5

330-351 SDFVRATATIPIQASLPFGWLI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

26-47

352-356 ATLQA linker 1-5

357-364 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

365-369 ATLQA linker 1-5

370-386 GVHFVCNLLLLFVIVYS ORF3a_protein@Malaysia(NC_045512@Malaysia:+:25393-26220) 76-92

387-391 ATLQA linker 1-5

392-412 VMFLARGIVFMCVDYCPI FFI nsp6@Cyprus(NC_045512@Cyprus:+: 10973-11842) 179-199

413-417 ATLQA linker 1-5

418-426 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788

427-431 ATLQA linker 1-5

432-445 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

446-450 ATLQA linker 1-5

451-466 AFKLNIKLLGVGGKPC nsp6(NC_045512:+:10973-11842) 268-283

467-471 ATLQA linker 1-5

472-485 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

486-490 ATLQA linker 1-5

491-511 QWNLVIGFLFLTWICLLQFAYmembrane_glycoprotein@Aruba(NC_045512@A ruba:+:26523-27191) 19-39 512-516 ATLQA linker 1-5

517-534 VTTVIFLARGIVFMCVEY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 179-196

535-539 ATLQA linker 1-5

540-556 LFFFLYENAFLPFVMGI nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+:10973-1 1842) 33-49

557-561 ATLQA linker 1-5

562-573 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

574-578 ATLQA linker 1-5

579-606 FTSDYYQLYSTQLSTYTGVEHVTFFIYN ORF3a_protein@Latvia(NC_045512@Latvia:+:25393-

207-234

607-611 ATLQA linker 1-5

612-621 SFKLKDCVMY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 107-116

622-626 ATLQA linker 1-5

627-641 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

1-23 QLALSKGVYFVCNLLLLFVTVYS ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

70-92

24-28 ATLQA linker 1-5

29-36 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

37-41 ATLQA linker 1-5

42-52 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

53-57 ATLQA linker 1-5

58-70 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

71-75 ATLQA linker 1-5

76-90 VDTSLSSLKLKDCVM nsp6@Latvia(NC_045512@Latvia:+:10973-11842) 101-115

91-95 ATLQA linker 1-5

96-104 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474 105-109 ATLQA linker 1-5 110-134 AAGLEAPFLYLYVLVYFLQSINFVR ORF3a_protein@Norway(NC_045512@Norway:+:25393-26220) 98-122

135-139 ATLQA linker 1-5 140-148 KHWPQIAQF nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 299-307 149-153 ATLQA linker 1-5 154-161 APLIELCV ORF8_protein(NC_045512:+:27894-28259) 55-62 162-166 ATLQA linker 1-5 167-188 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

206-227 189-193 ATLQA linker 1-5 194-201 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378 202-206 ATLQA linker 1-5

207-216 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840 217-221 ATLQA linker 1-5 222-238 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765 239-243 ATLQA linker 1-5 244-263 DANYFLCWHTNCYHYCIPYN QRF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220) 142-161 264-268 ATLQA linker 1-5 269-291 KEITVATSRTLSYYKLGASQRVA membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 166-188 292-296 ATLQA linker 1-5 297-306 LPFTINCQEL ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 84-93 307-311 ATLQA linker 1-5 312-320 APLIELCVD ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 55-63 321-325 ATLQA linker 1-5 326-334 DYYQLYSTQ ORF3a_protein(NC_045512:+:25393-26220) 210-218 335-339 ATLQA linker 1-5 340-358 VKDCVLLHSYFTSDYYQLY ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220) 197-215 359-363 ATLQA linker 1-5 364-373 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855 374-378 ATLQA linker 1-5 379-386 SDFVRATA ORF3a_protein(NC_045512:+:25393-26220) 26-33 387-391 ATLQA linker 1-5 392-401 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980 402-406 ATLQA linker 1-5 407-424 FLYENAFLPFAMGVIAMS nsp6@Mexico(NC_045512@Mexico :+ : 10973-11842) 36-53 425-429 ATLQA linker 1-5 430-442 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191) 119-131 443-447 ATLQA linker 1-5 448-469 SDFVRATATIPIRASLPFGWLI ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220) 26-47 470-474 ATLQA linker 1-5 475-503 FLYIIKLIFLWLLWPVTLACFVLAAVYRI membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 45-73 504-508 ATLQA linker 1-5 509-524 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 59-74 525-529 ATLQA linker 1-5 530-558 TLQCIMLVYCFLGYFCTCYFGLFCLLNRY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 203-231 559-563 ATLQA linker 1-5 564-586 VAAGLEAPFFYLYALVYFLQSIN QRF3a_protein@Ecuador(NC_045512@Ecuador:+:25393-26220) 97-119 587-591 ATLQA linker 1-5 592-599 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293 600-604 ATLQA linker 1-5 605-619 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 129-143 620-624 ATLQA linker 1-5 625-634 SPGVVNPVME ORF3a_protein@Brazil(NC_045512@Brazil:+:25393-26220)252-261 635-639 ATLQA linker 1-5 640-659 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-1256 1-25 KNPLLYDANYFLCWHTNCYDYCIPY QRF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

136-160 26-30 ATLQA linker 1-5 31-41 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146 42-46 ATLQA linker 1-5 47-60 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18 61-65 ATLQA linker 1-5 66-74 LKLKDCVMY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 105-113 75-79 ATLQA linker 1-5

80-99 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224 100-104 ATLQA linker 1-5

105-112 VVNPVMEP ORF3a_protein(NC_045512:+:25393-26220) 255-262

113-117 ATLQA linker 1-5

118-125 EHVQIHTI O R F3a_prote in (N C_045512 : + : 25393-26220) 242-249

126-130 ATLQA linker 1-5

131-140 ALLAVFHNAS QRF3a_protein@SmallSouthAmerica(NC_045512@SmallSouthAmerica: +:25393-26220)

51-60

141-145 ATLQA linker 1-5

146-164 VKDCVVLHSYFTSDYYQLY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 197-215 165-169 ATLQA linker 1-5

170-184 ALLAVFHSASKIITL ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 51-65

185-189 ATLQA linker 1-5

190-212 TTVMFLARGIVFMCVEYCPIFFI nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 177-199

213-217 ATLQA linker 1-5

218-240 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242 241-245 ATLQA linker 1-5

246-260 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629 261-265 ATLQA linker 1-5 266-282 INFVRIIMRLWLCLKCR QRF3a_protein@Mozambique(NC_045512@Mozambique:+:25393-26220) 118-134 283-287 ATLQA linker 1-5 288-301 KHWPQIAQFAPSAS nucleocapsid_phosphoprotein@Australia(NC_045512@Australia:+: 28274- 299-312 302-306 ATLQA linker 1-5 307-320 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-2 5384) 128-141 321-325 ATLQA linker 1-5 326-340 ALLAVFQSASKIITLORF3a_protein@Bangladesh(NC_045512@Bangladesh :+:25393-26220) 51-65 341-345 ATLQA linker 1-5 346-359 LMNVLTLVYKVYYG nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 139-152 360-364 ATLQA linker 1-5 365-373 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66 374-378 ATLQA linker 1-5 379-386 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203 387-391 ATLQA linker 1-5 392-401 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133 402-406 ATLQA linker 1-5 407-421 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384) 496-510 422-426 ATLQA linker 1-5 427-442 LMNVLTLFYKVYYGNA nsp6@Chile(NC_045512@Chile:+:10973-11842) 142-157 443-447 ATLQA linker 1-5 448-463 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19 464-468 ATLQA linker 1-5 469-488 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 209-228 489-493 ATLQA linker 1-5 494-508 VEHVTFFIYNKIVDE QRF3a_protein(NC_045512:+:25393-26220) 225-239 509-513 ATLQA linker 1-5 514-531 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404 532-536 ATLQA linker 1-5 537-550 TDTVVEHVTFFIYN ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 221-234 551-555 ATLQA linker 1-5 556-571 NYTVSCLPFTINCQEP ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 78-93 572-576 ATLQA linker 1-5 577-586 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844 587-591 ATLQA linker 1-5 592-601 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895 602-606 ATLQA linker 1-5 607-616 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173 617-621 ATLQA linker 1-5 622-635 TDTCVEHVTFFIYNORF3a_protein@Luxembourg(NC_045512@Luxembourg: +:25393-26220) 221-234 1 -12 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787 13-17 ATLQA linker 1-5 18-35 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161 -178 36-40 ATLQA linker 1-5 41-55 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368 56-60 ATLQA linker 1-5 61-73 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693 74-78 ATLQA linker 1-5 79-92 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509 93-97 ATLQA linker 1-5 98-107 NCYDYCIPYN O R F3a_prote in (N C_045512 : + : 25393-26220) 152-161 108-112 ATLQA linker 1-5 113-129 KDQVILLNKHIDAYKTF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 347-363 130-134 ATLQA linker 1-5 135-157 HQPYVVDDPCPIHFYSKWYIRVG ORF8_protein(NC_045512:+:27894-28259) 28-50 158-162 ATLQA linker 1-5 163-180 QLALFKGVHFVCNLLLLF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 70-87 181-185 ATLQA linker 1-5 186-197 DTSLKLKECVMY nsp6@SmallAsia(NC_045512@SmallAsia:+:10973-11842) 102-113 198-202 ATLQA linker 1-5 203-225 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061 226-230 ATLQA linker 1-5 231-249 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600 250-254 ATLQA linker 1-5 255-277 YALVYFLQSINFVIIIMRLWLCW QRF3a_protein@Denmark(NC_045512@Denmark:+:25393-26220) 109-131 278-282 ATLQA linker 1-5 283-298 HWPQIAQFAPSASAFF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 300-315 299-303 ATLQA linker 1-5 304-319 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001-1016 320-324 ATLQA linker 1-5 325-332 TQALPFIRQ nucleocapsid_phosphoprotein@Mozambique(NC_045512@Mozambique: +:28274-29533) 379-386 333-337 ATLQA linker 1-5 338-345 EVTPSGTW nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 323-330 346-350 ATLQA linker 1-5 351-362 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497 363-367 ATLQA linker 1-5 368-383 ATVAYFNMVYMPASWV nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 76-91 384-388 ATLQA linker 1-5 389-396 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742 397-401 ATLQA linker 1-5 402-415 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498 416-420 ATLQA linker 1-5 421 -442 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 125-146 443-447 ATLQA linker 1-5 448-472 VLVQSTQWSLFFFFYENAFLPFAMG nsp6@lceland(NC_045512@lceland:+:10973-11842) 24-48 473-477 ATLQA linker 1-5 478-499 GYQ PYRVVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525 500-504 ATLQA linker 1-5 505-529 VLVQSTQWSLFFFLYENAFLPFAMG nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 24-48 530-534 ATLQA linker 1-5 535-545 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68 546-550 ATLQA linker 1-5 551 -564 IHFYSKWYIRVGAK ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 39-52 565-569 ATLQA linker 1-5 570-579 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921 580-584 ATLQA linker 1-5 585-601 INFVRIIMRLWLCCKCR ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220) 118-134 602-606 ATLQA linker 1-5 607-630 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563- 205-228 631-635 ATLQA linker 1-5 636-647 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731 In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes with intervening linker sequences (and as set forth in Figure 19). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 9 concatemer P ^os _in_ ^conc atemer epitope gene pos_in_gene 1 1-16 YVRITGLYPTLNISYE helicase@SmallNorthAmerica(NC_045512@SmallNorthAmerica:+:162 37-18039)

246-261

1 17-26 PRRARSVRYP linker 1-10

1 27-49 TQLYLGGMSYYCKPHKPPISFPL helicase@lceland(NC_045512@lceland:+:16237-18039) 61-83

1 50-59 PRRARSVRYP linker 1-10

1 60-70 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

1088

1 71-80 PRRARSVRYP linker 1-10

1 81-90 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111

1 91-100 PRRARSVRYP linker 1-10

1 101-128 FTSDYYQLYSTQLSTYTGVEHVTFFIYN ORF3a_protein@Latvia(NC_045512@Latvia:+:25393-

26220) 207-234

1 129-138 PRRARSVRYP linker 1-10

1 139-154 NYTVSCLPFTINCQEP ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259)

78-93

1 155-164 PRRARSVRYP linker 1-10

1 165-184 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

1 185-194 PRRARSVRYP linker 1-10

1 195-204 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 434-443

1 205-214 PRRARSVRYP linker 1-10

1 215-228 TDTVVEHVTFFIYN ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 221-234

1 229-238 PRRARSVRYP linker 1-10

1 239-248 NVAFNVVNKG endoRNAse(NC_045512:+:19621 -20658) 4-13

1 249-258 PRRARSVRYP linker 1-10

1 259-275 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

1 276-285 PRRARSVRYP linker 1-10

1 286-307 SQHTMLVKQFDDYVYLPYPDPS RNA- dependent_RNA_polymerase@Estonia(NC_045512@Estonia:+:13442-1 3468+13468-16236) 814-835

1 308-317 PRRARSVRYP linker 1-10

1 318-337 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197

1 338-347 PRRARSVRYP linker 1-10

1 348-359 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

1 360-369 PRRARSVRYP linker 1-10

1 370-408 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

1 409-418 PRRARSVRYP linker 1-10

1 419-431 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480

1 432-441 PRRARSVRYP linker 1-10

1 442-450 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266

1 451-460 PRRARSVRYP linker 1-10

1 461-468 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

1 469-478 PRRARSVRYP linker 1-10

1 479-488 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

1 489-498 PRRARSVRYP linker 1-10

1 499-514 VREVLSDRELHLSWEV helicase(NC_045512:+:16237-18039) 154-169

1 515-524 PRRARSVRYP linker 1-10

1 525-532 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

1 533-542 PRRARSVRYP linker 1-10

1 543-553 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006

1 554-563 PRRARSVRYP linker 1-10

1 564-579 HWPQIAQFAPSASAFF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 300-315

1 580-589 PRRARSVRYP linker 1-10 1 590-600 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973

1 601-610 PRRARSVRYP linker 1-10

1 611-619 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

1 620-629 PRRARSVRYP linker 1-10

1 630-646 ILLNKHIDAYKTFPPIE nucleocapsid_phosphoprotein@Chile(NC_045512@Chile:+:28274-29 533)

351-367

1 647-656 PRRARSVRYP linker 1-10

1 657-675 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727

1 676-685 PRRARSVRYP linker 1-10

1 686-694 KFPLKLRGT 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 249-257

1 695-704 PRRARSVRYP linker 1-10

1 705-714 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980

1 715-724 PRRARSVRYP linker 1-10

1 725-735 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

1 736-745 PRRARSVRYP linker 1-10

1 746-755 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

1 756-765 PRRARSVRYP linker 1-10

1 766-775 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

1 776-785 PRRARSVRYP linker 1-10

1 786-800 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

1 801-810 PRRARSVRYP linker 1-10

1 811-824 TSACVLAAECTI FK nsp4(NC_045512:+:8555-10054) 147-160

1 825-834 PRRARSVRYP linker 1-10

1 835-852 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

470-487

1 853-862 PRRARSVRYP linker 1-10

1 863-876 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498

1 877-886 PRRARSVRYP linker 1-10

1 887-902 ATVAYF N M VYM PASWV nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 76-91

1 903-912 PRRARSVRYP linker 1-10

1 913-925 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349

1 926-935 PRRARSVRYP linker 1-10

1 936-952 LFFFLYENAFLPFVMGI nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+:10973-1 1842)

33-49

1 953-962 PRRARSVRYP linker 1-10

1 963-972 ALLAVFHNAS ORF3a_protein@SmallSouthAmerica(NC_045512@SmallSouthAmerica: +:25393-26220)

51-60

1 973-982 PRRARSVRYP linker 1-10

1 983-993 YDKLQFTSLEI helicase@Aruba(NC_045512@Aruba:+:16237-18039) 582-592

1 994-1003 PRRARSVRYP linker 1-10

1 1004-1011 SSNVANYQ helicase@Austria(NC_045512@Austria:+:16237-18039) 263-270

1 1012-1021 PRRARSVRYP linker 1-10

1 1022-1030 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

1 1031-1040 PRRARSVRYP linker 1-10

1 1041-1082 TTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR

ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-2825 9) 11-52

1 1083-1092 PRRARSVRYP linker 1-10

1 1093-1100 DMYSVMLT RNA-dependent_RNA_polymerase@Malaysia(NC_045512@Malaysia:+:1 3442-

13468+13468-16236) 901-908 1 1101-1110 PRRARSVRYP linker 1-10

1 1111-1126 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 331-346 1 1127-1136 PRRARSVRYP linker 1-10

1 1137-1167 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1211-1241

1 1168-1177 PRRARSVRYP linker 1-10

1 1178-1192 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-

25384) 496-510

1 1193-1202 PRRARSVRYP linker 1-10

1 1203-1219 KDQVILLNKHIDAYKTF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-

29533) 347-363

1 1220-1229 PRRARSVRYP linker 1-10

1 1230-1237 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

1 1238-1247 PRRARSVRYP linker 1-10

1 1248-1260 KLALGGSVAIKIT 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 160-172

1 1261-1270 PRRARSVRYP linker 1-10

1 1271 -1278 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

1 1279-1288 PRRARSVRYP linker 1-10

1 1289-1302 ITTVAAFHQECSLQ ORF8_protein@Aruba(NC_045512@Aruba:+:27894-28259) 10-23

1 1303-1312 PRRARSVRYP linker 1-10 1 1313-1328 LMNVLTLFYKVYYGNA nsp6@Chile(NC_045512@Chile:+:10973-11842) 142-157

1 1329-1338 PRRARSVRYP linker 1-10

1 1339-1361 HQPYVVDDPCPIHFYSKWYIRVG ORF8_protein(NC_045512:+:27894-28259) 28-50

1 1362-1371 PRRARSVRYP linker 1-10

1 1372-1395 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(NC_045512:+:27894-28259) 95-118

1 1396-1405 PRRARSVRYP linker 1-10

1 1406-1415 LPRVFSAVGN nsp4(NC_045512:+:8555-10054) 122-131

1 1416-1425 PRRARSVRYP linker 1-10

1 1426-1448 QLALSKGVYFVCNLLLLFVTVYS ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-

26220) 70-92

1 1449-1458 PRRARSVRYP linker 1-10

1 1459-1466 YDFAVSKG RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 420-427 1 1467-1476 PRRARSVRYP linker 1-10

1 1477-1502 YRLANECAQVLSEIVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Canada(NC_045512@Canada:+:13442-134 68+13468-16236) 653-678

1 1503-1512 PRRARSVRYP linker 1-10 1 1513-1520 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499 1 1521-1530 PRRARSVRYP linker 1-10 1 1531 -1538 YLKLRSDV nsp4(NC_045512:+:8555-10054) 427-434 1 1539-1548 PRRARSVRYP linker 1-10 1 1549-1567 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236 1 1568-1577 PRRARSVRYP linker 1-10 1 1578-1587 SFKLKDCVMY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 107-116 1 1588-1597 PRRARSVRYP linker 1-10 1 1598-1607 PRWYFYYLGT nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 106-115

1 1608-1617 PRRARSVRYP linker 1-10

1 1618-1636 CYDYCIPYNSVTSLIVITS ORF3a_protein@Netherlands(NC_045512@Netherlands:+:25393-

26220) 153-171

1 1637-1646 PRRARSVRYP linker 1-10

1 1647-1655 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579

1 1656-1665 PRRARSVRYP linker 1-10

1 1666-1674 GVVQQLPET endoRNAse(NC_045512:+:19621 -20658) 184-192

1 1675-1684 PRRARSVRYP linker 1-10

1 1685-1697 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

1 1698-1707 PRRARSVRYP linker 1-10

1 1708-1719 SVLLSMQGAVDI nsp7(NC_045512:+:11843-12091) 57-68

1 1720-1729 PRRARSVRYP linker 1-10

1 1730-1742 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

1 1743-1752 PRRARSVRYP linker 1-10

1 1753-1765 VKGLQPSVGPKQA endoRNAse(NC_045512:+:19621 -20658) 148-160

1 1766-1775 PRRARSVRYP linker 1-10

1 1776-1794 QLSLSKGFHFVCNLLLLFV ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220) 70-88

1 1795-1804 PRRARSVRYP linker 1-10

1 1805-1817 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

1 1818-1827 PRRARSVRYP linker 1-10

1 1828-1838 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

1 1839-1848 PRRARSVRYP linker 1-10

1 1849-1860 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

1 1861-1870 PRRARSVRYP linker 1-10

1 1871 -1884 RLTLGVYDYLVSTQ nsp6(NC_045512:+:10973-11842) 236-249

1 1885-1894 PRRARSVRYP linker 1-10

1 1895-1905 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

1 1906-1915 PRRARSVRYP linker 1-10

1 1916-1937 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-

25384) 125-146

1 1938-1947 PRRARSVRYP linker 1-10

1 1948-1955 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691

1 1956-1965 PRRARSVRYP linker 1-10

1 1966-1984 ANSVFNICQAVTANVNALL RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 690-708

1 1985-1994 PRRARSVRYP linker 1-10

1 1995-2004 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

743-752

1 2005-2014 PRRARSVRYP linker 1-10

1 2015-2034 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1048-1067 1 2035-2044 PRRARSVRYP linker 1-10

1 2045-2057 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

1 2058-2067 PRRARSVRYP linker 1-10

1 2068-2077 ISDYDYYRYN RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 450-459 1 2078-2087 PRRARSVRYP linker 1-10

1 2088-2095 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

1 2096-2105 PRRARSVRYP linker 1-10

1 2106-2127 LGGMSYYCKSHKPSISFPLCAN helicase@NewZealand(NC_045512@NewZealand:+:16237-

18039) 65-86

1 2128-2137 PRRARSVRYP linker 1-10

1 2138-2146 IQLSSYSLF 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 237-245

1 2147-2156 PRRARSVRYP linker 1-10

1 2157-2176 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 826-845 1 2177-2186 PRRARSVRYP linker 1-10

1 2187-2197 ETICAPLTVFF endoRNAse(NC_045512:+:19621 -20658) 113-123

1 2198-2207 PRRARSVRYP linker 1-10

1 2208-2226 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384)

607-625

1 2227-2236 PRRARSVRYP linker 1-10

1 2237-2246 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

1 2247-2256 PRRARSVRYP linker 1-10

1 2257-2270 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

1 2271-2280 PRRARSVRYP linker 1-10

1 2281-2296 NYTVSCSPFTINCQEP ORF8_protein@CostaRica(NC_045512@CostaRica:+:27894-28259)

78-93

1 2297-2306 PRRARSVRYP linker 1-10

1 2307-2317 MMFVKHKHAFL nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 57-67

1 2318-2327 PRRARSVRYP linker 1-10

1 2328-2341 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

1 2342-2351 PRRARSVRYP linker 1-10

1 2352-2360 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

1 2361-2370 PRRARSVRYP linker 1-10

1 2371 -2385 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 129-143

1 2386-2395 PRRARSVRYP linker 1-10

1 2396-2405 DGYVMHANYI 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 220-229

1 2406-2415 PRRARSVRYP linker 1-10

1 2416-2423 EHVQIHTI ORF3a_protein(NC_045512:+:25393-26220) 242-249

1 2424-2433 PRRARSVRYP linker 1-10

1 2434-2448 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

1 2449-2458 PRRARSVRYP linker 1-10

1 2459-2481 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

1 2482-2491 PRRARSVRYP linker 1-10

1 2492-2507 SLRCGACIRRPFLCCK helicase@Aruba(NC_045512@Aruba:+:16237-18039) 13-28

1 2508-2517 PRRARSVRYP linker 1-10

1 2518-2526 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

2 1-11 GPKVKYLYFIK nsp9(NC_045512:+:12686-13024) 82-92

2 12-21 PRRARSVRYP linker 1-10

2 22-33 TEISFMLWCKDG endoRNAse(NC_045512:+:19621 -20658) 325-336

2 34-43 PRRARSVRYP linker 1-10

2 44-61 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

2 62-71 PRRARSVRYP linker 1-10

2 72-79 WFTALTQH nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 52-59

2 80-89 PRRARSVRYP linker 1-10

2 90-99 LSVNPYVCNA helicase@Cyprus(NC_045512@Cyprus:+: 16237-18039) 43-52

2 100-109 PRRARSVRYP linker 1-10

2 110-124 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 680-694

2 125-134 PRRARSVRYP linker 1-10

2 135-149 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

2 150-159 PRRARSVRYP linker 1-10

2 160-180 VMFLARGIVFMCVDYCPI FFI nsp6@Cyprus(NC_045512@Cyprus:+: 10973-11842) 179-199

2 181-190 PRRARSVRYP linker 1-10

2 191-200 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895

2 201 -210 PRRARSVRYP linker 1-10 2 211-218 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

2 219-228 PRRARSVRYP linker 1-10

2 229-238 SPGVVNPVME ORF3a_protein@Brazil(NC_045512@Brazil:+:25393-26220) 252-261

2 239-248 PRRARSVRYP linker 1-10

2 249-258 KNTVCTVCGM nsp10(NC_045512:+: 13025-13441 ) 113-122

2 259-268 PRRARSVRYP linker 1-10

2 269-289 KLSYGIAIVREVLSDRELHLS helicase@Colombia(NC_045512@Colombia:+:16237-18039) 146-166

2 290-299 PRRARSVRYP linker 1-10

2 300-314 VEHVTFFIYNKIVDE ORF3a_protein(NC_045512:+:25393-26220) 225-239

2 315-324 PRRARSVRYP linker 1-10

2 325-332 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

2 333-342 PRRARSVRYP linker 1-10

2 343-351 VLGSLAATV nsp9(NC_045512:+:12686-13024) 102-110

2 352-361 PRRARSVRYP linker 1-10

2 362-370 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19

2 371 -380 PRRARSVRYP linker 1-10

2 381 -392 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24

2 393-402 PRRARSVRYP linker 1-10

2 403-410 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207

2 411 -420 PRRARSVRYP linker 1-10

2 421 -433 SMWALIISVTSNY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 160-172

2 434-443 PRRARSVRYP linker 1-10

2 444-462 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

2 463-472 PRRARSVRYP linker 1-10

2 473-480 YDFVVSKG RNA-dependent_RNA_polymerase@Japan(NC_045512@Japan:+:13442-1 3468+13468-

16236) 420-427

2 481 -490 PRRARSVRYP linker 1-10

2 491-498 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

2 499-508 PRRARSVRYP linker 1-10

2 509-530 QLALSKGVHFVCNLLLLFVTVY ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220)

70-91

2 531 -540 PRRARSVRYP linker 1-10

2 541-565 KNPLLYDANYFLCWHTNCYDYCIPY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

136-160

2 566-575 PRRARSVRYP linker 1-10

2 576-591 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

2 592-601 PRRARSVRYP linker 1-10

2 602-609 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817

2 610-619 PRRARSVRYP linker 1-10

2 620-633 LSPVALRQMSCAAG nsp9(NC_045512:+:12686-13024) 4-17

2 634-643 PRRARSVRYP linker 1-10

2 644-651 VQLRVIGH 3C-like_proteinase(NC_045512:+: 10055-10972) 73-80

2 652-661 PRRARSVRYP linker 1-10

2 662-685 TTVAAFHQECSLQLCTQHQPYVVD ORF8_protein@USA(NC_045512@USA:+:27894-28259) 11 -34

2 686-695 PRRARSVRYP linker 1-10

2 696-716 HPNCVNCLDDRCILHCANFNV RNA- d ependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 295-315

2 717-726 PRRARSVRYP linker 1-10

2 727-740 GASCCLYCRCHIDH nsp10(NC_045512:+: 13025-13441) 70-83

2 741 -750 PRRARSVRYP linker 1-10

2 751-760 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400

2 761 -770 PRRARSVRYP linker 1-10

2 771 -779 ISEHDYHIG ORF3a_protein@NorthMacedonia(NC_045512@NorthMacedonia:+:2539 3-26220) 179-187

2 780-789 PRRARSVRYP linker 1-10

2 790-800 CLPFTINCQKP ORF8_protein@Brazil(NC_045512@Brazil:+:27894-28259) 83-93

2 801-810 PRRARSVRYP linker 1-10

2 811-818 DVLYQPPQ nsp4(NC_045512:+:8555-10054) 484-491

2 819-828 PRRARSVRYP linker 1-10

2 829-842 APGCDVTDVTQLYL helicase@Aruba(NC_045512@Aruba:+:16237-18039) 52-65

2 843-852 PRRARSVRYP linker 1-10

2 853-860 SINVANYQ helicase@Mozambique(NC_045512@Mozambique:+:16237-18039) 263-270

2 861 -870 PRRARSVRYP linker 1-10

2 871-881 VVNAANVYLKH nsp3(NC_045512 : + :2720-8554) 239-249

2 882-891 PRRARSVRYP linker 1-10

2 892-916 VLVQSTQWSLFFFFYENAFLPFAMG nsp6@lceland(NC_045512@lceland:+:10973-11842) 24-48

2 917-926 PRRARSVRYP linker 1-10

2 927-939 QCVQLHNDILLAK nsp7(NC_045512:+:11843-12091) 31-43

2 940-949 PRRARSVRYP linker 1-10

2 950-982 YEPLTQDHVDILGPLSAQTGIAVLDMCASLKEL 3C-like_proteinase(NC_045512:+:10055-10972) 239-271 2 983-992 PRRARSVRYP linker 1-10

2 993-1006 TDTCVEHVTFFIYN ORF3a_protein@Luxembourg(NC_045512@Luxembourg:+:25393-26220) 221-234

2 1007-1016 PRRARSVRYP linker 1-10

2 1017-1026 YDANYFLCWH ORF3a_protein(NC_045512:+:25393-26220) 141-150

2 1027-1036 PRRARSVRYP linker 1-10

2 1037-1045 APLIELCVD ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 55-63

2 1046-1055 PRRARSVRYP linker 1-10

2 1056-1073 YNLLKDCPAVAKHDFFKF RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 87-104

2 1074-1083 PRRARSVRYP linker 1-10

2 1084-1098 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219

2 1099-1108 PRRARSVRYP linker 1-10

2 1109-1123 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+: 13442-

13468+13468-16236) 396-410 2 1124-1133 PRRARSVRYP linker 1-10 2 1134-1148 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+: 13442- 13468+13468-16236) 857-871

2 1149-1158 PRRARSVRYP linker 1-10

2 1159-1179 ALCEKALKYFPIDKCSRIIPA helicase@Colombia(NC_045512@Colombia:+:16237-18039) 316-336

2 1180-1189 PRRARSVRYP linker 1-10

2 1190-1212 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-

1061

2 1213 1222 PRRARSVRYP linker 1-10

2 1223-1239 GVHFVCNLLLLFVIVYS ORF3a_protein@Malaysia(NC_045512@Malaysia:+:25393-26220) 76-92

2 1240-1249 PRRARSVRYP linker 1-10

2 1250-1261 TFKVSIWNLDYI ORF6_protein(NC_045512:+:27202-27387) 21 -32

2 1262-1271 PRRARSVRYP linker 1-10

2 1272-1285 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

2 1286-1295 PRRARSVRYP linker 1-10

2 1296-1324 FAFACPDGVKHVYQLRARSVSPKLFIRQE ORF7a_protein(NC_045512:+:27394-27759) 63-91

2 1325-1334 PRRARSVRYP linker 1-10

2 1335-1343 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129

2 1344-1353 PRRARSVRYP linker 1-10

2 1354-1368 ALLAVFHSASKIITL ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 51 -65

2 1369-1378 PRRARSVRYP linker 1-10

2 1379-1392 IHFYSKWYIRVGAK ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-

28259) 39-52

2 1393-1402 PRRARSVRYP linker 1-10

2 1403-1413 SAPLIELCLDE ORF8_protein@Russia(NC_045512@Russia:+:27894-28259) 54-64

2 1414-1423 PRRARSVRYP linker 1-10

2 1424-1436 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902

2 1437-1446 PRRARSVRYP linker 1-10

2 1447-1478 MMFVKHKHAFLCLFLLPSFATVAYFNMVYMPA nsp6@lndonesia(NC_045512@lndonesia:+:10973-11842) 57-88

2 1479-1488 PRRARSVRYP linker 1-10

2 1489-1498 ISEHDYQIGG ORF3a_protein@FrenchGuiana(NC_045512@FrenchGuiana:+:25393-26 220)

179-188

2 1499-1508 PRRARSVRYP linker 1-10

2 1509-1516 SDDAVVCF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 759-766 2 1517-1526 PRRARSVRYP linker 1-10

2 1527-1544 CANFNVLFSTVFPPTSFG RNA- dependent_RNA_polymerase@China(NC_045512@China:+: 13442-13468+13468-16236) 310-327 2 1545-1554 PRRARSVRYP linker 1-10

2 1555-1583 SMWALIISVTSNYSGVVTIVMFLARGIVF nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+: 10973-11842) 160-188

1584-1593 PRRARSVRYP linker 1-10 1594-1610 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+: 13442- 13468+13468-16236) 877-893

2 1611-1620 PRRARSVRYP linker 1-10

2 1621 -1628 FNSVCRLM helicase@Aruba(NC_045512@Aruba:+:16237-18039) 422-429

2 1629-1638 PRRARSVRYP linker 1-10

2 1639-1647 SEAFLIGCN 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 202-210

2 1648-1657 PRRARSVRYP linker 1-10

2 1658-1671 KHWPQIAQFAPSAS nucleocapsid_phosphoprotein@Australia(NC_045512@Australia:+: 28274-29533) 299-312 1672-1681 PRRARSVRYP linker 1-10 1682-1698 INFVRIIMRLWLCCKCR ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220) 118-134 1699-1708 PRRARSVRYP linker 1-10 1709-1724 EEIIYNLLKDCPAVAK RNA- dependent_RNA_polymerase@Senegal(NC_045512@Senegal:+:13442-1 3468+13468-16236) 83-98

2 1725-1734 PRRARSVRYP linker 1-10

2 1735-1750 SRIIPARARVDCFDKF helicase@Brazil(NC_045512@Brazil:+:16237-18039) 331-346

2 1751-1760 PRRARSVRYP linker 1-10

2 1761-1771 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

2 1772-1781 PRRARSVRYP linker 1-10

2 1782-1793 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

2 1794-1803 PRRARSVRYP linker 1-10

2 1804-1812 ASQGLVASI RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 771-779 1813-1822 PRRARSVRYP linker 1-10 1823-1838 QLALSKGFHFVCNLLL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 70-85 1839-1848 PRRARSVRYP linker 1-10 1849-1871 TTVMFLARGIVFMCVEYCPIFFI nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 177-199 1872-1881 PRRARSVRYP linker 1-10 1882-1895 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608 1896-1905 PRRARSVRYP linker 1-10 1906-1913 TQALPHRQ nucleocapsid_phosphoprotein@Mozambique(NC_045512@Mozambique: +:28274-29533) 379-386 1914-1923 PRRARSVRYP linker 1-10

1924-1946 VAAGLEAPFFYLYALVYFLQSIN ORF3a_protein@Ecuador(NC_045512@Ecuador:+:25393-

6220) 97-119

1947-1956 PRRARSVRYP linker 1-10

1957-1979 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

2 1980-1989 PRRARSVRYP linker 1-10

2 1990-1997 AWLYAAVI 3C-like_proteinase(NC_045512:+: 10055-10972) 206-213

2 1998-2007 PRRARSVRYP linker 1-10

2 2008-2016 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

2 2017-2026 PRRARSVRYP linker 1-10

2 2027-2045 ECAQVLSETVMCGGSLYVK RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 658-676

2 2046-2055 PRRARSVRYP linker 1-10

2 2056-2071 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

2 2072-2081 PRRARSVRYP linker 1-10

2 2082-2099 VTTVIFLARGIVFMCVEY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 179-196

2 2100-2109 PRRARSVRYP linker 1-10

2 2110-2134 VLVQSTQWSLFFFLYENAFLPFAMG nsp6@Aruba(NC_045512@Aruba:+:10973-11842)

24-48

2 2135-2144 PRRARSVRYP linker 1-10

2 2145-2154 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021

2 2155-2164 PRRARSVRYP linker 1-10

2 2165-2177 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

2 2178-2187 PRRARSVRYP linker 1-10

2 2188-2196 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474

2 2197-2206 PRRARSVRYP linker 1-10

2 2207-2226 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 209-228

2 2227-2236 PRRARSVRYP linker 1-10

2 2237-2253 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384)

258-274

2 2254-2263 PRRARSVRYP linker 1-10

2 2264-2272 FEHIVYGDF endoRNAse(NC_045512:+:19621 -20658) 232-240

2 2273-2282 PRRARSVRYP linker 1-10

2 2283-2296 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

294-307

2 2297-2306 PRRARSVRYP linker 1-10

2 2307-2315 KHWPQIAQF nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 299-307

2 2316-2325 PRRARSVRYP linker 1-10

2 2326-2335 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

2 2336-2345 PRRARSVRYP linker 1-10

2 2346-2360 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

260-274 2 2361-2370 PRRARSVRYP linker 1-10

2 2371 -2388 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142

2 2389-2398 PRRARSVRYP linker 1-10

2 2399-2410 TRAKVGILCITS helicase@SouthKorea(NC_045512@SouthKorea:+:16237-18039) 566-577

2 2411-2420 PRRARSVRYP linker 1-10

2 2421 -2434 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

2 2435-2444 PRRARSVRYP linker 1-10

2 2445-2464 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-

1 256

2 2465-2474 PRRARSVRYP linker MO

2 2475-2488 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384)

5-18

2 2489-2498 PRRARSVRYP linker 1-10

2 2499-2506 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349

2 2507-2516 PRRARSVRYP linker 1-10

2 2517-2537 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 605-625

3 1-17 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

3 18-27 PRRARSVRYP linker 1-10

3 28-44 EVTPSGTWLTYTGAIKL nucleocapsid_phosphoprotein@Bulgaria(NC_045512@Bulgaria:+:28 274-29533) 323-339

3 45-54 PRRARSVRYP linker 1-10

3 55-68 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 142-155

3 69-78 PRRARSVRYP linker 1-10

3 79-100 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 206-227

3 101-110 PRRARSVRYP linker 1-10

3 111-120 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536

3 121-130 PRRARSVRYP linker 1-10

3 131-141 YDNLQFISLEI helicase@Austria(NC_045512@Austria:+:16237-18039) 582-592

3 142-151 PRRARSVRYP linker 1-10

3 152-178 AKYTQLCQYLNTLTLAVPYNMRVIHFG 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 45-71

3 179-188 PRRARSVRYP linker 1-10

3 189-203 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

3 204-213 PRRARSVRYP linker 1-10

3 214-221 ISEHDYQI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 179-186

3 222-231 PRRARSVRYP linker 1-10

3 232-245 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

3 246-255 PRRARSVRYP linker 1-10

3 256-266 ITNCVKMLCTH nsp10(NC_045512:+: 13025-13441) 38-48

3 267-276 PRRARSVRYP linker 1-10

3 277-284 VVNPVMEP ORF3a_protein(NC_045512:+:25393-26220) 255-262

3 285-294 PRRARSVRYP linker 1-10

3 295-314 HYQECVRGTTVLLKEPCSSG ORF7a_protein(NC_045512:+:27394-27759) 19-38

3 315-324 PRRARSVRYP linker 1-10

3 325-339 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

3 340-349 PRRARSVRYP linker 1-10

3 350-357 SSIVITSG ORF3a_protein@SouthKorea(NC_045512@SouthKorea:+:25393-26220) 165-172

3 358-367 PRRARSVRYP linker 1-10

3 368-377 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

3 378-387 PRRARSVRYP linker 1-10

3 388-405 DKACPLIAAVITREVGFV nsp4(NC_045512:+:8555-10054) 85-102

3 406-415 PRRARSVRYP linker 1-10

3 416-426 YCPRHVICTSE 3C-like_proteinase(NC_045512:+:10055-10972) 37-47

3 427-436 PRRARSVRYP linker 1-10

3 437-452 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

3 453-462 PRRARSVRYP linker 1-10

3 463-470 SSI VITSV ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 165-172

3 471 -480 PRRARSVRYP linker 1-10

3 481-509 FLYIIKLIFLWLLWPVTLACFVLAAVYRI membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 45-73

3 510-519 PRRARSVRYP linker 1-10

3 520-527 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

3 528-537 PRRARSVRYP linker 1-10

3 538-545 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

3 546-555 PRRARSVRYP linker 1-10

3 556-567 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54

3 568-577 PRRARSVRYP linker 1-10 3 578-588 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

3 589-598 PRRARSVRYP linker 1-10

3 599-611 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

3 612-621 PRRARSVRYP linker 1-10

3 622-633 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671

3 634-643 PRRARSVRYP linker 1-10

3 644-656 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42

3 657-666 PRRARSVRYP linker 1-10

3 667-676 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

3 677-686 PRRARSVRYP linker 1-10

3 687-699 YTELEPPCRFVTD nsp9(NC_045512:+:12686-13024) 66-78

3 700-709 PRRARSVRYP linker 1-10

3 710-717 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

3 718-727 PRRARSVRYP linker 1-10

3 728-741 RLNVGDYFVLTSHT helicase@Austria(NC_045512@Austria:+:16237-18039) 218-231

3 742-751 PRRARSVRYP linker 1-10

3 752-778 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

3 779-788 PRRARSVRYP linker 1-10

3 789-806 QLALFKGVHFVCNLLLLF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 70-87

3 807-816 PRRARSVRYP linker 1-10

3 817-839 KEITVATSRTLSYYKLGASQRVA membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 166-188

3 840-849 PRRARSVRYP linker 1-10

3 850-857 SQDLSVVS endoRNAse(NC_045512:+:19621 -20658) 308-315

3 858-867 PRRARSVRYP linker 1-10

3 868-877 EGSVRVVTTF nsp4(NC_045512:+:8555-10054) 207-216

3 878-887 PRRARSVRYP linker 1-10

3 888-904 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91 -107

3 905-914 PRRARSVRYP linker 1-10

3 915-930 AFKLNIKLLGVGGKPC nsp6(NC_045512:+:10973-11842) 268-283

3 931 -940 PRRARSVRYP linker 1-10

3 941-950 TLPVNVAFEL endoRNAse(NC_045512:+:19621 -20658) 48-57

3 951 -960 PRRARSVRYP linker 1-10

3 961 -968 TQALLQRQ nucleocapsid_phosphoprotein@CostaRica(NC_045512@CostaRica:+: 28274-29533) 379-386 969-978 PRRARSVRYP linker 1-10 979-989 SPGVFNPVMEP ORF3a_protein@Colombia(NC_045512@Colombia:+:25393-26220) 252-262 990-999 PRRARSVRYP linker 1-10 1000-1014 VCNLLLLFVTVYSHL ORF3a_protein@Croatia(NC_045512@Croatia:+:25393-26220) 80-94 1015-1024 PRRARSVRYP linker 1-10 1025-1049 AAGLEAPFLYLYVLVYFLQSINFVR ORF3a_protein@Norway(NC_045512@Norway:+:25393-

6220) 98-122 1050-1059 PRRARSVRYP linker 1-10 1060-1067 APLIELCV ORF8_protein(NC_045512:+:27894-28259) 55-62 1068-1077 PRRARSVRYP linker 1-10 1078-1098 HPNCVNCSDDRCILHCANFNV RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 295-315

3 1099-1108 PRRARSVRYP linker 1-10

3 1109-1123 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 368-382 3 1124-1133 PRRARSVRYP linker 1-10

3 1134-1153 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942

3 1154-1163 PRRARSVRYP linker 1-10

3 1164-1175 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

3 1176-1185 PRRARSVRYP linker 1-10

3 1186-1199 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

3 1200-1209 PRRARSVRYP linker 1-10

3 1210-1225 LVDFQVTIAEILLIIM ORF6_protein(NC_045512:+:27202-27387) 4-19

3 1226-1235 PRRARSVRYP linker 1-10

3 1236-1244 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390

3 1245-1254 PRRARSVRYP linker 1-10

3 1255-1274 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

3 1275-1284 PRRARSVRYP linker 1-10

3 1285-1294 GVGGKPCIKV nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 274-283

3 1295-1304 PRRARSVRYP linker 1-10

3 1305-1325 ELVIGAVILRGHLRIAGHHLG membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191)

137-157

3 1326-1335 PRRARSVRYP linker 1-10

3 1336-1345 TPLIQPIGAL nsp4(NC_045512:+:8555-10054) 269-278 3 1346-1355 PRRARSVRYP linker 1-10

3 1356-1369 TCFSVAALTNNVAF RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 394-407

3 1370-1379 PRRARSVRYP linker 1-10

3 1380-1402 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481

3 1403-1412 PRRARSVRYP linker 1-10

3 1413-1430 CANFNVLFSTVFPFTSFG RNA- dependent_RNA_polymerase@Nigeria(NC_045512@Nigeria:+:13442-1 3468+13468-16236) 310-327

3 1431-1440 PRRARSVRYP linker 1-10

3 1441 -1454 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

3 1455-1464 PRRARSVRYP linker 1-10

3 1465-1482 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178

3 1483-1492 PRRARSVRYP linker 1-10

3 1493-1524 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA- dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-16236 ) 632-663

3 1525-1534 PRRARSVRYP linker 1-10

3 1535-1549 SYFAIGLALYYPSAR helicase@Austria(NC_045512@Austria:+:16237-18039) 289-303

3 1550-1559 PRRARSVRYP linker 1-10

3 1560-1569 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

3 1570-1579 PRRARSVRYP linker 1-10

3 1580-1591 DTSLKLKECVMY nsp6@SmallAsia(NC_045512@SmallAsia:+:10973-11842) 102-113

3 1592-1601 PRRARSVRYP linker 1-10

3 1602-1617 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 348-363

1618-1627 PRRARSVRYP linker 1-10 1628-1664 VAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKC

ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 97-133

1665-1674 PRRARSVRYP linker 1-10 1675-1683 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708 1684-1693 PRRARSVRYP linker 1-10 1694-1713 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610 1714-1723 PRRARSVRYP linker 1-10 1724-1738 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319 1739-1748 PRRARSVRYP linker 1-10 1749-1759 ETTVDIVVFDE helicase@SmallAsia(NC_045512@SmallAsia:+:16237-18039) 365-375 1760-1769 PRRARSVRYP linker 1-10 1770-1793 TYASALWEIQQVVDADSKIVQLSE nsp8(NC_045512:+:12092-12685) 148-171 1794-1803 PRRARSVRYP linker 1-10 1804-1823 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411 1824-1833 PRRARSVRYP linker 1-10 1834-1847 DGCVPLNIIPLTTA nsp8(NC_045512:+:12092-12685) 112-125 1848-1857 PRRARSVRYP linker 1-10 1858-1866 KLMVVIPDY nsp8(NC_045512:+:12092-12685) 127-135 1867-1876 PRRARSVRYP linker 1-10 1877-1884 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829 1885-1894 PRRARSVRYP linker 1-10 1895-1908 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450 1909-1918 PRRARSVRYP linker 1-10 1919-1929 AALALLLLDRL nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 217-227 1930-1939 PRRARSVRYP linker 1-10 1940-1947 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478 1948-1957 PRRARSVRYP linker 1-10 1958-1966 DYYQLYSTQ ORF3a_protein(NC_045512:+:25393-26220) 210-218 1967-1976 PRRARSVRYP linker 1-10 1977-1992 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016 1993-2002 PRRARSVRYP linker 1-10 2003-2015 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329 2016-2025 PRRARSVRYP linker 1-10 2026-2036 GEVPVSIINNT endoRNAse(NC_045512:+:19621 -20658) 20-30 2037-2046 PRRARSVRYP linker 1-10 2047-2069 YALVYFLQSINFVIIIMRLWLCW ORF3a_protein@Denmark(NC_045512@Denmark:+:25393-

6220) 109-131 2070-2079 PRRARSVRYP linker 1-10 2080-2091 LKKLKKSLNVAK nsp8(NC_045512:+: 12092-12685) 35-46 2092-2101 PRRARSVRYP linker 1-10 2102-2109 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436 2110-2119 PRRARSVRYP linker 1-10 2120-2130 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191 ) 136-146 1-2140 PRRARSVRYP linker 1-10 1-2160 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) -224 1-2170 PRRARSVRYP linker 1-10 1-2182 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) -821 3-2192 PRRARSVRYP linker 1-10 3-2203 RFQLFIRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243 4-2213 PRRARSVRYP linker 1-10 4-2227 RNLQFIRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+:13442-

721-734 8-2237 PRRARSVRYP linker 1-10 8-2245 FNSVCRFM helicase@Malaysia(NC_045512@Malaysia:+:16237-18039) 422-429 6-2255 PRRARSVRYP linker 1-10 6-2270 IPIRASLPFGWLIVG ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 49 1-2280 PRRARSVRYP linker 1-10 1-2295 ALLAVFQSASKIITLORF3a_protein@Bangladesh(NC_045512@Bangladesh :+:25393-26220) 65 6-2305 PRRARSVRYP linker 1-10 6-2315 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173 6-2325 PRRARSVRYP linker 1-10 6-2335 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840 6-2345 PRRARSVRYP linker 1-10 6-2360 VDTSLSSLKLKDCVM nsp6@Latvia(NC_045512@Latvia:+:10973-11842) 101-115 1-2370 PRRARSVRYP linker 1-10 1-2379 YGIIWVATE leocapsid_phosphoprotein@SmallSouthAmerica(l\IC_045512@Small SouthAmerica:+:28274-29533) 128-136 0-2389 PRRARSVRYP linker 1-10 0-2408 ANSVFNICQSVTANVNALL RNA- NA_polymerase@Croatia(NC_045512@Croatia:+:13442-13468+13468- 16236) 690-708 9-2418 PRRARSVRYP linker 1-10 9-2428 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252 9-2438 PRRARSVRYP linker 1-10 9-2446 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145 7-2456 PRRARSVRYP linker 1-10 7-2465 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788 6-2475 PRRARSVRYP linker 1-10 6-2491 FLVLLPLVSIQCVNLT ace_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthAmeri ca:+:21563-25384) 4-19 2-2501 PRRARSVRYP linker 1-10 2-2511 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844 2-2521 PRRARSVRYP linker 1-10 2-2536 YNLLKGCPAVAKHDF RNA- NA_polymerase@Poland(NC_045512@Poland:+:13442-13468+13468-16 236) 87-101 4 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90 24 PRRARSVRYP linker 1-10 35 GKPVPYCYDTN nsp4(NC_045512:+:8555-10054) 164-174 45 PRRARSVRYP linker 1-10 57 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639 67 PRRARSVRYP linker 1-10 79 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497 89 PRRARSVRYP linker 1-10

4 90-113 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-

25384) 205-228

4 114-123 PRRARSVRYP linker 1-10

4 124-144 QWNLVIGFLFLTWICLLQFAYmembrane_glycoprotein@Aruba(NC_045512@A ruba:+:26523-27191) 19-39

4 145-154 PRRARSVRYP linker 1-10

4 155-176 SDFVRATATIPIQASLPFGWLI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

26-47

4 177-186 PRRARSVRYP linker 1-10

4 187-197 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291

4 198-207 PRRARSVRYP linker 1-10

4 208-215 ETQALPQR nucleocapsid_phosphoprotein@SmallNorthAmerica(NC_045512@Smal lNorthAmerica:+:28274-29533) 378-385

4 216-225 PRRARSVRYP linker 1-10

4 226-238 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191) 119-131

4 239-248 PRRARSVRYP linker 1-10

4 249-268 RLCAYCCNIVNVSLVKPSFY envelope_protein(NC_045512:+:26245-26472) 38-57

4 269-278 PRRARSVRYP linker 1-10 4 279-286 EVTPSGTW nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 323-330

4 287-296 PRRARSVRYP linker 1-10

4 297-306 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

4 307-316 PRRARSVRYP linker 1-10

4 317-325 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-1169

4 326-335 PRRARSVRYP linker 1-10

4 336-358 KNPLLYDANYFLCCHTNCYDYCI ORF3a_protein@Senegal(NC_045512@Senegal:+:25393-26220) 136-158

4 359-368 PRRARSVRYP linker 1-10

4 369-380 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

4 381 -390 PRRARSVRYP linker 1-10

4 391 -402 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

4 403-412 PRRARSVRYP linker 1-10

4 413-424 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362

4 425-434 PRRARSVRYP linker 1-10

4 435-446 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 231 -242

4 447-456 PRRARSVRYP linker 1-10

4 457-464 DQDVLFAY RNA-dependent_RNA_polymerase@FrenchGuiana(NC_045512@FrenchGu iana:+: 13442-

13468+13468-16236) 523-530

4 465-474 PRRARSVRYP linker 1-10

4 475-487 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

4 488-497 PRRARSVRYP linker 1-10

4 498-508 YDKLQFISLEI helicase@SouthAfrica(NC_045512@SouthAfrica:+:16237-18039) 582-592

4 509-518 PRRARSVRYP linker 1-10

4 519-526 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742

4 527-536 PRRARSVRYP linker 1-10

4 537-544 SDFVRATA ORF3a_protein(NC_045512:+:25393-26220) 26-33

4 545-554 PRRARSVRYP linker 1-10

4 555-563 ASQGLLASI RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-13468+13468-

16236) 771-779

4 564-573 PRRARSVRYP linker 1-10

4 574-583 PFTINCQEPK ORF8_protein@lndia(NC_045512@lndia:+:27894-28259) 85-94

4 584-593 PRRARSVRYP linker 1-10

4 594-601 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

4 602-611 PRRARSVRYP linker 1-10

4 612-625 LMNVLTLVYKVYYG nsp6@Aru ba (N C_045512@Aruba:+:10973-11842) 139-152

4 626-635 PRRARSVRYP linker 1-10

4 636-647 SVFQSASKIITL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 54-65

4 648-657 PRRARSVRYP linker 1-10

4 658-680 YLGGMSYYCKSHKLPISFPLCAN helicase@CostaRica(NC_045512@CostaRica:+:16237-18039)

64-86

4 681 -690 PRRARSVRYP linker 1-10

4 691-700 NCYDYCIPYN ORF3a_protein(NC_045512:+:25393-26220) 152-161

4 701-710 PRRARSVRYP linker 1-10

4 711-722 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

4 723-732 PRRARSVRYP linker 1-10

4 733-783 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

4 784-793 PRRARSVRYP linker 1-10

4 794-801 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

4 802-811 PRRARSVRYP linker 1-10

4 812-821 GLKLKDCVMY nsp6@Peru(NC_045512@Peru:+:10973-11842) 107-116

4 822-831 PRRARSVRYP linker 1-10

4 832-847 DKYVRNLQHRLYECLY RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba :+: 13442-

13468+13468-16236) 717-732

4 848-857 PRRARSVRYP linker 1-10

4 858-869 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

4 870-879 PRRARSVRYP linker 1-10

4 880-908 TLQCIMLVYCFLGYFCTCYFGLFCLLNRY nsp6@Aruba(NC_045512@Aruba:+:10973-11842)

203-231

4 909-918 PRRARSVRYP linker 1-10

4 919-933 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

4 934-943 PRRARSVRYP linker 1-10

4 944-951 DCATVHTA 2’-O-ribose_methyltransferase(NC_045512:+:20659-21552) 114-121

4 952-961 PRRARSVRYP linker 1-10

4 962-981 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

4 982-991 PRRARSVRYP linker 1-10

4 992-1001 LPFTINCQEL ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 84-93

4 1002-1011 PRRARSVRYP linker 1-10 4 1012-1031 DANYFLCWHTNCYHYCIPYN

ORF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220 ) 142-161

4 1032-1041 PRRARSVRYP linker 1-10

4 1042-1051 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

4 1052-1061 PRRARSVRYP linker 1-10

4 1062-1072 RQALLKTVQFC RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba :+: 13442-

13468+13468-16236) 183-193 4 1073-1082 PRRARSVRYP linker 1-10

4 1083-1090 TDVVYRAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 28-35 4 1091-1100 PRRARSVRYP linker 1-10

4 1101-1122 TLGVLVPHVGEIPVAYRKVLLR leader_protein(NC_045512:+:266-805) 103-124

4 1123-1132 PRRARSVRYP linker 1-10

4 1133-1142 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

667-676

4 1143-1152 PRRARSVRYP linker 1-10

4 1153-1165 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

4 1166-1175 PRRARSVRYP linker 1-10

4 1176-1183 VLSEARQH leader_protein(NC_045512:+:266-805) 38-45

4 1184-1193 PRRARSVRYP linker 1-10

4 1194-1216 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

4 1217-1226 PRRARSVRYP linker 1-10

4 1227-1244 KGFCDLKGKYVQIPTTCA nsp10(NC_045512:+: 13025-13441 ) 87-104

4 1245-1254 PRRARSVRYP linker 1-10

4 1255-1264 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487

4 1265-1274 PRRARSVRYP linker 1-10

4 1275-1284 NLIIKNLSKS ORF6_protein(NC_045512:+:27202-27387) 34-43

4 1285-1294 PRRARSVRYP linker 1-10

4 1295-1316 IAMACLVGLMWLSYFIASFRLF membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 82-103

4 1317-1326 PRRARSVRYP linker 1-10

4 1327-1351 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

4 1352-1361 PRRARSVRYP linker 1-10

4 1362-1380 VKDCVVLHSYFTSDYYQLY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220)

197-215

4 1381-1390 PRRARSVRYP linker 1-10

4 1391 -1398 TFSVLACY 3C-like_proteinase(NC_045512:+: 10055-10972) 111-118

4 1399-1408 PRRARSVRYP linker 1-10

4 1409-1420 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

4 1421-1430 PRRARSVRYP linker 1-10

4 1431-1448 SQHTMLVKQGDDYVYLPY RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 814-831 4 1449-1458 PRRARSVRYP linker 1-10

4 1459-1484 YRLANECAQVLSEMVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 653-678

4 1485-1494 PRRARSVRYP linker 1-10

4 1495-1508 IRNLQHRLYECLYR RNA- dependent_RNA_polymerase@Austria(NC_045512@Austria:+:13442-1 3468+13468-16236) 720-733

4 1509-1518 PRRARSVRYP linker 1-10

4 1519-1534 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31

4 1535-1544 PRRARSVRYP linker 1-10

4 1545-1554 LAWPLIVTAL nsp8(NC_045512:+:12092-12685) 180-189

4 1555-1564 PRRARSVRYP linker 1-10

4 1565-1581 LTQYNRYLALYNKYKYF nsp4(NC_045512:+:8555-10054) 438-454

4 1582-1591 PRRARSVRYP linker 1-10

4 1592-1608 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 4-20 4 1609-1618 PRRARSVRYP linker 1-10

4 1619-1626 IAANTVIW endoRNAse(NC_045512:+:19621 -20658) 79-86

4 1627-1636 PRRARSVRYP linker 1-10

4 1637-1647 CYTPSKLIEYT nsp4(NC_045512:+:8555-10054) 133-143

4 1648-1657 PRRARSVRYP linker 1-10

4 1658-1665 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

67-74

4 1666-1675 PRRARSVRYP linker 1-10

4 1676-1691 SEFSSLPSYAAFATAQ nsp8(NC_045512:+:12092-12685) 4-19

4 1692-1701 PRRARSVRYP linker 1-10

4 1702-1715 ESVVKDCVVLHSYF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220)

194-207 4 1716-1725 PRRARSVRYP linker 1-10

4 1726-1747 GYQ PYRVVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

4 1748-1757 PRRARSVRYP linker 1-10

4 1758-1772 EVPANSTVLSFCAFA nsp10(NC_045512:+: 13025-13441 ) 6-20

4 1773-1782 PRRARSVRYP linker 1-10

4 1783-1798 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

4 1799-1808 PRRARSVRYP linker 1-10

4 1809-1825 INFVRIIMRLWLCLKCR ORF3a_protein@Mozambique(NC_045512@Mozambique:+:25393-

26220) 118-134

4 1826-1835 PRRARSVRYP linker 1-10

4 1836-1848 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

4 1849-1858 PRRARSVRYP linker 1-10

4 1859-1876 FLYENAFLPFAMGVIAMS nsp6@Mexico(NC_045512@Mexico:+:10973-11842) 36-53

4 1877-1886 PRRARSVRYP linker 1-10

4 1887-1897 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373

4 1898-1907 PRRARSVRYP linker 1-10

4 1908-1915 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

4 1916-1925 PRRARSVRYP linker 1-10

4 1926-1944 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

4 1945-1954 PRRARSVRYP linker 1-10

4 1955-1968 DYDCVSFCYMHHME 3C-like_proteinase(NC_045512:+:10055-10972) 153-166

4 1969-1978 PRRARSVRYP linker 1-10

4 1979-2000 SDFVRATATIPIRASLPFGWLI ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-

26220) 26-47

4 2001-2010 PRRARSVRYP linker 1-10

4 2011-2020 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

4 2021-2030 PRRARSVRYP linker 1-10

4 2031 -2038 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

4 2039-2048 PRRARSVRYP linker 1-10

4 2049-2063 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

354-368

4 2064-2073 PRRARSVRYP linker 1-10

4 2074-2090 VPQEHYVRITGLYPTLN helicase@Aruba(NC_045512@Aruba:+:16237-18039) 241-257

4 2091-2100 PRRARSVRYP linker 1-10

4 2101-2112 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

4 2113-2122 PRRARSVRYP linker 1-10

4 2123-2133 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

4 2134-2143 PRRARSVRYP linker 1-10

4 2144-2162 VKDCVLLHSYFTSDYYQLY ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220)

197-215

4 2163-2172 PRRARSVRYP linker 1-10

4 2173-2180 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

4 2181-2190 PRRARSVRYP linker 1-10

4 2191-2206 FSNVTWFFIAIFIVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384)

59-74

4 2207-2216 PRRARSVRYP linker 1-10

4 2217-2231 FIYVRITGLYPTLNIL helicase@lndonesia(NC_045512@lndonesia:+: 16237-18039)

245-259

4 2232-2241 PRRARSVRYP linker 1-10

4 2242-2261 DDRCILFICANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+: 13442-

13468+13468-16236) 303-322 4 2262-2271 PRRARSVRYP linker 1-10

4 2272-2281 SSVLHSTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

4 2282-2291 PRRARSVRYP linker 1-10

4 2292-2299 GSCGSVGF 3C-like_proteinase(NC_045512:+: 10055-10972) 143-150

4 2300-2309 PRRARSVRYP linker 1-10

4 2310-2324 YFTSDYYQLYSTQLI ORF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220)

206-220

4 2325-2334 PRRARSVRYP linker 1-10

4 2335-2343 LKLKDCVMY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 105-113

4 2344-2353 PRRARSVRYP linker 1-10

4 2354-2368 RIIPARARVECFDKF helicase@Aruba(NC_045512@Aruba:+:16237-18039) 332-346

4 2369-2378 PRRARSVRYP linker 1-10

4 2379-2388 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

4 2389-2398 PRRARSVRYP linker 1-10

4 2399-2421 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278

4 2422-2431 PRRARSVRYP linker 1-10

4 2432-2439 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

4 2440-2449 PRRARSVRYP linker 1-10 4 2450-2463 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-

25384) 128-141

4 2464-2473 PRRARSVRYP linker 1-10

4 2474-2483 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348

4 2484-2493 PRRARSVRYP linker 1-10

4 2494-2515 LLYDANYFLCWHINCYDYCIPY ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-

26220) 139-160

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes with intervening linker sequences (and as set forth in Figure 20). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 10 concat pos_in_concat epitope gene pos_in_gene

1 1-12 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

1 13-22 PRRARSVRYP linker 1-10

1 23-36 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

142-155

1 37-46 PRRARSVRYP linker 1-10

1 47-63 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

1 64-73 PRRARSVRYP linker 1-10

1 74-89 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

1 90-99 PRRARSVRYP linker 1-10

1 100-107 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

1 108-117 PRRARSVRYP linker 1-10

1 118-129 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

1 130-139 PRRARSVRYP linker 1-10

1 140-147 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

1 148-157 PRRARSVRYP linker 1-10

1 158-172 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319

1 173-182 PRRARSVRYP linker 1-10

1 183-192 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

1 193-202 PRRARSVRYP linker 1-10

1 203-210 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

1 211 -220 PRRARSVRYP linker 1-10

1 221 -247 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

1 248-257 PRRARSVRYP linker 1-10

1 258-273 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

331-346

1 274-283 PRRARSVRYP linker 1-10

1 284-299 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

348-363

1 300-309 PRRARSVRYP linker 1-10

1 310-323 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608

1 324-333 PRRARSVRYP linker 1-10

1 334-348 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237

1 349-358 PRRARSVRYP linker 1-10

1 359-368 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 743-752

1 369-378 PRRARSVRYP linker 1-10

1 379-390 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

1 391 -400 PRRARSVRYP linker 1-10

1 401-408 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

1 409-418 PRRARSVRYP linker 1-10

1 419-428 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

1 429-438 PRRARSVRYP linker 1-10

1 439-446 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

1 447-456 PRRARSVRYP linker 1-10 1 457-464 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

1 465-474 PRRARSVRYP linker 1-10

1 475-491 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

877-893

1 492-501 PRRARSVRYP linker 1-10

1 502-511 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

1 512-521 PRRARSVRYP linker 1-10

1 522-535 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450

1 536-545 PRRARSVRYP linker 1-10

1 546-558 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

1 559-568 PRRARSVRYP linker 1-10

1 569-588 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

826-845

1 589-598 PRRARSVRYP linker 1-10

1 599-613 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

1 614-623 PRRARSVRYP linker 1-10

1 624-646 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

1 647-656 PRRARSVRYP linker 1-10

1 657-666 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

1 667-676 PRRARSVRYP linker 1-10

1 677-684 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

1 685-694 PRRARSVRYP linker 1-10

1 695-706 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

1 707-716 PRRARSVRYP linker 1-10

1 717-736 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

1 737-746 PRRARSVRYP linker 1-10

1 747-763 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

1 764-773 PRRARSVRYP linker 1-10

1 774-783 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

1 784-793 PRRARSVRYP linker 1-10

1 794-832 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

1 833-842 PRRARSVRYP linker 1-10

1 843-862 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

2 1-13 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

2 14-23 PRRARSVRYP linker 1-10

2 24-40 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

4-20

2 41-50 PRRARSVRYP linker 1-10

2 51-64 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

721-734

2 65-74 PRRARSVRYP linker 1-10

2 75-87 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

2 88-97 PRRARSVRYP linker 1-10

2 98-107 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

2 108-117 PRRARSVRYP linker 1-10

2 118-126 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

2 127-136 PRRARSVRYP linker 1-10

2 137-147 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

2 148-157 PRRARSVRYP linker 1-10

2 158-165 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

2 166-175 PRRARSVRYP linker 1-10

2 176-184 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

2 185-194 PRRARSVRYP linker 1-10

2 195-202 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

2 203-212 PRRARSVRYP linker 1-10

2 213-222 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

2 223-232 PRRARSVRYP linker 1-10

2 233-247 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

368-382

2 248-257 PRRARSVRYP linker 1-10

2 258-265 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

2 266-275 PRRARSVRYP linker 1-10

2 276-283 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

2 284-293 PRRARSVRYP linker 1-10

2 294-325 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

2 326-335 PRRARSVRYP linker 1-10

2 336-348 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131

2 349-358 PRRARSVRYP linker 1-10

2 359-367 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708 368-377 PRRARSVRYP linker 1-10 378-390 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349 391 -400 PRRARSVRYP linker 1-10 401-423 S H G KQVVS D I D YVP LKSAT C I TR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476 424-433 PRRARSVRYP linker 1-10 434-446 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42 447-456 PRRARSVRYP linker 1-10 457-469 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902 470-479 PRRARSVRYP linker 1-10 480-490 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373 491 -500 PRRARSVRYP linker 1-10 501-510 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 434-443 511-520 PRRARSVRYP linker 1-10 521-528 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 67-74 529-538 PRRARSVRYP linker 1-10 539-549 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973 550-559 PRRARSVRYP linker 1-10 560-579 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942 580-589 PRRARSVRYP linker 1-10 590-599 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252 600-609 PRRARSVRYP linker 1-10 610-621 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671 622-631 PRRARSVRYP linker 1-10 632-643 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639 644-653 PRRARSVRYP linker 1-10 654-672 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600 673-682 PRRARSVRYP linker 1-10 683-692 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348 693-702 PRRARSVRYP linker 1-10 703-717 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219 718-727 PRRARSVRYP linker 1-10 728-747 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-1256 748-757 PRRARSVRYP linker 1-10 758-770 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171 771 -780 PRRARSVRYP linker 1-10 781-799 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450 800-809 PRRARSVRYP linker 1-10 810-821 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494 822-831 PRRARSVRYP linker 1-10 832-847 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541 1-10 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536 11-20 PRRARSVRYP linker 1-10 21-29 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129 30-39 PRRARSVRYP linker 1-10 40-62 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278 63-72 PRRARSVRYP linker 1-10 73-84 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497 85-94 PRRARSVRYP linker 1-10 95-109 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629 110-119 PRRARSVRYP linker 1-10 120-170 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

171-180 PRRARSVRYP linker 1-10 181-195 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 396-410 196-205 PRRARSVRYP linker 1-10 206-213 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829 214-223 PRRARSVRYP linker 1-10 224-243 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197 244-253 PRRARSVRYP linker 1-10 254-261 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372 262-271 PRRARSVRYP linker 1-10 272-283 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821 284-293 PRRARSVRYP linker 1-10 294-309 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31 310-319 PRRARSVRYP linker 1-10 320-330 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146 331 -340 PRRARSVRYP linker 1-10 341 -352 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24 353-362 PRRARSVRYP linker 1-10 363-382 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645 383-392 PRRARSVRYP linker 1-10 393-411 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236 412-421 PRRARSVRYP linker 1-10 422-444 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481 445-454 PRRARSVRYP linker 1-10 455-464 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400 465-474 PRRARSVRYP linker 1-10 475-484 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248 485-494 PRRARSVRYP linker 1-10 495-508 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928 509-518 PRRARSVRYP linker 1-10 519-528 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921 529-538 PRRARSVRYP linker 1-10 539-553 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881 554-563 PRRARSVRYP linker 1-10 564-581 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178 582-591 PRRARSVRYP linker 1-10 592-602 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006 603-612 PRRARSVRYP linker 1-10 613-637 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478 638-647 PRRARSVRYP linker 1-10 648-657 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487 658-667 PRRARSVRYP linker 1-10 668-676 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440 677-686 PRRARSVRYP linker 1-10 687-698 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242 699-708 PRRARSVRYP linker 1-10 709-720 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955 721 -730 PRRARSVRYP linker 1-10 731-739 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788 740-749 PRRARSVRYP linker 1-10 750-759 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021 760-769 PRRARSVRYP linker 1-10 770-780 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291 781 -790 PRRARSVRYP linker 1-10 791-803 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135 804-813 PRRARSVRYP linker 1-10 814-821 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742 822-831 PRRARSVRYP linker 1-10 832-849 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 470-487 1-10 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881 11-20 PRRARSVRYP linker 1-10 21-38 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404 39-48 PRRARSVRYP linker 1-10 49-62 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191 63-72 PRRARSVRYP linker 1-10 73-80 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131 81-90 PRRARSVRYP linker 1-10 91-99 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270 100-109 PRRARSVRYP linker 1-10 110-131 GYQ PYRVVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525 132-141 PRRARSVRYP linker 1-10 142-150 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390 151-160 PRRARSVRYP linker 1-10 161-170 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111 171-180 PRRARSVRYP linker 1-10 181-200 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 303-322 201-210 PRRARSVRYP linker 1-10 211-218 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349 219-228 PRRARSVRYP linker 1-10 229-248 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610 249-258 PRRARSVRYP linker 1-10 259-266 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817 267-276 PRRARSVRYP linker 1-10 277-289 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480 290-299 PRRARSVRYP linker 1-10 300-307 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54 4 308-317 PRRARSVRYP linker 1-10

4 318-332 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 857-871

4 333-342 PRRARSVRYP linker 1-10

4 343-354 VRTNVYLAVFDK nsp3(NC_045512: + :2720-8554) 351 -362

4 355-364 PRRARSVRYP linker 1-10

4 365-374 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

4 375-384 PRRARSVRYP linker 1-10

4 385-395 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

4 396-405 PRRARSVRYP linker 1-10

4 406-413 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

4 414-423 PRRARSVRYP linker 1-10

4 424-434 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

4 435-444 PRRARSVRYP linker 1-10

4 445-461 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91 -107

4 462-471 PRRARSVRYP linker 1-10

4 472-479 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691

4 480-489 PRRARSVRYP linker 1-10

4 490-502 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

4 503-512 PRRARSVRYP linker 1-10

4 513-528 VREVLSDRELHLSWEV helicase(NC_045512:+:16237-18039) 154-169

4 529-538 PRRARSVRYP linker 1-10

4 539-554 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

4 555-564 PRRARSVRYP linker 1-10

4 565-580 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016

4 581 -590 PRRARSVRYP linker 1-10

4 591-600 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

4 601-610 PRRARSVRYP linker 1-10

4 611-620 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

4 621 -630 PRRARSVRYP linker 1-10

4 631-641 VVNAANVYLKH nsp3(NC_045512 : + :2720-8554) 239-249

4 642-651 PRRARSVRYP linker 1-10

4 652-665 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

4 666-675 PRRARSVRYP linker 1-10

4 676-686 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

4 687-696 PRRARSVRYP linker 1-10

4 697-716 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

4 717-726 PRRARSVRYP linker 1-10

4 727-734 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207

4 735-744 PRRARSVRYP linker 1-10

4 745-752 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

4 753-762 PRRARSVRYP linker 1-10

4 763-771 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

4 772-781 PRRARSVRYP linker 1-10

4 782-794 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

4 795-804 PRRARSVRYP linker 1-10

4 805-813 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579

4 814-823 PRRARSVRYP linker 1-10

4 824-833 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

4 834-843 PRRARSVRYP linker 1-10

4 844-851 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes with intervening linker sequences (and as set forth in Figure 21). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 11 concatemer P ^os _in_ ^conc at epitope gene pos_in_gene

1 1-12 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

1 13-22 PRRARSVRYP linker 1-10

1 23-36 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

142-155

1 37-46 PRRARSVRYP linker 1-10

1 47-61 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368

1 62-71 PRRARSVRYP linker 1-10

1 72-86 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

1 87-96 PRRARSVRYP linker 1-10

1 97-104 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

1 105-114 PRRARSVRYP linker 1-10

1 115-126 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

1 127-136 PRRARSVRYP linker 1-10

1 137-147 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

1 148-157 PRRARSVRYP linker 1-10

1 158-171 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

1 172-181 PRRARSVRYP linker 1-10

1 182-196 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

857-871

1 197-206 PRRARSVRYP linker 1-10

1 207-214 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

1 215-224 PRRARSVRYP linker 1-10

1 225-244 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

1 245-254 PRRARSVRYP linker 1-10

1 255-264 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

1 265-274 PRRARSVRYP linker 1-10

1 275-285 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

1 286-295 PRRARSVRYP linker 1-10

1 296-313 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

470-487

1 314-323 PRRARSVRYP linker 1-10

1 324-339 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

348-363

1 340-349 PRRARSVRYP linker 1-10

1 350-360 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291

1 361 -370 PRRARSVRYP linker 1-10

1 371-385 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

1 386-395 PRRARSVRYP linker 1-10

1 396-404 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-1169

1 405-414 PRRARSVRYP linker 1-10

1 415-426 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24

1 427-436 PRRARSVRYP linker 1-10

1 437-448 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

1 449-458 PRRARSVRYP linker 1-10

1 459-468 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746

1 469-478 PRRARSVRYP linker 1-10

1 479-488 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

1 489-498 PRRARSVRYP linker 1-10

1 499-509 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

1 510-519 PRRARSVRYP linker 1-10

1 520-535 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31

1 536-545 PRRARSVRYP linker 1-10

1 546-561 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409

1 562-571 PRRARSVRYP linker 1-10

1 572-580 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

1 581 -590 PRRARSVRYP linker 1-10

1 591-613 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

1 614-623 PRRARSVRYP linker 1-10

1 624-638 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384)

680-694

1 639-648 PRRARSVRYP linker 1-10

1 649-656 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207

1 657-666 PRRARSVRYP linker 1-10

1 667-689 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

1 690-699 PRRARSVRYP linker 1-10

1 700-712 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

1 713-722 PRRARSVRYP linker 1-10

1 723-738 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654 1 739-748 PRRARSVRYP linker 1-10

1 749-761 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

1 762-771 PRRARSVRYP linker 1-10

1 772-783 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

1 784-793 PRRARSVRYP linker 1-10

1 794-801 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

1 802-811 PRRARSVRYP linker 1-10

1 812-838 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

1 839-848 PRRARSVRYP linker 1-10

1 849-856 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

1 857-866 PRRARSVRYP linker 1-10

1 867-877 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

1 878-887 PRRARSVRYP linker 1-10

1 888-906 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384) 607-625

1 907-916 PRRARSVRYP linker 1-10

1 917-928 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

1 929-938 PRRARSVRYP linker 1-10

1 939-951 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

1 952-961 PRRARSVRYP linker 1-10

1 962-976 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

1 977-986 PRRARSVRYP linker 1-10

1 987-1009 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

1 1010-1019 PRRARSVRYP linker 1-10

1 1020-1033 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 294-307

1 1034-1043 PRRARSVRYP linker 1-10

1 1044-1057 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18

1 1058-1067 PRRARSVRYP linker 1-10

1 1068-1076 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

1 1077-1086 PRRARSVRYP linker 1-10

1 1087-1106 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

1 1107-1116 PRRARSVRYP linker 1-10

1 1117-1127 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

1 1128-1137 PRRARSVRYP linker 1-10

1 1138-1169 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA- dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-16236 ) 632-663

1 1170-1179 PRRARSVRYP linker 1-10

1 1180-1192 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191) 119-131

1 1193-1202 PRRARSVRYP linker 1-10

1 1203-1213 VVNAANVYLKH nsp3(NC_045512 : + :2720-8554) 239-249

2 1-13 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

2 14-23 PRRARSVRYP linker 1-10

2 24-40 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 4-20

2 41-50 PRRARSVRYP linker 1-10

2 51-64 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

2 65-74 PRRARSVRYP linker 1-10

2 75-84 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980

2 85-94 PRRARSVRYP linker 1-10

2 95-110 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

2 111-120 PRRARSVRYP linker 1-10

2 121-129 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

2 130-139 PRRARSVRYP linker 1-10

2 140-159 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224

2 160-169 PRRARSVRYP linker 1-10

2 170-181 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

2 182-191 PRRARSVRYP linker 1-10

2 192-204 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

2 205-214 PRRARSVRYP linker 1-10

2 215-222 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829

2 223-232 PRRARSVRYP linker 1-10

2 233-249 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 877-893

2 250-259 PRRARSVRYP linker 1-10

2 260-270 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146

2 271 -280 PRRARSVRYP linker 1-10

2 281 -290 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

2 291 -300 PRRARSVRYP linker 1-10 301 -316 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 331-346 317-326 PRRARSVRYP linker 1-10 327-334 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54 335-344 PRRARSVRYP linker 1-10 345-362 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161 -178 363-372 PRRARSVRYP linker 1-10 373-394 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 125-146 395-404 PRRARSVRYP linker 1-10 405-412 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478 413-422 PRRARSVRYP linker 1-10 423-432 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840 433-442 PRRARSVRYP linker 1-10 443-456 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691 457-466 PRRARSVRYP linker 1-10 467-476 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400 477-486 PRRARSVRYP linker 1-10 487-501 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629 502-511 PRRARSVRYP linker 1-10 512-521 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021 522-531 PRRARSVRYP linker 1-10 532-548 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384) 258-274 549-558 PRRARSVRYP linker 1-10 559-566 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691 567-576 PRRARSVRYP linker 1-10 577-593 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91 -107 594-603 PRRARSVRYP linker 1-10 604-614 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006 615-624 PRRARSVRYP linker 1-10 625-639 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219 640-649 PRRARSVRYP linker 1-10 650-660 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373 661 -670 PRRARSVRYP linker 1-10 671-690 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942 691 -700 PRRARSVRYP linker 1-10 701 -720 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

1048-1067

721 -730 PRRARSVRYP linker 1-10

731-738 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742 739-748 PRRARSVRYP linker 1-10 749-760 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54 761 -770 PRRARSVRYP linker 1-10 771-778 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499 779-788 PRRARSVRYP linker 1-10 789-802 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608 803-812 PRRARSVRYP linker 1-10 813-827 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82 828-837 PRRARSVRYP linker 1-10 838-847 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133 848-857 PRRARSVRYP linker 1-10 858-867 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895 868-877 PRRARSVRYP linker 1-10 878-892 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237 893-902 PRRARSVRYP linker 1-10 903-915 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902 916-925 PRRARSVRYP linker 1-10 926-935 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252 936-945 PRRARSVRYP linker 1-10 946-960 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 129-143 961 -970 PRRARSVRYP linker 1-10 971 -981 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-

982-991 PRRARSVRYP linker 1-10

992-1001 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

1002-1011 PRRARSVRYP linker 1-10

1012-1025 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

1026-1035 PRRARSVRYP linker 1-10

1036-1043 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996 2 1044-1053 PRRARSVRYP linker 1-10

2 1054-1062 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788

2 1063-1072 PRRARSVRYP linker 1-10

2 1073-1085 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

2 1086-1095 PRRARSVRYP linker 1-10

2 1096-1105 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676

2 1106-1115 PRRARSVRYP linker 1-10

2 1116-1123 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

2 1124-1133 PRRARSVRYP linker 1-10

2 1134-1153 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 209-228

2 1154-1163 PRRARSVRYP linker 1-10

2 1164-1171 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

2 1172-1181 PRRARSVRYP linker 1-10

2 1182-1200 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236

3 1-10 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536

3 11-20 PRRARSVRYP linker 1-10

3 21-29 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129

3 30-39 PRRARSVRYP linker 1-10

3 40-62 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278

3 63-72 PRRARSVRYP linker 1-10

3 73-80 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

3 81-90 PRRARSVRYP linker 1-10

3 91-99 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474

3 100-109 PRRARSVRYP linker 1-10

3 110-140 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1211-1241

3 141-150 PRRARSVRYP linker 1-10

3 151-163 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

3 164-173 PRRARSVRYP linker 1-10

3 174-187 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

3 188-197 PRRARSVRYP linker 1-10

3 198-207 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

3 208-217 PRRARSVRYP linker 1-10

3 218-225 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

3 226-235 PRRARSVRYP linker 1-10

3 236-243 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

3 244-253 PRRARSVRYP linker 1-10

3 254-262 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

3 263-272 PRRARSVRYP linker 1-10

3 273-284 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242

3 285-294 PRRARSVRYP linker 1-10

3 295-307 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42

3 308-317 PRRARSVRYP linker 1-10

3 318-329 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639

3 330-339 PRRARSVRYP linker 1-10

3 340-349 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 743-752

3 350-359 PRRARSVRYP linker 1-10

3 360-379 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

3 380-389 PRRARSVRYP linker 1-10

3 390-428 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

3 429-438 PRRARSVRYP linker 1-10

3 439-446 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

3 447-456 PRRARSVRYP linker 1-10

3 457-474 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

3 475-484 PRRARSVRYP linker 1-10

3 485-504 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-1256

3 505-514 PRRARSVRYP linker 1-10

3 515-537 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

3 538-547 PRRARSVRYP linker 1-10

3 548-559 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

3 560-569 PRRARSVRYP linker 1-10

3 570-577 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

3 578-587 PRRARSVRYP linker 1-10

3 588-599 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497

3 600-609 PRRARSVRYP linker 1-10

3 610-626 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

3 627-636 PRRARSVRYP linker 1-10 637-651 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

368-382

652-661 PRRARSVRYP linker 1-10

662-671 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 434-443

672-681 PRRARSVRYP linker 1-10

682-700 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

701-710 PRRARSVRYP linker 1-10

711-720 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

721-730 PRRARSVRYP linker 1-10

731-745 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319

746-755 PRRARSVRYP linker 1-10

756-768 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135 769-778 PRRARSVRYP linker 1-10

779-787 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

788-797 PRRARSVRYP linker 1-10

798-809 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671

810-819 PRRARSVRYP linker 1-10

820-833 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498

834-843 PRRARSVRYP linker 1-10

844-854 FFSNVTWFFIVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

855-864 PRRARSVRYP linker 1-10

865-880 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

881-890 PRRARSVRYP linker 1-10

891-900 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

901-910 PRRARSVRYP linker 1-10 911-918 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349 919-928 PRRARSVRYP linker 1-10 929-942 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

943-952 PRRARSVRYP linker 1-10 953-966 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450 967-976 PRRARSVRYP linker 1-10 977-991 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384) 496-510

992-1001 PRRARSVRYP linker 1-10

1002-1009 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

1010-1019 PRRARSVRYP linker 1-10

1020-1027 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

1028-1037 PRRARSVRYP linker 1-10

1038-1045 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

67-74

1046-1055 PRRARSVRYP linker 1-10

1056-1068 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349

1069-1078 PRRARSVRYP linker 1-10

1079-1088 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

1089-1098 PRRARSVRYP linker 1-10

1099-1114 FSNVTWFFIAIFIVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384)

59-74

1115-1124 PRRARSVRYP linker 1-10

1125-1136 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

1137-1146 PRRARSVRYP linker 1-10

1147-1156 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

1157-1166 PRRARSVRYP linker 1-10

1167-1174 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

1175-1184 PRRARSVRYP linker 1-10

1185-1194 SSVLFISTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

1195-1204 PRRARSVRYP linker 1-10

1205-1212 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

I-10 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

I I-20 PRRARSVRYP linker 1-10

21-42 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

206-227

43-52 PRRARSVRYP linker 1-10

53-66 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

721-734

67-76 PRRARSVRYP linker 1-10

77-89 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

90-99 PRRARSVRYP linker 1-10

100-113 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

114-123 PRRARSVRYP linker 1-10 124-174 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

175-184 PRRARSVRYP linker 1-10

185-204 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 826-845 205-214 PRRARSVRYP linker 1-10 215-225 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973 226-235 PRRARSVRYP linker 1-10 236-255 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 303-322 256-265 PRRARSVRYP linker 1-10 266-278 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480 279-288 PRRARSVRYP linker 1-10 289-296 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420 297-306 PRRARSVRYP linker 1-10 307-314 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817 315-324 PRRARSVRYP linker 1-10 325-339 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 396-410 340-349 PRRARSVRYP linker 1-10 350-359 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173 360-369 PRRARSVRYP linker 1-10 370-378 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266 379-388 PRRARSVRYP linker 1-10 389-398 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487 399-408 PRRARSVRYP linker 1-10 409-431 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481 432-441 PRRARSVRYP linker 1-10 442-455 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-2 5384) 128-141 456-465 PRRARSVRYP linker 1-10 466-482 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765 483-492 PRRARSVRYP linker 1-10 493-502 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348 503-512 PRRARSVRYP linker 1-10 513-527 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733 528-537 PRRARSVRYP linker 1-10 538-549 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577 550-559 PRRARSVRYP linker 1-10 560-572 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984 573-582 PRRARSVRYP linker 1-10 583-602 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610 603-612 PRRARSVRYP linker 1-10 613-621 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579 622-631 PRRARSVRYP linker 1-10 632-640 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19 641 -650 PRRARSVRYP linker 1-10 651 -672 GYQ PYRVVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525 673-682 PRRARSVRYP linker 1-10 683-693 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819 694-703 PRRARSVRYP linker 1-10 704-712 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708 713-722 PRRARSVRYP linker 1-10 723-734 VRTNVYLAVFDK nsp3(NC_045512: + :2720-8554) 351 -362 735-744 PRRARSVRYP linker 1-10 745-763 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727 764-773 PRRARSVRYP linker 1-10 774-783 GTNLPLQLGF 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 102-111 784-793 PRRARSVRYP linker 1-10 794-802 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390 803-812 PRRARSVRYP linker 1-10 813-831 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600 832-841 PRRARSVRYP linker 1-10 842-861 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197 862-871 PRRARSVRYP linker 1-10 872-887 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

888-897 PRRARSVRYP linker 1-10

898-909 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241 910-919 PRRARSVRYP linker 1-10 4 920-939 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

4 940-949 PRRARSVRYP linker 1-10

4 950-965 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016

4 966-975 PRRARSVRYP linker 1-10

4 976-989 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

4 990-999 PRRARSVRYP linker 1-10

4 1000-1011 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821

4 1012-1021 PRRARSVRYP linker 1-10

4 1022-1046 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

4 1047-1056 PRRARSVRYP linker 1-10

4 1057-1072 VREVLSDRELHLSWEV helicase(NC_045512:+:16237-18039) 154-169

4 1073-1082 PRRARSVRYP linker 1-10

4 1083-1106 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-25384 ) 205-228

4 1107-1116 PRRARSVRYP linker 1-10

4 1117-1126 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

4 1127-1136 PRRARSVRYP linker 1-10

4 1137-1144 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

4 1145-1154 PRRARSVRYP linker 1-10

4 1155-1175 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 605-625

4 1176-1185 PRRARSVRYP linker 1-10

4 1186-1203 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

125-142

In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes with intervening linker sequences (and as set forth in Figure 22). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 12 contig pos_in_contig epitope gene pos_in_gene

1 1-11 YDKLQFISLEI helicase@SouthAfrica(NC_045512@SouthAfrica:+:16237-18039) 582-592

1 12-21 PRRARSVRYP linker 1-10

1 22-39 YNLLKDCPAVAKHDFFKF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-

13468+13468-16236) 87-104

1 40-49 PRRARSVRYP linker 1-10

1 50-63 SDRVVFVLWAHGFE 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 178-191

1 64-73 PRRARSVRYP linker 1-10

1 74-82 TENLLLYID nsp3(NC_045512:+:2720-8554) 432-440

1 83-92 PRRARSVRYP linker 1-10

1 93-111 ANSVFNICQSVTANVNALL RNA-dependent_RNA_polymerase@Croatia(NC_045512@Croatia:+:134 42-

13468+13468-16236) 690-708

1 112-121 PRRARSVRYP linker 1-10

1 122-130 AGFSLWVYK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 504-512

1 131-140 PRRARSVRYP linker 1-10

1 141-148 DQDVLFAY RNA-dependent_RNA_polymerase@FrenchGuiana(NC_045512@FrenchGu iana:+:13442-

13468+13468-16236) 523-530

1 149-158 PRRARSVRYP linker 1-10

1 159-168 ETFVTHSKGL nsp2(NC_045512:+:806-2719) 527-536

1 169-178 PRRARSVRYP linker 1-10

1 179-186 SDDAVVCF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

16236) 759-766

1 187-196 PRRARSVRYP linker 1-10

1 197-208 AKLLHKPIVWHV nsp3(NC_045512:+:2720-8554) 1165-1176

1 209-218 PRRARSVRYP linker 1-10 1 219-226 FNSVCRFM helicase@Malaysia(NC_045512@Malaysia:+:16237-18039) 422-429

1 227-236 PRRARSVRYP linker 1-10

1 237-247 YELKHGTFTCA nsp3(NC_045512:+:2720-8554) 996-1006

1 248-257 PRRARSVRYP linker 1-10

1 258-267 DVVAIDYKHY nsp3(NC_045512:+:2720-8554) 1148-1157

1 268-277 PRRARSVRYP linker 1-10

1 278-285 KAVFISPY helicase(NC_045512:+:16237-18039) 508-515

1 286-295 PRRARSVRYP linker 1-10

1 296-303 ARDLSLQF nsp3(NC_045512:+:2720-8554) 1652-1659

1 304-313 PRRARSVRYP linker 1-10

1 314-331 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161 -178

1 332-341 PRRARSVRYP linker 1-10

1 342-355 TCFSVAALTNNVAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba :+: 13442-

13468+13468-16236) 394-407

1 356-365 PRRARSVRYP linker 1-10

1 366-381 SRIIPARARVDCFDKF helicase@Brazil(NC_045512@Brazil:+:16237-18039) 331-346

1 382-391 PRRARSVRYP linker 1-10

1 392-406 SYELQTPFEIKLAKK nsp2(NC_045512:+:806-2719) 68-82

1 407-416 PRRARSVRYP linker 1-10

1 417-437 KLSYGIAIVREVLSDRELHLS helicase@Colombia(NC_045512@Colombia:+:16237-18039) 146-166

1 438-447 PRRARSVRYP linker 1-10

1 448-469 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 206-227

1 470-479 PRRARSVRYP linker 1-10

1 480-493 LKEILVTYNCCDDD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 142-155

1 494-503 PRRARSVRYP linker 1-10

1 504-519 VREVLSDRELHLSWEV helicase(NC_045512:+:16237-18039) 154-169

1 520-529 PRRARSVRYP linker 1-10

1 530-539 QEHYVRITGL helicase(NC_045512:+:16237-18039) 243-252

1 540-549 PRRARSVRYP linker 1-10

1 550-559 RHSLSHFVNL nsp3(NC_045512:+:2720-8554) 1697-1706

1 560-569 PRRARSVRYP linker 1-10

1 570-577 MADLVYAL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 124-131

1 578-587 PRRARSVRYP linker 1-10

1 588-595 PEHSLAEY nsp2(NC_045512:+:806-2719) 200-207

1 596-605 PRRARSVRYP linker 1-10

1 606-621 FRELGVVHNQDVNLHS RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 348-363

1 622-631 PRRARSVRYP linker 1-10

1 632-642 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191 ) 149-159

1 643-652 PRRARSVRYP linker 1-10

1 653-672 FCKLHNWNCVNCDTFCAGST nsp3(NC_045512:+:2720-8554) 1626-1645

1 673-682 PRRARSVRYP linker 1-10

1 683-690 CLNRVCTN nsp3(NC_045512:+:2720-8554) 1342-1349

1 691 -700 PRRARSVRYP linker 1-10

1 701 -720 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

1048-1067

1 721 -730 PRRARSVRYP linker 1-10

1 731-749 ANSVFNICQAVTANVNALL RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba :+: 13442-

13468+13468-16236) 690-708

1 750-759 PRRARSVRYP linker 1-10

1 760-776 PNFVFPLNSIIKTIQPR nsp2(NC_045512:+:806-2719) 91 -107

1 777-786 PRRARSVRYP linker 1-10

1 787-799 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

1 800-809 PRRARSVRYP linker 1-10

1 810-817 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

1 818-827 PRRARSVRYP linker 1-10

1 828-840 AFASEAARVVRSI nsp2(NC_045512:+:806-2719) 355-367

1 841 -850 PRRARSVRYP linker 1-10

1 851 -863 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984

1 864-873 PRRARSVRYP linker 1-10

1 874-887 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18

1 888-897 PRRARSVRYP linker 1-10

1 898-912 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

1 913-922 PRRARSVRYP linker 1-10

1 923-931 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

1 932-941 PRRARSVRYP linker 1-10

1 942-950 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11 -19

1 951 -960 PRRARSVRYP linker 1-10 1 961-973 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131

1 974-983 PRRARSVRYP linker 1-10

1 984-996 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81 -93

1 997-1006 PRRARSVRYP linker 1-10

1 1007-1014 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203

1 1015-1024 PRRARSVRYP linker 1-10

1 1025-1032 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

1 1033-1042 PRRARSVRYP linker 1-10

1 1043-1058 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19

1 1059-1068 PRRARSVRYP linker 1-10

1 1069-1076 SSNVANYQ helicase@Austria(NC_045512@Austria:+:16237-18039) 263-270

1 1077-1086 PRRARSVRYP linker 1-10

1 1087-1101 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-

25384) 496-510

1 1102-1111 PRRARSVRYP linker 1-10

1 1112-1121 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

1 1122-1131 PRRARSVRYP linker 1-10

1 1132-1139 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

1 1140-1149 PRRARSVRYP linker 1-10

1 1150-1165 DKYVRNLQHRLYECLY RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 717-732 1 1166-1175 PRRARSVRYP linker 1-10

1 1176-1191 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

1 1192-1201 PRRARSVRYP linker 1-10

1 1202-1219 LFVVEVVDKYFDCYDGGC RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 470-487

1 1220-1229 PRRARSVRYP linker 1-10

1 1230-1241 HEFCSQHTMLVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 810-821

1 1242-1251 PRRARSVRYP linker 1-10

1 1252-1259 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

1 1260-1269 PRRARSVRYP linker 1-10

1 1270-1277 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742

1 1278-1287 PRRARSVRYP linker 1-10

1 1288-1295 NNLVVMAY nsp2(NC_045512:+:806-2719) 413-420

1 1296-1305 PRRARSVRYP linker 1-10

1 1306-1317 FRSSVLFISTRDL surface glycoprotein@Nigeria(NC 045512@Nigeria:+:21563-25384) 43-54

1 1318-1327 PRRARSVRYP linker 1-10

1 1328-1335 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

1 1336-1345 PRRARSVRYP linker 1-10

1 1346-1365 GYLPQNAVVKIYCPACHNSE nsp2(NC_045512:+:806-2719) 178-197

1 1366-1375 PRRARSVRYP linker 1-10

1 1376-1385 VTGLFKDCSK 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 4-13

1 1386-1395 PRRARSVRYP linker 1-10

1 1396-1403 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

1 1404-1413 PRRARSVRYP linker 1-10

1 1414-1427 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

1 1428-1437 PRRARSVRYP linker 1-10

1 1438-1446 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788

1 1447-1456 PRRARSVRYP linker 1-10

1 1457-1475 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

1 1476-1485 PRRARSVRYP linker 1-10

1 1486-1496 FFSNVTWFFIVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

1 1497-1506 PRRARSVRYP linker 1-10

1 1507-1519 FQTLLALFIRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

2 1 -20 IRRPFLCCKCCYDHVISTSH helicase(NC_045512:+:16237-18039) 20-39

2 21-30 PRRARSVRYP linker 1-10

2 31-38 LPINVIVFnsp3(NC_045512:+:2720-8554) 1718-1725

2 39-48 PRRARSVRYP linker 1-10

2 49-69 HPNCVNCSDDRCILHCANFNV RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 295-315 2 70-79 PRRARSVRYP linker 1-10

2 80-92 GVNLVAVPTGYVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 114-126

2 93-102 PRRARSVRYP linker 1-10

2 103-116 IRNLQHRLYECLYR RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-

13468+13468-16236) 720-733

2 117-126 PRRARSVRYP linker 1-10

2 127-143 VPQEHYVRITGLYPTLN helicase@Aruba(NC_045512@Aruba:+:16237-18039) 241-257 144-153 PRRARSVRYP linker 1-10

154-164 RQALLKTVQFC RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

6236) 183-193

165-174 PRRARSVRYP linker 1-10

175-182 YDKLVSSF nsp3(NC_045512:+:2720-8554) 365-372

183-192 PRRARSVRYP linker 1-10

193-212 KLTCATTRQVVNVVTTKIAL nsp3(NC_045512:+:2720-8554) 1923-1942

213-222 PRRARSVRYP linker 1-10

223-233 VVNAANVYLKH nsp3(NC_045512:+:2720-8554) 239-249

234-243 PRRARSVRYP linker 1-10

244-257 TKDVVECLKLSHQS nsp3(NC_045512:+:2720-8554) 1830-1843

258-267 PRRARSVRYP linker 1-10

268-276 YDLSVVNAR helicase(NC_045512:+:16237-18039) 382-390

277-286 PRRARSVRYP linker 1-10

287-296 ACIDCSARHI nsp3(NC_045512:+:2720-8554) 1872-1881

297-306 PRRARSVRYP linker 1-10

307-316 NYQCGHYKHI nsp3(NC_045512:+:2720-8554) 1012-1021

317-326 PRRARSVRYP linker 1-10

327-336 KACVEEVTTT nsp3(NC_045512:+:2720-8554) 415-424

337-346 PRRARSVRYP linker 1-10

347-354 FNSVCRLM helicase@Aruba(NC_045512@Aruba:+:16237-18039) 422-429

355-364 PRRARSVRYP linker 1-10

365-379 FKELLVYAADPAMHA RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236)

368-382

380-389 PRRARSVRYP linker 1-10

390-399 SVELKHFFFA RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 434-443

400-409 PRRARSVRYP linker 1-10

410-418 RSVYPVASP nsp2(NC_045512:+:806-2719) 121-129

419-428 PRRARSVRYP linker 1-10

429-446 CANFNVLFSTVFPFTSFG RNA-dependent_RNA_polymerase@Nigeria(NC_045512@Nigeria:+:134 42-

13468+13468-16236) 310-327

2 447-456 PRRARSVRYP linker 1-10

2 457-469 ANFCALILAYCNK nsp3(NC_045512:+:2720-8554) 890-902

2 470-479 PRRARSVRYP linker 1-10

2 480-495 TVLKKCKSAFYILPSI nsp3(NC_045512:+:2720-8554) 526-541

2 496-505 PRRARSVRYP linker 1-10

2 506-520 ERFVSLAIDAYPLTK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 857-871

2 521 -530 PRRARSVRYP linker 1-10

2 531-543 IVKFISTCACEIV nsp2(NC_045512:+:806-2719) 468-480

2 544-553 PRRARSVRYP linker 1-10

2 554-561 DSYFVVKR RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 67-74

2 562-571 PRRARSVRYP linker 1-10

2 572-591 DDRCILHCANFNVLFSTVFP RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 303-322

2 592-601 PRRARSVRYP linker 1-10

2 602-610 VTANVNALL RNA-dependent_RNA_polymerase(NC_045512:+: 13442-13468+13468-16236) 700-708

2 611-620 PRRARSVRYP linker 1-10

2 621-640 LQKAAITILDGISQYSLRLI nsp2(NC_045512:+:806-2719) 382-401

2 641 -650 PRRARSVRYP linker 1-10

2 651-673 SHGKQVVSDIDYVPLKSATCITR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 454-476

2 674-683 PRRARSVRYP linker 1-10

2 684-696 YAKPFLNKVVSTT nsp3(NC_045512:+:2720-8554) 1323-1335

2 697-706 PRRARSVRYP linker 1-10

2 707-733 FSASTSAFVETVKGLDYKAFKQIVESC nsp2(NC_045512:+:806-2719) 300-326

2 734-743 PRRARSVRYP linker 1-10

2 744-758 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368

2 759-768 PRRARSVRYP linker 1-10

2 769-778 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840

2 779-788 PRRARSVRYP linker 1-10

2 789-800 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

2 801-810 PRRARSVRYP linker 1-10

2 811-819 TEIYQAGST surface glycoprotein@Aruba(NC 045512@Aruba:+:21563-25384) 466-474

2 820-829 PRRARSVRYP linker 1-10

2 830-839 GTNLPLQLGF 3’-to-5’ 5Xonuclease(NC_045512:+:18040-19620) 102-111

2 840-849 PRRARSVRYP linker 1-10

2 850-861 FSNVTWFHAIVS surface_g glyycopprotein@@Ghana((NC__045512@@Ghana:+:21563-25384)) 59-70

2 862-871 PRRARSVRYP linker 1-10

2 872-895 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-

25384) 205-228 2 896-905 PRRARSVRYP linker 1-10

2 906-915 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895

2 916-925 PRRARSVRYP linker 1-10

2 926-941 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 59-74

2 942-951 PRRARSVRYP linker 1-10

2 952-966 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

2 967-976 PRRARSVRYP linker 1-10

2 977-994 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

2 995-1004 PRRARSVRYP linker 1-10

2 1005-1023 ECAQVLSETVMCGGSLYVK RNA- dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-13468 +13468-16236) 658-676

2 1024-1033 PRRARSVRYP linker 1-10

2 1034-1048 INAACRKVQHMVVKA 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 305-319

2 1049-1058 PRRARSVRYP linker 1-10

2 1059-1072 RLNVGDYFVLTSHT helicase@Austria(NC_045512@Austria:+:16237-18039) 218-231

2 1073-1082 PRRARSVRYP linker 1-10

2 1083-1091 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-

1 266

2 1092-1101 PRRARSVRYP linker 1-10

2 1102-1126 SDIDITFLKKDAPYIVGDVVQEGVL nsp3(NC_045512:+:2720-8554) 454-478

2 1127-1136 PRRARSVRYP linker 1-10

2 1137-1151 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway :+:21563-25384)

129-143

2 1152-1161 PRRARSVRYP linker 1-10

2 1162-1175 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384)

485-498

2 1176-1185 PRRARSVRYP linker 1-10

2 1186-1199 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

2 1200-1209 PRRARSVRYP linker 1-10

2 1210-1221 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 230-241

2 1222-1231 PRRARSVRYP linker 1-10

2 1232-1239 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

2 1240-1249 PRRARSVRYP linker 1-10

2 1250-1263 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

2 1264-1273 PRRARSVRYP linker 1-10

2 1274-1294 ALCEKALKYFPIDKCSRIIPA helicase@Colombia(NC_045512@Colombia:+:16237-18039) 316-336

2 1295-1304 PRRARSVRYP linker 1-10

2 1305-1316 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

2 1317-1326 PRRARSVRYP linker 1-10

2 1327-1336 KCAYWVPRAS nsp2(NC_045512:+:806-2719) 239-248

2 1337-1346 PRRARSVRYP linker 1-10

2 1347-1358 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

2 1359-1368 PRRARSVRYP linker 1-10

2 1369-1380 IEVQGYKSVNIT nsp3(NC_045512:+:2720-8554) 13-24

2 1381-1390 PRRARSVRYP linker 1-10

2 1391-1404 FGTVYEKLKPVLDW nsp2(NC_045512:+:806-2719) 437-450

2 1405-1414 PRRARSVRYP linker 1-10

2 1415-1424 FCLEASFNYL nsp3(NC_045512:+:2720-8554) 1391 -1400

2 1425-1434 PRRARSVRYP linker 1-10

2 1435-1445 YDKLQFTSLEI helicase@Aruba(NC_045512@Aruba:+:16237-18039) 582-592

2 1446-1455 PRRARSVRYP linker 1-10

2 1456-1466 DNVLSTFISAA nsp3(NC_045512:+:2720-8554) 1809-1819

2 1467-1476 PRRARSVRYP linker 1-10

2 1477-1484 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

2 1485-1494 PRRARSVRYP linker 1-10

2 1495-1504 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

3 1 -8 QIGVVREF helicase(NC_045512:+:16237-18039) 492-499

3 9-18 PRRARSVRYP linker 1-10

3 19-40 LGGMSYYCKSHKPSISFPLCAN helicase@NewZealand(NC_045512@NewZealand:+:16237-18039) 65-86

3 41-50 PRRARSVRYP linker 1-10

3 51-60 DPIHSLRVCV nsp3(NC_045512:+:2720-8554) 339-348

3 61-70 PRRARSVRYP linker 1-10

3 71-88 SQHTMLVKQGDDYVYLPY RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442- 13468+13468-16236) 814-831

3 89-98 PRRARSVRYP linker 1-10 3 99-107 ASQGLLASI RNA-dependent_RNA_polymerase@Austria(NC_045512@Austria:+:134 42-13468+13468-

16236) 771-779

3 108-117 PRRARSVRYP linker 1-10

3 118-143 YRLANECAQVLSEMVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 653-678

3 144-153 PRRARSVRYP linker 1-10

3 154-185 IMASLVLARKHTTCCSLSHRFYRLANECAQVL RNA-dependent_RNA_polymerase(NC_045512:+:13442-

13468+13468-16236) 632-663

3 186-195 PRRARSVRYP linker 1-10

3 196-212 LECNVKTTEVVGDIILK nsp3(NC_045512:+:2720-8554) 1244-1260

3 213-222 PRRARSVRYP linker 1-10

3 223-236 SYLFQHANLDSCKR nsp3(NC_045512:+:2720-8554) 915-928

3 237-246 PRRARSVRYP linker 1-10

3 247-256 LSVNPYVCNA helicase@Cyprus(NC_045512@Cyprus:+:16237-18039) 43-52

3 257-266 PRRARSVRYP linker 1-10

3 267-277 EQYVFCTVNAL helicase(NC_045512:+:16237-18039) 353-363

3 278-287 PRRARSVRYP linker 1-10

3 288-297 VQQESPFVMM nsp3(NC_045512:+:2720-8554) 980-989

3 298-307 PRRARSVRYP linker 1-10

3 308-316 MPVCVETKA nsp3(NC_045512:+:2720-8554) 571-579

3 317-326 PRRARSVRYP linker 1-10

3 327-349 YLGGMSYYCKSHKLPISFPLCAN helicase@CostaRica(NC_045512@CostaRica:+:16237-18039)

64-86

3 350-359 PRRARSVRYP linker 1-10 3 360-375 RKIFVDGVPFVVSTGY RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

331-346

3 376-385 PRRARSVRYP linker 1-10 3 386-397 VPVVDSYY S LLM RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 231-242 3 398-407 PRRARSVRYP linker 1-10 3 408-417 VMCGGSLYVK RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 667-676 3 418-427 PRRARSVRYP linker 1-10 3 428-435 DMYSVMLT RNA-dependent_RNA_polymerase@Malaysia(NC_045512@Malaysia:+:1 3442-

13468+13468-16236) 901-908

3 436-445 PRRARSVRYP linker 1-10

3 446-453 GVYCCREH nsp2(NC_045512:+:806-2719) 47-54

3 454-463 PRRARSVRYP linker 1-10

3 464-478 YNLLKGCPAVAKHDF RNA-dependent_RNA_polymerase@Poland(NC_045512@Poland:+:13442 -

13468+13468-16236) 87-101

3 479-488 PRRARSVRYP linker 1-10

3 489-500 NIGCNHTGVVGE nsp2(NC_045512:+:806-2719) 250-261

3 501-510 PRRARSVRYP linker 1-10

3 511-532 SQHTMLVKQFDDYVYLPYPDPS RNA- dependent_RNA_polymerase@Estonia(NC_045512@Estonia:+:13442-1 3468+13468-16236) 814-835

3 533-542 PRRARSVRYP linker 1-10

3 543-550 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

3 551-560 PRRARSVRYP linker 1-10

3 561-574 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

3 575-584 PRRARSVRYP linker 1-10

3 585-596 VTMPLGYVTHGL nsp3(NC_045512:+:2720-8554) 628-639

3 597-606 PRRARSVRYP linker 1-10

3 607-645 GCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGL helicase(NC_045512:+:16237-18039) 54-92

3 646-655 PRRARSVRYP linker 1-10

3 656-686 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1211-1241

3 687-696 PRRARSVRYP linker 1-10

3 697-708 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

3 709-718 PRRARSVRYP linker 1-10

3 719-737 DKSAFVNLKQLPFFYYSDS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 432-450

3 738-747 PRRARSVRYP linker 1-10

3 748-763 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001-1016

3 764-773 PRRARSVRYP linker 1-10

3 774-782 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

3 783-792 PRRARSVRYP linker 1-10

3 793-807 RIIPARARVECFDKF helicase@Aruba(NC_045512@Aruba:+:16237-18039) 332-346

3 808-817 PRRARSVRYP linker 1-10

3 818-831 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384)

58-71

832-841 PRRARSVRYP linker 1-10

842-855 EGVVDYGARFYFYT nsp3(NC_045512:+:2720-8554) 595-608

856-865 PRRARSVRYP linker 1-10 3 866-887 GYQPYRVVVLSFELLHAPATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

3 888-897 PRRARSVRYP linker 1-10

3 898-916 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384) 607-625

3 917-926 PRRARSVRYP linker 1-10

3 927-941 FSVAALTNNVAFQTV RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 396-410

3 942-951 PRRARSVRYP linker 1-10

3 952-959 TDVVYRAF RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 28-35

3 960-969 PRRARSVRYP linker 1-10

3 970-981 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497

3 982-991 PRRARSVRYP linker 1-10

3 992-999 PSFLGRYM nsp3(NC_045512:+:2720-8554) 822-829

3 1000-1009 PRRARSVRYP linker 1-10

3 1010-1028 KLNVGDYFVLTSHTVMPLS helicase(NC_045512:+:16237-18039) 218-236

3 1029-1038 PRRARSVRYP linker 1-10

3 1039-1054 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

3 1055-1064 PRRARSVRYP linker 1-10

3 1065-1074 SVLNDILARL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 971-980

3 1075-1084 PRRARSVRYP linker 1-10

3 1085-1107 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-

1061

3 1108-1117 PRRARSVRYP linker 1-10

3 1118-1135 CANFNVLFSTVFPPTSFG RNA- dependent_RNA_polymerase@China(NC_045512@China:+: 13442-13468+13468-16236) 310-327

3 1136-1145 PRRARSVRYP linker 1-10

3 1146-1159 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

294-307

3 1160-1169 PRRARSVRYP linker 1-10

3 1170-1191 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-

25384) 125-146

3 1192-1201 PRRARSVRYP linker 1-10

3 1202-1210 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161-

1169

3 1211-1220 PRRARSVRYP linker 1-10

3 1221-1237 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384) 258-274

3 1238-1247 PRRARSVRYP linker 1-10

3 1248-1267 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-

1256

3 1268-1277 PRRARSVRYP linker 1-10

3 1278-1288 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384) 1078-1088

3 1289-1298 PRRARSVRYP linker 1-10

3 1299-1308 NEFYAYLRKH RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236) 743-752

3 1309-1318 PRRARSVRYP linker 1-10

3 1319-1332 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-

25384) 128-141

3 1333-1342 PRRARSVRYP linker 1-10

3 1343-1359 YADVFHLYLQYIRKLHD RNA-dependent_RNA_polymerase(NC_045512:+: 13442-

13468+13468-16236) 877-893

3 1360-1369 PRRARSVRYP linker 1-10 3 1370-1384 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 680-694

3 1385-1394 PRRARSVRYP linker 1-10 3 1395-1404 KSASVYYSQL nsp3(NC_045512:+:2720-8554) 1737-1746 3 1405-1414 PRRARSVRYP linker 1-10 3 1415-1430 ANSIVCRFDTRVLSNL 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 394-409 3 1431-1440 PRRARSVRYP linker 1-10 3 1441-1448 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-

1266

3 1449-1458 PRRARSVRYP linker 1-10

3 1459-1478 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 209-228

3 1479-1488 PRRARSVRYP linker 1-10

3 1489-1502 APGCDVTDVTQLYL helicase@Aruba(NC_045512@Aruba:+:16237-18039) 52-65

4 1-12 VRTNVYLAVFDK nsp3(NC_045512:+:2720-8554) 351-362 4 13-22 PRRARSVRYP linker 1-10 4 23-33 KGVQIPCTCGK nsp3(NC_045512:+:2720-8554) 963-973 4 34-43 PRRARSVRYP linker 1-10

4 44-66 NHDLYCQVHGNAHVASCDAIMTR 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 256-278

4 67-76 PRRARSVRYP linker 1-10

4 77-84 YDFAVSKG RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+: 13442-13468+13468-

16236) 420-427

4 85-94 PRRARSVRYP linker 1-10

4 95-104 ISDYDYYRYN RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 450-459

4 105-114 PRRARSVRYP linker 1-10

4 115-122 FKLASHMY nsp3(NC_045512:+:2720-8554) 96-103

4 123-132 PRRARSVRYP linker 1-10

4 133-147 SYFAIGLALYYPSAR helicase@Austria(NC_045512@Austria:+:16237-18039) 289-303

4 148-157 PRRARSVRYP linker 1-10

4 158-166 ASQGLVASI RNA-dependent_RNA_polymerase@Aruba(NC_045512@Aruba:+:13442-1 3468+13468-

16236) 771-779

4 167-176 PRRARSVRYP linker 1-10

4 177-186 VVADAVIKTL nsp3(NC_045512:+:2720-8554) 56-65

4 187-196 PRRARSVRYP linker 1-10

4 197-208 SSPDAVTAYNGY nsp3(NC_045512:+:2720-8554) 660-671

4 209-218 PRRARSVRYP linker 1-10

4 219-226 SINVANYQ helicase@Mozambique(NC_045512@Mozambique:+:16237-18039) 263-270

4 227-236 PRRARSVRYP linker 1-10

4 237-245 SRELKVTFF nsp3(NC_045512:+:2720-8554) 1134-1142

4 246-255 PRRARSVRYP linker 1-10

4 256-267 TRAKVGILCIMS helicase(NC_045512:+:16237-18039) 566-577

4 268-277 PRRARSVRYP linker 1-10

4 278-287 GVITHDVSSA helicase(NC_045512:+:16237-18039) 478-487

4 288-297 PRRARSVRYP linker 1-10

4 298-317 SEAVEAPLVGTPVCINGLML nsp2(NC_045512:+:806-2719) 591-610

4 318-327 PRRARSVRYP linker 1-10

4 328-338 AVHECFVKRVD 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 281-291

4 339-348 PRRARSVRYP linker 1-10

4 349-362 RNLQHRLYECLYRN RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

721-734

4 363-372 PRRARSVRYP linker 1-10

4 373-388 SLRCGACIRRPFLCCK helicase@Aruba(NC_045512@Aruba:+:16237-18039) 13-28

4 389-398 PRRARSVRYP linker 1-10

4 399-411 KASCTLSEQLDFI nsp2(NC_045512:+:806-2719) 30-42

4 412-421 PRRARSVRYP linker 1-10

4 422-438 AQSFLNRVCGVSAARLT RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

4-20

4 439-448 PRRARSVRYP linker 1-10

4 449-463 QIELKFNPPALQDAY nsp3(NC_045512:+:2720-8554) 867-881

4 464-473 PRRARSVRYP linker 1-10

4 474-491 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142

4 492-501 PRRARSVRYP linker 1-10

4 502-516 HYVRITGLYPTLNIL helicase@lndonesia(NC_045512@lndonesia:+:16237-18039) 245-259

4 517-526 PRRARSVRYP linker 1-10

4 527-534 YDFVVSKG RNA-dependent_RNA_polymerase@Japan(NC_045512@Japan:+:13442-1 3468+13468-

16236) 420-427

4 535-544 PRRARSVRYP linker 1-10

4 545-564 YVYLPYPDPSRILGAGCFVD RNA-dependent_RNA_polymerase(NC_045512:+:13442-13468+13468-1 6236)

826-845

4 565-574 PRRARSVRYP linker 1-10

4 575-625 HFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARV helicase(NC_045512:+:16237-18039) 290-340

4 626-635 PRRARSVRYP linker 1-10

4 636-655 RAKHYVYIGDPAQLPAPRTL helicase(NC_045512:+:16237-18039) 392-411

4 656-665 PRRARSVRYP linker 1-10

4 666-678 WNVVRIKIVQMLS 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 159-171

4 679-688 PRRARSVRYP linker 1-10

4 689-696 IETISLAG nsp3(NC_045512:+:2720-8554) 684-691

4 697-706 PRRARSVRYP linker 1-10

4 707-717 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146

4 718-727 PRRARSVRYP linker 1-10

4 728-746 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 709-727

4 747-756 PRRARSVRYP linker 1-10

4 757-766 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173

4 767-776 PRRARSVRYP linker 1-10

4 777-792 TGLHPTQAPTHLSVDT 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 16-31 4 793-802 PRRARSVRYP linker 1-10

4 803-823 HPNCVNCLDDRCILHCANFNV RNA- dependent_RNA_polymerase@Australia(NC_045512@Australia:+: 13442-13468+13468-16236) 295-315

4 824-833 PRRARSVRYP linker 1-10

4 834-844 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

4 845-854 PRRARSVRYP linker 1-10

4 855-874 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224

4 875-884 PRRARSVRYP linker 1-10

4 885-895 KESVQTFFKLV nsp2(NC_045512:+:806-2719) 492-502

4 896-905 PRRARSVRYP linker 1-10

4 906-928 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

4 929-938 PRRARSVRYP linker 1-10

4 939-955 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

4 956-965 PRRARSVRYP linker 1-10

4 966-977 TRAKVGILCITS helicase@SouthKorea(NC_045512@SouthKorea:+:16237-18039) 566-577

4 978-987 PRRARSVRYP linker 1-10

4 988-998 YDNLQFISLEI helicase@Austria(NC_045512@Austria:+:16237-18039) 582-592

4 999-1008 PRRARSVRYP linker 1-10

4 1009-1021 AIKCVPQADVEWK3’-to-5’_exonuclease(NC_045512:+:18040-1962 0) 337-349

4 1022-1031 PRRARSVRYP linker 1-10

4 1032-1044 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

4 1045-1054 PRRARSVRYP linker 1-10

4 1055-1067 ATNVVIKVCEFQF surface_glycoprotein(NC_045512:+:21563-25384) 123-135

4 1068-1077 PRRARSVRYP linker 1-10

4 1078-1087 SSVLFISTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

4 1088-1097 PRRARSVRYP linker 1-10

4 1098-1105 RVEAFEYY nsp3(NC_045512:+:2720-8554) 810-817

4 1106-1115 PRRARSVRYP linker 1-10

4 1116-1141 YRLANECAQVLSEIVMCGGSLYVKPG RNA- dependent_RNA_polymerase@Canada(NC_045512@Canada:+:13442-134 68+13468-16236) 653-678

4 1142-1151 PRRARSVRYP linker 1-10

4 1152-1174 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

4 1175-1184 PRRARSVRYP linker 1-10

4 1185-1205 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384) 605-625

4 1206-1215 PRRARSVRYP linker 1-10

4 1216-1227 YPSLETIQITIS nsp3(NC_045512:+:2720-8554) 1483-1494

4 1228-1237 PRRARSVRYP linker 1-10

4 1238-1247 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

4 1248-1257 PRRARSVRYP linker 1-10

4 1258-1273 EEIIYNLLKDCPAVAK RNA- dependent_RNA_polymerase@Senegal(NC_045512@Senegal:+:13442-1 3468+13468-16236) 83-98

4 1274-1283 PRRARSVRYP linker 1-10

4 1284-1298 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

4 1299-1308 PRRARSVRYP linker 1-10

4 1309-1331 TIATYCTGSIPCSVCLSGLDSLD nsp3(NC_045512:+:2720-8554) 1459-1481

4 1332-1341 PRRARSVRYP linker 1-10

4 1342-1364 TQLYLGGMSYYCKPHKPPISFPL helicase@lceland(NC_045512@lceland:+:16237-18039) 61-83

4 1365-1374 PRRARSVRYP linker 1-10

4 1375-1385 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616

4 1386-1395 PRRARSVRYP linker 1-10

4 1396-1406 IEELFYSYATH 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 363-373

4 1407-1416 PRRARSVRYP linker 1-10

4 1417-1431 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

4 1432-1441 PRRARSVRYP linker 1-10

4 1442-1456 RTCCLCDRRATCFST 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 205-219

4 1457-1466 PRRARSVRYP linker 1-10

4 1467-1474 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478

4 1475-1484 PRRARSVRYP linker 1-10

4 1485-1494 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

4 1495-1504 PRRARSVRYP linker 1-10

4 1505-1519 TYACWHHSIGFDYVY 3’-to-5’_exonuclease(NC_045512:+:18040-19620) 223-237 In certain embodiments, the vaccine comprises or expresses at least one of the concatemers of epitopes with intervening linker sequences (and as set forth in Figure 23). In certain embodiments, the vaccine comprises or expresses at least two of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses three of the concatemers set forth below. In certain embodiments, the vaccine comprises or expresses all the concatemers set forth below.

Table 13 mmunoprec P ^os _in_ ^conc atemer epitopes gene P ^os J ⁿ _gene

1 1-23 QLALSKGVYFVCNLLLLFVTVYS ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 70-92

1 24-33 PRRARSVRYP linker 1-10

1 34-48 AYYVGYLQPRTFLLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 260-274

1 49-58 PRRARSVRYP linker 1-10

1 59-69 SELVIGAVILR membrane_glycoprotein(NC_045512:+:26523-27191) 136-146

1 70-79 PRRARSVRYP linker 1-10

1 80-90 RFQLHRSYLTP surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 233-243

1 91-100 PRRARSVRYP linker 1-10

1 101-108 PVLKGVKL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1259-1266

1 109-118 PRRARSVRYP linker 1-10

1 119-131 RSVASQSIIAYTM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 681-693

1 132-141 PRRARSVRYP linker 1-10

1 142-156 VDTSLSSLKLKDCVM nsp6@Latvia(NC_045512@Latvia:+:10973-11842) 101-115

1 157-166 PRRARSVRYP linker 1-10

1 167-185 QLSLSKGFHFVCNLLLLFV ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220) 70-88

1 186-195 PRRARSVRYP linker 1-10

1 196-205 NCYDYCIPYN ORF3a_protein(NC_045512:+:25393-26220) 152-161

1 206-215 PRRARSVRYP linker 1-10

1 216-232 KDQVILLNKHIDAYKTF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 347-363

1 233-242 PRRARSVRYP linker 1-10

1 243-252 PFTINCQEPK ORF8_protein@lndia(NC_045512@lndia:+:27894-28259) 85-94

1 253-262 PRRARSVRYP linker 1-10

1 263-285 HQPYVVDDPCPIHFYSKWYIRVG ORF8_protein(NC_045512:+:27894-28259) 28-50

1 286-295 PRRARSVRYP linker 1-10

1 296-304 YGIIWVATE nucleocapsid_phosphoprotein@SmallSouthAmerica(NC_045512@Smal lSouthAmerica:+:28274-29533) 128-136

1 305-314 PRRARSVRYP linker 1-10

1 315-332 QLALFKGVHFVCNLLLLF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 70-87

1 333-342 PRRARSVRYP linker 1-10

1 343-357 ALLAVFHSASKIITL ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 51-65

1 358-367 PRRARSVRYP linker 1-10

1 368-375 STFKCYGV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 371-378

1 376-385 PRRARSVRYP linker 1-10

1 386-393 EIYQAGSK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 471-478

1 394-403 PRRARSVRYP linker 1-10

1 404-417 RLTLGVYDYLVSTQ nsp6(NC_045512:+:10973-11842) 236-249

1 418-427 PRRARSVRYP linker 1-10

1 428-442 VCNLLLLFVTVYSHL ORF3a_protein@Croatia(NC_045512@Croatia:+:25393-26220) 80-94

1 443-452 PRRARSVRYP linker 1-10

1 453-472 DANYFLCWHTNCYHYCIPYN ORF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220) 142-161

1 473-482 PRRARSVRYP linker 1-10

1 483-498 GSNVFQTRAGCLIGAE surface_glycoprotein(NC_045512:+:21563-25384) 639-654

1 499-508 PRRARSVRYP linker 1-10

1 509-525 INFVRIIMRLWLCLKCR ORF3a_protein@Mozambique(NC_045512@Mozambique:+:25393-26220) 118-134

1 526-535 PRRARSVRYP linker 1-10

1 536-544 AAAYYVGYL surface_glycoprotein(NC_045512:+:21563-25384) 262-270

1 545-554 PRRARSVRYP linker 1-10

1 555-565 AALALLLLDRL nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 217-227 1 566-575 PRRARSVRYP linker 1-10

1 576-589 IKVCEFQFCNDPYY surface_glycoprotein@CostaRica(NC_045512@CostaRica:+:21563-2 5384)

128-141

1 590-599 PRRARSVRYP linker 1-10

1 600-609 ISEHDYQIGG ORF3a_protein@FrenchGuiana(NC_045512@FrenchGuiana:+:25393-26 220) 179-188

1 610-619 PRRARSVRYP linker 1-10

1 620-628 DYYQLYSTQ ORF3a_protein(NC_045512:+:25393-26220) 210-218

1 629-638 PRRARSVRYP linker 1-10

1 639-657 VKDCVLLHSYFTSDYYQLY ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220) 197-215

1 658-667 PRRARSVRYP linker 1-10

1 668-679 FNCYFPLQSYGF surface_glycoprotein(NC_045512:+:21563-25384) 486-497

1 680-689 PRRARSVRYP linker 1-10

1 690-699 ARDLICAQKF surface_glycoprotein(NC_045512:+:21563-25384) 846-855

1 700-709 PRRARSVRYP linker 1-10

1 710-727 IKVCEFQFCNDPFLGVYH surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 125-142

1 728-737 PRRARSVRYP linker 1-10

1 738-758 VMFLARGIVFMCVDYCPI FFI nsp6@Cyprus(NC_045512@Cyprus:+: 10973-11842) 179-199

1 759-768 PRRARSVRYP linker 1-10

1 769-782 GFNCYSPLQSYGFQ surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 485-498

1 783-792 PRRARSVRYP linker 1-10

1 793-814 QLALSKGVHFVCNLLLLFVTVY ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220)

70-91

1 815-824 PRRARSVRYP linker 1-10

1 825-838 ANPVLPFNDGVYFA surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 77-90

1 839-848 PRRARSVRYP linker 1-10

1 849-870 SDFVRATATIPIRASLPFGWLI ORF3a_protein@Belgium(NC_045512@Belgium:+:25393-26220)

26-47

1 871 -880 PRRARSVRYP linker 1-10

1 881 -900 PINLVRGLPQGFSVLEPLVD surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-25384)

209-228

1 901-910 PRRARSVRYP linker 1-10

1 911-932 GYQ PYRVVVLS F E L LH A PATVC surface_glycoprotein(NC_045512:+:21563-25384) 504-525

1 933-942 PRRARSVRYP linker 1-10

1 943-959 ILLNKHIDAYKTFPPIE nucleocapsid_phosphoprotein@Chile(NC_045512@Chile:+:28274-29 533)

351-367

1 960-969 PRRARSVRYP linker 1-10

1 970-987 LNDLCFTNVYADSFVIRG surface_glycoprotein(NC_045512:+:21563-25384) 387-404

1 988-997 PRRARSVRYP linker 1-10

1 998-1020 KNPLLYDANYFLCCHTNCYDYCI ORF3a_protein@Senegal(NC_045512@Senegal:+:25393-26220) 136-158

1 1021-1030 PRRARSVRYP linker 1-10

1 1031-1052 IAMACLVGLMWLSYFIASFRLF membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 82-103

1 1053-1062 PRRARSVRYP linker 1-10

1 1063-1085 VAAGLEAPFFYLYALVYFLQSIN ORF3a_protein@Ecuador(NC_045512@Ecuador:+:25393-

26220) 97-119

1 1086-1095 PRRARSVRYP linker 1-10

1 1096-1123 FTSDYYQLYSTQLSTYTGVEHVTFFIYN

ORF3a_protein@Latvia(NC_045512@Latvia:+:25393-26220) 207-234

1 1124-1133 PRRARSVRYP linker 1-10

1 1134-1148 EFQFCNYPFLGVYHK surface_glycoprotein@Norway(NC_045512@Norway :+:21563-25384)

129-143

1 1149-1158 PRRARSVRYP linker 1-10

1 1159-1179 ELVIGAVILRGHLRIAGHHLG membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191)

137-157

1 1180-1189 PRRARSVRYP linker 1-10

1 1190-1201 ISVTTEILPVSM surface_glycoprotein(NC_045512:+:21563-25384) 720-731

2 1-8 TQALLQRQ nucleocapsid_phosphoprotein@CostaRica(NC_045512@CostaRica:+: 28274-29533)

379-386

2 9-18 PRRARSVRYP linker 1-10

2 19-43 KNPLLYDANYFLCWHTNCYDYCIPY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 136-160

2 44-53 PRRARSVRYP linker 1-10

2 54-61 REGVFVSN surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 1087-1094

2 62-71 PRRARSVRYP linker 1-10

2 72-83 FRSSVLHSTQDL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 43-54

2 84-93 PRRARSVRYP linker 1-10

2 94-104 LRIAGHHLGRC membrane_glycoprotein(NC_045512:+:26523-27191) 149-159

2 105-114 PRRARSVRYP linker 1-10 2 115-128 FFSNVTWFHAIHVS surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 58-71

2 129-138 PRRARSVRYP linker 1-10

2 139-147 LKLKDCVMY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 105-113

2 148-157 PRRARSVRYP linker 1-10

2 158-166 EPLLKGVKL surface_glycoprotein@Croatia(NC_045512@Croatia:+:21563-25384 ) 1258-1266

2 167-176 PRRARSVRYP linker 1-10

2 177-192 NYTVSCSPFTINCQEP ORF8_protein@CostaRica(NC_045512@CostaRica:+:27894-28259) 78-93

2 193-202 PRRARSVRYP linker 1-10

2 203-211 ISEHDYHIG ORF3a_protein@NorthMacedonia(NC_045512@NorthMacedonia:+:2539 3-26220) 179-187

2 212-221 PRRARSVRYP linker 1-10

2 222-232 CLPFTINCQKP ORF8_protein@Brazil(NC_045512@Brazil:+:27894-28259) 83-93

2 233-242 PRRARSVRYP linker 1-10

2 243-250 SSIVITSG ORF3a_protein@SouthKorea(NC_045512@SouthKorea:+:25393-26220) 165-172

2 251 -260 PRRARSVRYP linker 1-10

2 261-268 WFTALTQH nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 52-59

2 269-278 PRRARSVRYP linker 1-10

2 279-286 ETQALPQR nucleocapsid_phosphoprotein@SmallNorthAmerica(NC_045512@Smal lNorthAmerica:+:28274-29533) 378-385

2 287-296 PRRARSVRYP linker 1-10

2 297-320 LGSLVVRCSFYEDFLEYHDVRVVL ORF8_protein(NC_045512:+:27894-28259) 95-118

2 321 -330 PRRARSVRYP linker 1-10

2 331 -352 INLVRDLPQGFSALEPLVDLPI surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 206-227

2 353-362 PRRARSVRYP linker 1-10

2 363-374 DTSLKLKECVMY nsp6@SmallAsia(NC_045512@SmallAsia:+:10973-11842) 102-113

2 375-384 PRRARSVRYP linker 1-10

2 385-407 RVDFCGKGYHLMSFPQSAPHGVV surface_glycoprotein(NC_045512:+:21563-25384) 1039-1061

2 408-417 PRRARSVRYP linker 1-10

2 418-427 GVGGKPCIKV nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 274-283

2 428-437 PRRARSVRYP linker 1-10

2 438-459 LLYDANYFLCWHINCYDYCIPY ORF3a_protein@Estonia(NC_045512@Estonia:+:25393-26220) 139-160

2 460-469 PRRARSVRYP linker 1-10

2 470-484 VNCTEVPVAIHADQL surface_glycoprotein(NC_045512:+:21563-25384) 615-629

2 485-494 PRRARSVRYP linker 1-10

2 495-509 YFTSDYYQLYSTQLI ORF3a_protein@lndonesia(NC_045512@lndonesia:+:25393-26220) 206-220

2 510-519 PRRARSVRYP linker 1-10

2 520-532 ATNVVIKVCEFQF su rfa ce_g ly co p ro te i n ( N C_045512:+:21563-25384) 123-135

2 533-542 PRRARSVRYP linker 1-10

2 543-556 KHWPQIAQFAPSAS nucleocapsid_phosphoprotein@Australia(NC_045512@Australia:+: 28274-

29533) 299-312

2 557-566 PRRARSVRYP linker 1-10

2 567-576 LPFTINCQEL ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-28259) 84-93

2 577-586 PRRARSVRYP linker 1-10

2 587-595 VFSQCVNLT surface_glycoprotein@Egypt(NC_045512@Egypt:+:21563-25384) 11-19

2 596-605 PRRARSVRYP linker 1-10

2 606-626 AVLYQGVNCTEVPFAIHADQL surface_glycoprotein@SmallAfrica(NC_045512@SmallAfrica:+:215 63-

25384) 605-625

2 627-636 PRRARSVRYP linker 1-10

2 637-644 EVTPSGTW nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 323-330

2 645-654 PRRARSVRYP linker 1-10

2 655-666 SVFQSASKIITL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 54-65

2 667-676 PRRARSVRYP linker 1-10

2 677-684 AEVQIDRL surface_glycoprotein(NC_045512:+:21563-25384) 989-996

2 685-694 PRRARSVRYP linker 1-10

2 695-703 FFSNVTWFH surface_glycoprotein(NC_045512:+:21563-25384) 58-66

2 704-713 PRRARSVRYP linker 1-10

2 714-721 SDFVRATA ORF3a_protein(NC_045512:+:25393-26220) 26-33

2 722-731 PRRARSVRYP linker 1-10

2 732-742 MMFVKHKHAFL nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 57-67

2 743-752 PRRARSVRYP linker 1-10

2 753-762 GNCDVVIGIV surface_glycoprotein(NC_045512:+:21563-25384) 1124-1133

2 763-772 PRRARSVRYP linker 1-10

2 773-787 TYGVGYQPYRVVVLS surface_glycoprotein@Australia(NC_045512@Australia:+:21563-2 5384)

496-510

2 788-797 PRRARSVRYP linker 1-10

2 798-819 NVVIKVCEFQFCNYPFLGVYYH surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 125-146 820-829 PRRARSVRYP linker 1-10 830-843 ETKCTLKSFTVEKG surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 294-307 844-853 PRRARSVRYP linker 1-10 854-869 FLVLLPLVSSQCVNLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 4-19 870-879 PRRARSVRYP linker 1-10 880-890 VLYQGVNCTEV surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 606-616 891 -900 PRRARSVRYP linker 1-10 901-929 FLYIIKLIFLWLLWPVTLACFVLAAVYRI membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 45-73

930-939 PRRARSVRYP linker 1-10

940-954 VEHVTFFIYNKIVDE ORF3a_protein(NC_045512:+:25393-26220) 225-239 955-964 PRRARSVRYP linker 1-10 965-979 ARSVARQSIIAYTMS surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 680-694

980-989 PRRARSVRYP linker 1-10

990-1018 TLQCIMLVYCFLGYFCTCYFGLFCLLN RY nsp6@Aruba(NC_045512@Aruba:+: 10973-11842) 203-231

1019-1028 PRRARSVRYP linker 1-10

1029-1045 LFFFLYENAFLPFVMGI nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+: 10973-11842) 33-49

1046-1055 PRRARSVRYP linker 1-10

1056-1074 AIPINFTISVTTEILPVSM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

709-727

1075-1084 PRRARSVRYP linker 1-10

1085-1094 KQYGDCLGDI surface_glycoprotein(NC_045512:+:21563-25384) 835-844

1095-1104 PRRARSVRYP linker 1-10

1105-1121 INFVRIIMRLWLCCKCR ORF3a_protein@Australia(NC_045512@Australia:+:25393-26220)

118-134

1122-1131 PRRARSVRYP linker 1-10

1132-1148 SAAYYVGYLQLRTFLLK surface_glycoprotein@ltaly(NC_045512@ltaly:+:21563-25384)

258-274

1149-1158 PRRARSVRYP linker 1-10

1159-1168 SFKLKDCVMY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 107-116

1169-1178 PRRARSVRYP linker 1-10

1179-1197 QVAVLYQDVNCTEVPVAIH surface_glycoprotein@China(NC_045512@China:+:21563-25384)

607-625

1198-1207 PRRARSVRYP linker 1-10

1208-1227 MTSCCSCLKGCCSCGSCCKF surface_glycoprotein(NC_045512:+:21563-25384) 1237-

1-37 VAAGLEAPFLYLYALVYFLQSINFVRIIMRLWLCWKC ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 97-133

38-47 PRRARSVRYP linker 1-10 48-65 IKDLPKEITVATSRTLSY membrane_glycoprotein(NC_045512:+:26523-27191 ) 161-178 66-75 PRRARSVRYP linker 1-10 76-90 ISNCVADYSVLYNSA surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 354-368 91-100 PRRARSVRYP linker 1-10 101-113 ISSVLNDILSRLD surface_glycoprotein@Bangladesh(NC_045512@Bangladesh:+:21563 -25384) 972-984 114-123 PRRARSVRYP linker 1-10

124-136 SMWALIISVTSNY nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 160-172

137-146 PRRARSVRYP linker 1-10

147-160 TSGVGYQPYRVVVL surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 496-509

161-170 PRRARSVRYP linker 1-10

171-190 FPQSAPHGVVFLHVTYVPAQ surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384)

1048-1067

191 -200 PRRARSVRYP linker 1-10 201-208 VVNPVMEP ORF3a_protein(NC_045512:+:25393-26220) 255-262 209-218 PRRARSVRYP linker 1-10 219-228 PRWYFYYLGT nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 106-115 229-238 PRRARSVRYP linker 1-10 239-246 EHVQIHTI O R F3a_prote in (N C_045512 : + : 25393-26220) 242-249

247-256 PRRARSVRYP linker 1-10

257-285 SMWALIISVTSNYSGVVTIVMFLARGIVF nsp6@SmallSouthAmerica(NC_045512@SmallSouthAmerica:+: 10973-11842) 160-188

286-295 PRRARSVRYP linker 1-10

296-303 APLIELCV ORF8_protein(NC_045512:+:27894-28259) 55-62

304-313 PRRARSVRYP linker 1-10

314-355 TTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGAR ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 11-52

356-365 PRRARSVRYP linker 1-10

366-388 TTVMFLARGIVFMCVEYCPIFFI nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 177-199 3 389-398 PRRARSVRYP linker 1-10

3 399-408 KQYGDCLGNI surface_glycoprotein@Jordan(NC_045512@Jordan:+:21563-25384) 831-840

3 409-418 PRRARSVRYP linker 1-10

3 419-441 LIAIVMVTIMLCCITSCCSCLKG surface_glycoprotein@Mozambique(NC_045512@Mozambique:+:21563 -25384) 1220-1242

3 442-451 PRRARSVRYP linker 1-10

3 452-467 QLALSKGFHFVCNLLL ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220) 70-85

3 468-477 PRRARSVRYP linker 1-10

3 478-485 ISEHDYQI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 179-186

3 486-495 PRRARSVRYP linker 1-10

3 496-507 ALGKLQDVVNQN surface_glycoprotein(NC_045512:+:21563-25384) 944-955

3 508-517 PRRARSVRYP linker 1-10

3 518-530 NPVLPFNDGVYFA surface_glycoprotein(NC_045512:+:21563-25384) 81-93

3 531 -540 PRRARSVRYP linker 1-10

3 541 -556 HWPQIAQFAPSASAFF nucleocapsid_phosphoprotein@Aruba(NC_045512@Aruba:+:28274-29 533) 300-315

3 557-566 PRRARSVRYP linker 1-10

3 567-582 LQS LQTYVT QQ L I RAA surface_glycoprotein(NC_045512:+:21563-25384) 1001 -1016

3 583-592 PRRARSVRYP linker 1-10

3 593-601 APLIELCVD ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-28259) 55-63

3 602-611 PRRARSVRYP linker 1-10

3 612-619 TQALPHRQ nucleocapsid_phosphoprotein@Mozambique(NC_045512@Mozambique: +:28274-29533) 379-386

3 620-629 PRRARSVRYP linker 1-10

3 630-644 ALLAVFQSASKIITLORF3a_protein@Bangladesh(NC_045512@Bangladesh :+:25393-26220) 51-65

3 645-654 PRRARSVRYP linker 1-10

3 655-668 LMNVLTLVYKVYYG nsp6@Aru ba (N C_045512@Aruba:+:10973-11842) 139-152

3 669-678 PRRARSVRYP linker 1-10

3 679-697 CYDYCIPYNSVTSLIVITS ORF3a_protein@Netherlands(NC_045512@Netherlands:+:25393-2622 0) 153-171

3 698-707 PRRARSVRYP linker 1-10

3 708-724 GVHFVCNLLLLFVIVYS ORF3a_protein@Malaysia(NC_045512@Malaysia:+:25393-26220) 76-92

3 725-734 PRRARSVRYP linker 1-10

3 735-742 SVDCTMYI surface_glycoprotein(NC_045512:+:21563-25384) 735-742

3 743-752 PRRARSVRYP linker 1-10

3 753-760 KLGASQRV membrane_glycoprotein(NC_045512:+:26523-27191) 180-187

3 761 -770 PRRARSVRYP linker 1-10

3 771-788 FLYENAFLPFAMGVIAMS nsp6@Mexico(NC_045512@Mexico:+:10973-11842) 36-53

3 789-798 PRRARSVRYP linker 1-10

3 799-810 FRSSVLHSTRDL surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 43-54

3 811-820 PRRARSVRYP linker 1-10

3 821-833 LLNVPLHGTILTR membrane_glycoprotein(NC_045512:+:26523-27191 ) 119-131

3 834-843 PRRARSVRYP linker 1-10

3 844-868 VLVQSTQWSLFFFFYENAFLPFAMG nsp6@lceland(NC_045512@lceland:+:10973-11842) 24-48

3 869-878 PRRARSVRYP linker 1-10

3 879-886 AALQIPFA surface_glycoprotein(NC_045512:+:21563-25384) 892-899

3 887-896 PRRARSVRYP linker 1-10

3 897-912 FLVLLPLVSIQCVNLT surface_glycoprotein@SmallNorthAmerica(NC_045512@SmallNorthA merica:+:21563-25384) 4-19

3 913-922 PRRARSVRYP linker 1-10

3 923-943 QWNLVIGFLFLTWICLLQFAYmembrane_glycoprotein@Aruba(NC_045512@A ruba:+:26523-27191) 19-39

3 944-953 PRRARSVRYP linker 1-10

3 954-978 VLVQSTQWSLFFFLYENAFLPFAMG nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 24-48

3 979-988 PRRARSVRYP linker 1-10

3 989-999 SPGVFNPVMEP ORF3a_protein@Colombia(NC_045512@Colombia:+:25393-26220) 252-262

3 1000-1009 PRRARSVRYP linker 1-10

3 1010-1017 ISNCVADY surface_glycoprotein(NC_045512:+:21563-25384) 358-365

3 1018-1027 PRRARSVRYP linker 1-10

3 1028-1041 TDTVVEHVTFFIYN ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 221-234

3 1042-1051 PRRARSVRYP linker 1-10

3 1052-1067 NYTVSCLPFTINCQEP ORF8_protein@Bangladesh(NC_045512@Bangladesh:+:27894-

28259) 78-93

3 1068-1077 PRRARSVRYP linker 1-10

3 1078-1087 TQNVLYENQK surface_glycoprotein(NC_045512:+:21563-25384) 912-921

3 1088-1097 PRRARSVRYP linker 1-10

3 1098-1108 HFPRKGVFVSN surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384)

1078-1088

3 1109-1118 PRRARSVRYP linker 1-10

3 1119-1128 AGAALQIPFA surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 886-895

3 1129-1138 PRRARSVRYP linker 1-10 3 1139-1148 FEYVSQPFLM surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 164-173

3 1149-1158 PRRARSVRYP linker 1-10

3 1159-1172 TDTCVEHVTFFIYNORF3a_protein@Luxembourg(NC_045512@Luxembourg: +:25393-26220) 221-234

3 1173-1182 PRRARSVRYP linker 1-10

3 1183-1197 EFQFCNDPFLGVYYH surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 132-146

4 1 -10 YDANYFLCWH ORF3a_protein(NC_045512:+:25393-26220) 141-150

4 11-20 PRRARSVRYP linker 1-10

4 21-32 EVFAQVKQIYKT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 776-787

4 33-42 PRRARSVRYP linker 1-10

4 43-53 SAPLIELCLDE ORF8_protein@Russia(NC_045512@Russia:+:27894-28259) 54-64

4 54-63 PRRARSVRYP linker 1-10

4 64-87 TTVAAFHQECSLQLCTQHQPYVVD ORF8_protein@USA(NC_045512@USA:+:27894-28259) 11 -34

4 88-97 PRRARSVRYP linker 1-10

4 98-111 LVLLPLVSSQCVNF surface_glycoprotein@Brazil(NC_045512@Brazil:+:21563-25384) 5-18

4 112-121 PRRARSVRYP linker 1-10

4 122-135 SVASQSIIAYTMSL surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 678-691

4 136-145 PRRARSVRYP linker 1-10

4 146-154 SPDVDLADI surface_glycoprotein@Chile(NC_045512@Chile:+:21563-25384) 1161 -1169

4 155-164 PRRARSVRYP linker 1-10

4 165-184 PINLVRGLPQGFSALEPLVD surface_glycoprotein@Austria(NC_045512@Austria:+:21563-25384 ) 205-224

4 185-194 PRRARSVRYP linker 1-10

4 195-203 TEIYQAGST surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 466-474

4 204-213 PRRARSVRYP linker 1-10

4 214-238 AAGLEAPFLYLYVLVYFLQSINFVR ORF3a_protein@Norway(NC_045512@Norway:+:25393-26220) 98-122

4 239-248 PRRARSVRYP linker 1-10

4 249-258 ALLAVFHNAS ORF3a_protein@SmallSouthAmerica(NC_045512@SmallSouthAmerica: +:25393-26220) 51-60

4 259-268 PRRARSVRYP linker 1-10

4 269-277 KHWPQIAQF nucleocapsid_phosphoprotein(NC_045512:+:28274-29533) 299-307

4 278-287 PRRARSVRYP linker 1-10

4 288-306 VKDCVVLHSYFTSDYYQLY ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 197-215

4 307-316 PRRARSVRYP linker 1-10

4 317-347 YIWLGFIAGLIAIVMVTIMLCCMTSCCSCLK surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-

25384) 1211-1241

4 348-357 PRRARSVRYP linker 1-10

4 358-370 FQTLLALHRSYLT surface_glycoprotein@Aruba(NC_045512@Aruba:+:21563-25384) 234-246

4 371 -380 PRRARSVRYP linker 1-10

4 381 -412 MMFVKHKHAFLCLFLLPSFATVAYFNMVYMPA nsp6@lndonesia(NC_045512@lndonesia:+:10973-11842) 57-88

4 413-422 PRRARSVRYP linker 1-10

4 423-439 CSNLLLQYGSFCTQLNR surface_glycoprotein(NC_045512:+:21563-25384) 749-765

4 440-449 PRRARSVRYP linker 1-10

4 450-468 LEILDITPCSFGGVSVITP surface_glycoprotein(NC_045512:+:21563-25384) 582-600

4 469-478 PRRARSVRYP linker 1-10

4 479-501 YALVYFLQSINFVIIIMRLWLCW ORF3a_protein@Denmark(NC_045512@Denmark:+:25393-26220) 109-131

4 502-511 PRRARSVRYP linker 1-10

4 512-534 KEITVATSRTLSYYKLGASQRVA membrane_glycoprotein@Aruba(NC_045512@Aruba:+:26523-27191) 166-188

4 535-544 PRRARSVRYP linker 1-10

4 545-554 GLKLKDCVMY nsp6@Peru(NC_045512@Peru:+:10973-11842) 107-116

4 555-564 PRRARSVRYP linker 1-10

4 565-577 NFRVQPTESIVRF surface_glycoprotein(NC_045512:+:21563-25384) 317-329

4 578-587 PRRARSVRYP linker 1-10

4 588-595 SSI VITSV ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 165-172

4 596-605 PRRARSVRYP linker 1-10

4 606-619 ESVVKDCVVLHSYF ORF3a_protein@CostaRica(NC_045512@CostaRica:+:25393-26220) 194-207

4 620-629 PRRARSVRYP linker 1-10

4 630-651 SDFVRATATIPIQASLPFGWLI ORF3a_protein@Aruba(NC_045512@Aruba:+:25393-26220) 26-47

4 652-661 PRRARSVRYP linker 1-10

4 662-684 GKIQDSLFSTASALGKLQDVVNQ surface_glycoprotein@NorthMacedonia(NC_045512@NorthMacedonia :+:21563-25384) 928-950

4 685-694 PRRARSVRYP linker 1-10

4 695-710 ATVAYFNMVYMPASWV nsp6@Aruba(NC_045512@Aruba:+:10973-11842) 76-91

4 711-720 PRRARSVRYP linker 1-10

4 721-728 SLIDLQEL surface_glycoprotein(NC_045512:+:21563-25384) 1196-1203 4 729-738 PRRARSVRYP linker 1-10

4 739-748 SVLNDILARL surfface__gglyycopprotein@@Aruba((NC__045512@@Aruba:+:21563- 25384)) 971-980

4 749-758 PRRARSVRYP linker 1-10

4 759-766 YDPLQPEL surface_glycoprotein(NC_045512:+:21563-25384) 1138-1145

4 767-776 PRRARSVRYP linker 1-10

4 777-784 FTGCVIAW surface_glycoprotein(NC_045512:+:21563-25384) 429-436

4 785-794 PRRARSVRYP linker 1-10

4 795-803 EVFAQVKQI surface_glycoprotein(NC_045512:+:21563-25384) 780-788

4 804-813 PRRARSVRYP linker 1-10

4 814-829 LMNVLTLFYKVYYGNA nsp6@Chile(NC_045512@Chile:+:10973-11842) 142-157

4 830-839 PRRARSVRYP linker 1-10

4 840-856 EVTPSGTWLTYTGAIKL nucleocapsid_phosphoprotein@Bulgaria(NC_045512@Bulgaria:+:28 274-29533) 323-339

4 857-866 PRRARSVRYP linker 1-10

4 867-882 AFKLNIKLLGVGGKPC nsp6(NC_045512:+:10973-11842) 268-283

4 883-892 PRRARSVRYP linker 1-10

4 893-906 GFNCYFPLQPYGFQ surface_glycoprotein@SmallSouthAmerica(NC_045512@SmallSouthA merica:+:21563-25384) 481-494

4 907-916 PRRARSVRYP linker 1-10

4 917-926 SSVLHSTQDF surface_glycoprotein@Norway(NC_045512@Norway:+:21563-25384) 45-54

4 927-936 PRRARSVRYP linker 1-10

4 937-950 ITTVAAFHQECSLQ ORF8_protein@Aruba(NC_045512@Aruba:+:27894-28259) 10-23

4 951-960 PRRARSVRYP linker 1-10

4 961-976 FSNVTWFHAIHVSGTN surface_glycoprotein@Peru(NC_045512@Peru:+:21563-25384) 59-74

4 977-986 PRRARSVRYP linker 1-10

4 987-1004 VTTVIFLARGIVFMCVEY nsp6@Malaysia(NC_045512@Malaysia:+:10973-11842) 179-196

4 1005-1014 PRRARSVRYP linker 1-10

4 1015-1025 FFSNVTWFHVS surface_glycoprotein@Nigeria(NC_045512@Nigeria:+:21563-25384 ) 58-68

4 1026-1035 PRRARSVRYP linker 1-10

4 1036-1049 IHFYSKWYIRVGAK ORF8_protein@Mozambique(NC_045512@Mozambique:+:27894-

28259) 39-52

4 1050-1059 PRRARSVRYP linker 1-10

4 1060-1071 FSNVTWFHAIVS surface_glycoprotein@Ghana(NC_045512@Ghana:+:21563-25384) 59-70

4 1072-1081 PRRARSVRYP linker 1-10

4 1082-1096 IPIRASLPFGWLIVG ORF3a_protein@lceland(NC_045512@lceland:+:25393-26220)

35-49

4 1097-1106 PRRARSVRYP linker 1-10

4 1107-1114 TDAVDCAL surface_glycoprotein(NC_045512:+:21563-25384) 286-293

4 1115-1124 PRRARSVRYP linker 1-10

4 1125-1136 FQTLLHRSYLTP surface_glycoprotein@SmallAsia(NC_045512@SmallAsia:+:21563-2 5384)

230-241

4 1137-1146 PRRARSVRYP linker 1-10

4 1147-1170 PINLVRDLPQGFSVLEPLVDLPIG surface_glycoprotein@Belgium(NC_045512@Belgium:+:21563-25384 ) 205-228

4 1171-1180 PRRARSVRYP linker 1-10

4 1181-1190 SPGVVNPVME ORF3a_protein@Brazil(NC_045512@Brazil:+:25393-26220)252-261

4 1191-1200 PRRARSVRYP linker 1-10

4 1201-1215 TISVTTEILPVSMAK surface_glycoprotein@Mexico(NC_045512@Mexico:+:21563-25384) 719-733

Immune Response Enhancing Components:

In certain embodiments, the vaccines comprise or are capable of expressing one or more additional components to enhance the immune response to the one or more viral immunogens. These components may include, for example, targeting molecules, elements which enhance antigen processing, immunostimulatory molecules such as cytokines and other adjuvants. In certain embodiments, the vaccine comprises one or more fusion polypeptides comprising the one or more additional components and one or more concatemers of epitopes. The additional components include but are not limited to one or more targeting molecules/motifs. In certain embodiments where the vaccine comprises more than more concatemer, each concatemer is fused to one or more targeting molecules. The targeting molecules may be the same for all immunogens in the vaccine or different.

It is known in the art that targeting the immunogen to antigen presenting cells (APCs), including but not limited to dendritic cells, or enhancing antigen processing by APCs enhances immunogenicity.

In specific embodiments, the fusion protein comprises one or more CD74 or fragment thereof and one or more concatemer(s) of epitopes. In certain embodiments, the fusion protein comprises the CD74 transmembrane and cytoplasmic domain and one or more concatemer(s) of epitopes. In certain embodiments, the CD74 transmembrane and cytoplasmic domain has the sequence set forth below:

HRRRSRSCREDQKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRGALYTGFSILVT LLLAGQ

ATTAYFLY

In specific embodiments, the fusion protein comprises one or more human leukocyte antigen (HI_A) or fragment thereof and the one or more immunogen or fragment thereof. In specific embodiments, the fusion protein comprises the HI_A transmembrane and cytoplasmic domain and immunogen or fragment thereof.

In specific embodiment, the HI_A fragment comprises the following sequence:

MVKCATLSVDSGQASDSSAAQTYSGGKRDSSKRRWMVAAVVAGTIVAGLLVLGAIIG V

In certain embodiments, the targeting moiety is a chimeric targeting moiety comprising portions of different molecules. For example, the targeting moiety may comprise the cytoplasmic domain from one molecule fused to the transmembrane domain of another molecule. In certain embodiments, the targeting moiety comprises the CD74 cytoplasmic domain fused to an HI_A transmembrane sequence. In specific embodiments, the targeting moiety comprises the following sequence:

HRRRSRSCREDQKPVMDDQRDLISNNEQLPMLGRRPGAPESKCSRWMVAAVVAGTIV AGLLV

LGAIIGV Other elements:

The proteins of the present invention may also include tags. Appropriate tags are known in the art and include but are not limited to HA-, FLAG®- or myc- or alpha tags.

Exemplary Vaccines

Non-limiting exemplary vaccines or concatemers expressed by exemplary vaccines are set forth in the figures.

Vaccine Formulations

The vaccines formulations may also comprise pharmaceutically acceptable carriers, excipients and/or adjuvants. Adjuvants and carriers suitable for administering genetic vaccines and immunogens are known in the art. Conventional carriers and adjuvants are for example reviewed in Kiyono et al. 1996.

A vaccine adjuvant is a component that potentiates the immune responses to an antigen and/or modulates it towards the desired immune responses. A vaccine may include one or more adjuvants. Exemplary adjuvants include mineral salts including but not limited to aluminium salts (such as amorphous aluminum hydroxyphosphate sulfate (AAHS), aluminum hydroxide, aluminum phosphate, potassium aluminum sulfate (Alum)) and calcium phosphate gels; Oil emulsions and surfactant based formulations, including but not limited to MF59 (microfluidised detergent mmunoprec oil-in-water emulsion), QS21 (purified saponin), AS02 [SBAS2] (oil-in- water emulsion + MPL + QS-21), Montanide ISA-51 and ISA-720 ( mmunoprec water-in-oil emulsion); Particulate adjuvants, including but not limited to virosomes (unilamellar liposomal vehicles incorporating influenza haemagglutinin), AS04 ([SBAS4] Al salt with MPL), ISCOMS (structured complex of saponins and lipids), polylactide co-glycolide (PLG). And ; microbial derivatives (natural and synthetic), including but not limited to monophosphoryl lipid A (MPL), Detox (MPL + M. Phlei cell wall skeleton), AGP [RC-529] (synthetic acylated monosaccharide), DC_Chol (lipoidal immunostimulators able to self mmunopr into liposomes), OM-174 (lipid A derivative), CpG motifs (synthetic oligonucleotides containing immunostimulatory CpG motifs), modified LT and CT (genetically modified bacterial toxins to provide non-toxic adjuvant effects); endogenous human immunomodulators, including but not limited to hGM-CSF or hlL-12 (cytokines that can be administered either as protein or plasmid encoded), Immudaptin (C3d tandem array) and inert vehicles, such as gold particles. The vaccine formulations may also comprise a stabilizer. Suitable stabilizer are known in the art and include but are not limited to amino acids, antioxidants, cyclodextrins, proteins, sugars/ sugar alcohols, and surfactants. See for example Morefield, AAPS J. 2011 Jun; 13(2): 191— 200; https://www.ncbi.nlm.nih.qov/pmc/articles/PMC3085699/).

The vaccine can be incorporated into liposomes, microspheres or other polymer matrices. Liposomes can consist of phospholipids or other lipids, and can be nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer.

Previously, it has been found that a SARS-CoV-2 SAM lipid nanoparticle (LNP) vaccine induced high neutralizing antibody titers in mice (McKay et al. , Nat Commun 11, 3523 (2020). https://doi.orq/10.1038/s41467-020-17409-9). Briefly, the LNP (described in US patent US10,221,127) contains an ionizable cationic lipid phosphatidylcholine/cholesterol/PEG-lipid. The SAM RNA were encapsulated in LNP using a self-assembly process in which an aqueous solution of SAM RNA at pH = 4.0 is rapidly mixed with an ethanolic lipid mixture. LNP.

Accordingly, in certain embodiments, the vaccines formulations comprise lipid nanoparticle delivery formulations of nucleic acid-based vaccines. Optionally, the lipid is cationic. Appropriate cationic lipids are known in the art. Non-limiting examples include phosphatidylcholine/cholesterol/PEG-lipid, C12-200, dimethyldioctadecylammonium (DDA), 1,2- dioleoyl-3-trimethylammonium propane (DOTAP) or 1,2-dilinoleyloxy-3-dimethylaminopropane (DLinDMA). Also see for example, U.S. Patent No. 10,221,127 (incorporated by reference) and Reichmuth AM et al. (Therapeutic Delivery. 2016 ;7(5):319-334. DOI: 10.4155/tde-2016-0006). In specific embodiments, the vaccines formulations comprise lipid nanoparticle delivery formulations of SAM RNA vaccines. In specific embodiments, the LNPs comprise an ionizable cationic lipid (phosphatidylcholine:cholesterol/PEG-lipid (50:10:38.5:1.5 mol/mol). In certain embodiments, the RNA to total lipid ratio in the LNP is approximately 0.05 (wt/wt). In certain embodiments, the LNPs have a diameter of ~80 nm.

In other embodiments, Charge-Altering Releasable Transporters (CARTs) as a mRNA delivery platform. Accordingly, in certain embodiments, the vaccines viral vector-based vaccines or nucleic acid- based vaccines. In specific embodiments, the vaccines are SAM RNA-based vaccines. Optionally, the SAM vaccines are in lipid nanoparticle formulations.

Method of Vaccination

Also provided herein is a method of treating, protecting against, and/or preventing disease associated with the infectious agent in a subject in need thereof by administering the vaccine to the subject. For example, a worker skilled in the art would readily appreciate that a SARS-CoV- 2 vaccine may be used treating, protecting against, and/or preventing disease associated with SARS-CoV-2 (i.e. COVID 19). Administration of the vaccine to the subject can induce or elicit a specific immune response against the vaccine target in the subject.

The subject may be a human or other animals, including but not limited to other mammals, such as non-human primates, cats, dogs, equines (including but not limited to horses, donkeys and zebras), camels, sheep, goats, and bovines (including but not limited to cows).

The induced immune response can be used to treat, prevent, and/or protect against disease related to the vaccine target. For example, a SARS-CoV-2 vaccine to the subject can induce or elicit a specific immune response against the SARS-CoV-2 in the subject. The induced immune response provides the subject administered the vaccine with protection against the vaccine target, such as a SARS-CoV-2 vaccine provides resistance to SARS-CoV-2.

The induced immune response can include an induced humoral immune response and/or an induced cellular immune response. The induced humoral immune response can include IgG antibodies and/or neutralizing antibodies that are reactive to the antigen. The induced cellular immune response can include a CD8+ T cell response.

The number of vaccine doses for effective treatment can be 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10.

In certain embodiments, a single type of vaccine is used. In other embodiments, multiple types of vaccines are used. For example, in certain embodiments, a prime and boost strategy of vaccination is used. In such embodiments, one vaccine expresses epitopes are linked to CD74/HI_A targeting sequences is used (this may promote DC cross priming of T cells). A second vaccine expresses epitopes that lack all signal sequences and transmembrane domains is used (this may promote endogenous antigen presentation). These may be administered together or in 2 separate immunization of priming and boosting to promote optimum T cell response.

The vaccine can be formulated in accordance with standard techniques well known to those skilled in the pharmaceutical art. Such compositions can be administered in dosages and by techniques well known to those skilled in the medical arts taking into consideration such factors as the age, sex, weight, and condition of the particular subject, and the route of administration. The subject can be a mammal, such as a human, an equine, a bovine, a pig, a sheep, a camel, a cat, a dog, a rat, or a mouse.

The vaccine can be administered prophylactically or therapeutically. In prophylactic administration, the vaccines can be administered in an amount sufficient to induce an immune response. In therapeutic applications, the vaccines are administered to a subject in need thereof in an amount sufficient to elicit a therapeutic effect. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition of the vaccine regimen administered, the manner of administration, the stage and severity of the disease, the general state of health of the patient, and the judgment of the prescribing physician.

The vaccine can be administered by methods well known in the art as described in Donnelly et al. (Ann. Rev. Immunol. 15:617-648 (1997)); Feigner et al. (U.S. Pat. No. 5,580,859, issued Dec. 3, 1996); Feigner (U.S. Pat. No. 5,703,055, issued Dec. 30, 1997); and Carson et al. (U.S. Pat. No. 5,679,647, issued Oct. 21, 1997). The nucleic acid of the vaccine can be complexed to particles or beads that can be administered to an individual, for example, using a vaccine gun. One skilled in the art would know that the choice of a pharmaceutically acceptable carrier, including a physiologically acceptable compound, depends, for example, on the route of administration of the expression vector.

The vaccine can be delivered via a variety of routes. Typical delivery routes include parenteral administration, e.g., intradermal, intramuscular or subcutaneous delivery. Other routes include oral administration, intranasal, and intravaginal routes. The vaccine can be delivered to the interstitial spaces of tissues of an individual (Feigner et al., U.S. Pat. Nos. 5,580,859 and 5,703,055. The vaccine can also be administered to muscle, or can be administered via intradermal or subcutaneous injections, or transdermally, such as by iontophoresis. Epidermal administration of the vaccine can also be employed. Epidermal administration can involve mechanically or chemically irritating the outermost layer of epidermis to stimulate an immune response to the irritant (Carson et al., U.S. Pat. No. 5,679,647, the contents of which are incorporated herein by reference in its entirety).

The vaccine can also be formulated for administration via the nasal passages. Formulations suitable for nasal administration, wherein the carrier is a solid, can include a coarse powder having a particle size, for example, in the range of about 10 to about 500 microns which is administered in the manner in which snuff is taken, i.e. , by rapid inhalation through the nasal passage from a container of the powder held close up to the nose. The formulation can be a nasal spray, nasal drops, or by aerosol administration by nebulizer. The formulation can include aqueous or oily solutions of the vaccine.

The vaccine can be a liquid preparation such as a suspension, syrup or elixir. The vaccine can also be a preparation for parenteral, subcutaneous, intradermal, intramuscular or intravenous administration (e.g., injectable administration), such as a sterile suspension or emulsion.

The vaccine can be administered via electroporation, such as by a method described in U.S. Pat. No. 7,664,545. The electroporation can be by a method and/or apparatus described in U.S. Pat. Nos. 6,302,874; 5,676,646; 6,241,701; 6,233,482; 6,216,034; 6,208,893; 6,192,270; 6,181,964; 6,150,148; 6,120,493; 6,096,020; 6,068,650; and 5,702,359. The electroporation may be carried out via a minimally invasive device.

A method of inducing an antigen- specific immune response in a subject, the method comprising administering to the subject the vaccine comprising at least one nucleic acid sequence of SEQ ID NO. 1- 51 or a mutated variant thereof capable of expressing a polypeptide in an amount effective to produce an antigen- specific immune response in the subject.

EXAMPLES

EXAMPLE 1: IDENTIFICATION AND QUANTIFICATION OF PEPTIDES ELUTED FROM HLA MOLECULES FROM CULTURED CELLS AND FROM PATIENT SAMPLES.

Peptide analysis from cultured cells: Peptide epitopes in the SARS-CoV-2 proteins will be mapped. Using human THP-1 (monocytic) and Calu-3 (lung epithelial) cells, we will treat them with a recombinant version of each SARS-CoV-2 protein. The duration of antigen exposure will be optimized for maximum presentation. After antigen challenge, we will first collect host- processed, HLA-bound peptides from the cells by immunoprecipitation (IP) of the HI_A, followed by peptide elution using acid stripping (as performed previously). We will use anti-HLA-A (IgG EP1395Y, Abeam 52922), anti HLA-B (lgG1 JOAN-1, Thermo MA1-35410), and anti-HLA-C (IgG EPR6749, Abeam 126722) antibodies to mmunoprecipitated human HLA I proteins and their ligands. For MHC II, we will use the L243 antibody against HLA-DRB1 (lgG2a, Abeam 136320), or other antibodies against several variants, such as the HL-40 antibody against HLA- DR and -DP (lgG2a, Abeam 8085). The IgG will be conjugated to magnetic Protein G beads and cross-linked with disuccinimidyl suberate so that the IgG is not eluted and the beads can be re used. Post-challenge, cells will be solubilized in a detergent-containing buffer, and HI_A molecules will be immunoprecipitated with the IgG conjugated magnetic beads. HI_A-bound peptides will then be eluted in 10% acetic acid, separated from larger proteins by a 5000 molecular weight cutoff filter and then detected by mass spectrometry, as performed previously.

Peptide analysis from COVID-19 Patient Cohort: Vancouver General Hospital (VGH) and Surrey Memorial Hospital (SMH) receive >70% of SARS-CoV-2 patients in British Columbia who require hospitalization. As of March 30, 2020, 56 patients have been enrolled in the two centers (VGH & SMH). Clinical care will be guided by the discretion of attending intensive care physicians in accordance with the international guidelines for COVID-19 management from the Surviving Sepsis Campaign and the British Columbia COVID-19 Therapeutics Committee recommendations. Clinical data include: date of ICU admission, sex, age, symptoms of viral illness, comorbidities, length of ICU and hospital stay, length of mechanical ventilation, development of acute respiratory distress syndrome, medications administered specific to treatment of SARS-CoV-2, length of other treatment modalities. PBMCs will be collected on day 14 and day 21. We will experimentally mapping peptide epitopes in the SARS-CoV-2 proteins, in a manner similar to the peptide analysis from cultured cells. We will obtain COVID-19 patient peripheral blood mononuclear cells (PBMCs) from the COVID-19 patient cohort in Vancouver. We will elute the HLA-bound SARS-CoV-2 peptides from the PBMCs, and map the peptides using Mass Spectrometry.

HLA haplotype sequencing: In order to begin to understand if some HLA genes confer resistance or susceptibility to SARS-CoV-2, as has been noted for other human coronaviruses, we will sequence HLA genes from COVID-19 patients. From the COVID-19 patient PBMC samples, all HLA Class I and Class II HLA genes will be sequenced at single base-pair resolution. 0.6-1.4pg of high-quality genomic DNA (gDNA) is required for the amplification of HLA-A, HLA-B, HLA-C, HLA-DRB1/3, HLA-DRB4, HLA-DRB5, HLADPA1, HLA-DPB1, HLA- DQA1 and HLA-DQB1 regions. Each patient will be genotyped once. The next generation sequencing tool for HLA typing, Holotype HLA v3.0 (Omixon), is a set of predetermined PCR primers and reagents that provides deep and even coverage of the whole gene region for all 11 HLA class 1 and class 2 genes, with balance between alleles at the same locus. Targeted whole gene libraries will be multiplexed and sequenced on the lllumina MiSeq platform using the 300- cycle Standard flow cell. Data Analysis of fastq files will be done using the Omixon Twin v4.0.1 Software. Polymorphic sites will be identified within all the regions.

EXAMPLE 2: CREATION OF HLA TETRAMERS FOR USE IN VACCINE TESTING AND EVALUATION OF PATIENT IMMUNE STATUS:

HLA tetramers are essentially four HLA molecules together in a tetramer, such that their peptide-binding pockets are exposed. Specific kits for making tetramers with specific HLA haplotypes will be purchased from Mbl International Corp, i.e. QuickSwitch Quant HLA-A*02:01 Tetramer Kit-APC (#TB-7300-K2). These HLA tetramer molecules can then be loaded with a relevant peptide, identified by the studies above. In a tetramer assay, these HLA-tetramers are used to detect T cell with receptors that recognize the peptide: HLA complex. The HLA tetramers are further labeled with a fluorophore (Tetramer Staining Guide, MBL Int. Corp.), allowing tetramer-bound T-cells to be analyzed with flow cytometry. This enables us to quantitate and to investigate the specificity and functionality of the cellular immune response to a SARS-CoV-2 viral infection and to an eventual vaccine administration, as HLA tetramer binding to a T cell indicates that a person has encountered the pathogen previously and built an immune response to that pathogen. Mapping HLA-peptide epitopes of SARS-CoV-2 proteins will allow generation of HLA Tetramers, which can then be used to quantify T cell specificity in human populations. A tetramer reagent such as this would be invaluable for monitoring patients’ immune responses in real time and may inform clinical treatment and vaccine performance.

EXAMPLE 3: CREATION OF “STRING-OF-BEADS” VACCINES FOR COVID-19 Self-Amplifying mRNA (SAM) Vaccines production: I “String-of-Beads” SAM candidates vaccines will be produced asdescribed above.

Lipid nanoparticle (LNP) formulation of the RNA-based vaccines: SAM vaccine candidates will be encapsulated state-of-the-art lipid nanoparticles based on clinically approved formulations. Encapsulation uses a self-assembly process, in which an aqueous solution of mRNA at pH = 4.0 is rapidly mixed with a solution of lipids dissolved in ethanol. LNPs to be used in this study are similar in composition to those described previously, which contain an ionizable cationic lipid (phosphatidylcholine:cholesterol/PEG-lipid (50:10:38.5:1.5 mol/mol)) and will be encapsulated at an RNA to total lipid ratio of -0.05 (wt/wt). This should result in LNPs with a diameter of -80 nm as measured by dynamic light scattering using a Zetasizer Nano ZS (Malvern Instruments Ltd., Malvern, UK) instrument. All SAM-LNP formulations will be stored at -80 °C at a concentration of mRNA of -1 pg/pl.

Validation of recombinant gene and protein expression: Human HEK293 cell and hamster BHK-21 cells will be transfected with the SAM-lipid nanoparticle formulations. RT-PCR and Western blots will be used to test for expression of the constructs from the vaccine candidates. Cell lysates will be run on SDS-PAGE gels and Western blots will be performed with FLAG- specific antibodies.

Testing vaccines in a hamster COVID-19 disease model. The SAM-lipid nanoparticle (SAM- LNP) vaccines will be tested in a hamster model of COVID-19. Vaccine constructs will be tested for their performance in evoking immune responses against the SARS-CoV-2 spike protein and to elicit protection in a SARS-CoV-2 lethal viral challenge model in Syrian hamsters.

Hamster Vaccination: SAM-LNPs vaccine candidates will be diluted in phosphate-buffered saline (PBS) and injected into animals intramuscularly (i.m.) with a 3/1 Occ 29½G insulin syringe. Four sites of injection (30 pi each) over the lower back will be used. For a dose response curve, hamsters will be vaccinated (Primed) on day 0 and receive a booster injection on day 14. Groups will consist of a minimum of 5 animals per group for each vaccine tested, and a minimum of 3 dose ranges (e.g. 0.005mg/kg - 0.250mg/kg) will be used for each vaccine23. A control group of unimmunized hamsters will be included. Body weights will be determined every day.

Measuring Cellular Immune Responses: Peripheral blood monocytic cells (PBMCs) will be obtained on day 0, 7, 14 and 28 post-infection. We will harvest PBMCs to compare lymphocyte populations (T cell: CD4+, CD8+; B cell) using hamster-specific antibodies available from the Monoclonal Antibody Center at Washington State University. Inflammatory cytokines profiling will be undertaken using ELISA kits (MBL Inti) in samples collected at day 0, 4, 7, 14, 28 after challenge. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) will also be used to verify cytokine production from isolated cells and tissues, as previously described. Using blood obtained from the vaccinated hamsters above, we will screen for the production of antibodies which bind to recombinant SARS-CoV-2 proteins, using screening assays, e.g. Western blot; ELISA assay; EliSpot.

Viral Challenge: The optimal dose of vaccine to use will be determined from the dose response trial. Hamsters will be vaccinated (Primed) on day 0 and receive a booster injection on day 14. Groups will consist of a minimum of 15 animals per group for each vaccine tested. At 28 days post vaccination, hamsters will be challenged with SARS-CoV-2 at a dose of 10e5 pfu in roughly 30 pi PBS via intranasal administration. Hamsters will be monitored every day for temperature, weight, and survival. Losing over 20% of their body weight will be considered a humane endpoint, and animals will be sacrificed. Tissues and cells will be harvested and examined, as described above, and bronchoalveolar lavage cell suspension will also be obtained at time of mortality.

EXAMPLE 4: COM BINATORIALLY IDENTIFIED EPITOPES AND EXPERIMENTAL DATA

There appears to be a good concordance between the epitopes identified by the method described in PCT/CA2021/051666 (incorporated by reference) and those found experimentally in infection survivors. With typical parameters, the method described in PCT/CA2021/051666 would identify 251 highly immunogenic loci that are needed to confer a broad population-wide immunity against SARS- CoV-2, and 113 of those (or the 63% of the 180 detected ones) correspond with peptides that have been identified in survivors. It should also be noted that the dataset of detected peptides is by no means exhaustive as it is derived from a sample of survivors that is not representative of the general population, so more of the peptides predicted by PCT/CA2021/0516 might in fact be present in the general population. A pre-gene breakdown of the results is included in the following Table.

In more detail, this is the full list of viral loci, with whether they have been predicted/detected:

It should also be noted that, according to the contents of the current invention and depending on the viral gene, the method described in PCT/CA2021/0516 was used to predict peptides coming from both the wild-type virus and from variants. A table detailing the viral loci, the corresponding number of wild-type and variant peptides, and the corresponding number of HLA I & II alleles that are expected to be protected by these specific sets of peptides, is enclosed below.

Although various embodiments of the invention are disclosed herein, many adaptations and modifications may be made within the scope of the invention in accordance with the common general knowledge of those skilled in this art. Such modifications include the substitution of known equivalents for any aspect of the invention in order to achieve the same result in substantially the same way. Numeric ranges are inclusive of the numbers defining the range. The word “comprising” is used herein as an open ended term, substantially equivalent to the phrase “including, but not limited to”, and the word “comprises” has a corresponding meaning. As used herein, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a thing” includes more than one such thing. Citation of references herein is not an admission that such references are prior art to an embodiment of the present invention. The invention includes all embodiments and variations substantially as hereinbefore described and with reference to the examples and drawings. Titles, headings, or the like are provided to enhance the reader’s comprehension of this document, and should not be read as limiting the scope of the present invention.