WO2023240159A2 - Sars-cov-2 multi-antigen universal vaccines - Google Patents
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Definitions
- the present invention relates to vaccines, for example, viral vaccines, such as those directed to coronaviruses, e.g., pan-coronavirus vaccines.
- viral vaccines such as those directed to coronaviruses, e.g., pan-coronavirus vaccines.
- BACKGROUND OF THE INVENTION While the Wuhan Hu1 variant of SARS-CoV-2 is the ancestral reference virus, Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), and Delta (lineage B.1.617.2) variants of concern (VOCs) subsequently emerged in Brazil, India, and South Africa vaccines from 2020 to 2022.
- the most recent SARS CoV-2 variants including multiple heavily mutated Omicron (B.1.1.529) sub-variants, have prolonged the COVID-19 pandemic. These new variants emerged since December 2020 at a much higher rate, consistent with the accumulation of two mutations per month, and strong selective pressure on the immunologically important SARS-CoV-2 genes.
- the Alpha, Beta, Gamma, Delta, and Omicron Variants are defined as Variants of Concern (VOC) based on their high transmissibility associated with increased hospitalizations and deaths. This is a result of reduced neutralization by antibodies generated by previous variants and/or by the first-generation COVID-19 vaccines, together with failures of treatments and diagnostics. Dr.
- the Spike protein is a surface predominant antigen of SARS-CoV-2 that is involved in the docking and penetration of the virus into the target host cells.
- the Spike protein is the main target of the first-generation COVID-19 subunit vaccines aiming mainly at inducing neutralizing antibodies.
- first-generation COVID-19 vaccines Nearly 56% of the 10 billion doses of first-generation COVID-19 vaccines are based on the Spike antigen alone, while the remaining 44% of the COVID-19 vaccines were based on whole virion inactivated (WVI) vaccines. Both the Spike-based COVID-19 sub-unit vaccines and the whole virion-inactivated vaccines were successful. However, because the Spike protein is the most mutated SARS-CoV-2 antigen, these first-generation vaccines lead to immune evasion by many new variants and subvariants, such as the Omicron XBB1.5 sub-variant.
- the second-generation COVID-19 vaccines should be focused not only on the highly variable Spike protein but also on other highly conserved structural and non-structural SARS-CoV-2 antigens capable of inducing protection mediated by not only neutralizing antibodies but also by cross-reactive CD4 + and CD8 + T cells.
- BRIEF SUMMARY OF THE INVENTION It is an objective of the present invention to provide compositions and methods featuring a universal pre-emptive coronavirus vaccine as specified in the independent claims. Embodiments of the invention are given in the dependent claims. Embodiments of the present invention can be freely combined with each other if they are not mutually exclusive.
- the present invention features a universal pre-emptive pan-Coronavirus vaccine composition, wherein the composition comprising at least two of: (i) one or more conserved coronavirus B-cell target epitopes selected from SEQ ID NO: 23-31, or a combination thereof; (ii) one or more conserved coronavirus CD4+ T cell target epitopes selected from SEQ ID NO: 17-22, or a combination thereof; and (iii) one or more conserved coronavirus CD8+ T cell target epitopes selected from SEQ ID NO: 1-16, or a combination thereof.
- An at least one epitope of the composition is derived from a non-spike protein.
- the target epitopes are derived from a SARS-CoV-2 protein selected from a group consisting of: ORF1ab protein, Spike glycoprotein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein and ORF10 protein.
- one or more of the one or more epitopes may be part of one or more large sequences. The one or more large sequences are highly conserved among human and animal Coronaviruses.
- At least one large sequence is a whole protein sequence expressed by SARS-CoV-2, a partial protein sequence expressed by SARS-CoV-2, or a combination thereof.
- the large sequences are selected from Variants of Concern or Variants of Interest.
- the one or more large sequences are derived from a whole protein sequence expressed by SARS-CoV-2.
- the one or more large sequences are derived from a partial protein sequence expressed by SARS-CoV-2.
- the one or more large sequences is derived from a full-length spike glycoprotein.
- the one or more large sequences is derived from a partial spike glycoprotein.
- the one or more large sequences comprises Spike glycoprotein (S) or a portion thereof, Nucleoprotein or a portion thereof, and protein encoded by ORF1a/b or a portion thereof.
- the one or more conserved epitopes may be derived from one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold.
- the one or more large sequences may be derived from one or more of: one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold. past, current, and future coronavirus outbreaks.
- the one or more SARS-CoV-2 human strains or variants in current circulation are selected from: strain B.1.177; strain B.1.160, strain B.1.1.7; strain B.1.351; strain P.1; strain B.1.427/B.1.429; strain B.1.258; strain B.1.221; strain B.1.367; strain B.1.1.277; strain B.1.1.302; strain B.1.525; strain B.1.526, strain S:677H; strain S:677P; strain B.1.1.529-Omicron (BA.1); strain B.1.1.529-Omicron (BA.2); and strain B.1.617.2-Delta.
- the one or more coronaviruses that cause the common cold are selected from: 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus, and HKU1 beta coronavirus.
- the vaccine composition protects against disease caused by one or more coronavirus variants or coronavirus subvariants.
- the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants wherein the coronavirus variants comprise alpha, beta, gamma, delta, and omicron.
- the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus.
- the vaccine composition protects against infection and reinfection of coronavirus variants or coronavirus subvariants.
- the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants, wherein the coronavirus variants comprise alpha, beta, gamma, delta, and omicron.
- the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus.
- the vaccine composition protects against infection or reinfection of one or more coronavirus variants or coronavirus subvariant. In some embodiments, the vaccine composition protects against infection or reinfection of multiple coronavirus variants or coronavirus subvariants. In some embodiments, the vaccine composition protects against infection or re-infection caused by one coronavirus variants or coronavirus subvariants. In some embodiments, the vaccine composition induces strong and long-lasting protection mediated by antibodies (Abs), CD4+ T helper (Th1) cells, and/or CD8+ cytotoxic T-cells (CTL).
- Abs antibodies
- Th1 CD4+ T helper
- CTL CD8+ cytotoxic T-cells
- the composition protects against Sarbecoviruses, wherein sarbecoviruses comprise SARS-CoV1 or SARS-CoV2.
- the composition may further comprise a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
- the composition may further comprise a composition that promotes T cell proliferation, wherein the composition that promotes T cell proliferation is IL-7 or IL-15.
- One of the unique and inventive technical features of the present invention is the use of highly conserved epitopes.
- the technical feature of the present invention advantageously provides for a universal vaccine composition that will protect from future human outbreaks and deter future zoonosis. None of the presently known prior references or work has the unique inventive technical feature of the present invention.
- the present invention also includes a pre-emptive pan-coronavirus vaccine composition
- a pre-emptive pan-coronavirus vaccine composition comprising: at least two conserved coronavirus antigens selected from: (i) a conserved coronavirus Spike protein; (ii) a conserved coronavirus NSP2 protein; (iii) a conserved coronavirus NSP3 protein; (iv) a conserved coronavirus NSP14 protein; and (v) a conserved coronavirus Nucleoprotein.
- the aforementioned proteins or antigens may refer to portions of a particular entire protein.
- the present invention also includes a pre-emptive pan-coronavirus vaccine composition
- a pre-emptive pan-coronavirus vaccine composition comprising: at least two conserved coronavirus antigens selected from: (i) a conserved coronavirus Spike protein or a portion thereof; (ii) a conserved coronavirus NSP2 protein or a portion thereof; (iii) a conserved coronavirus NSP3 protein or a portion thereof; (iv) a conserved coronavirus NSP14 protein or a portion thereof; and (v) a conserved coronavirus Nucleoprotein or a portion thereof.
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP2 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the Spike protein (or a portion thereof) comprises one or more proline substitutions.
- the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof).
- the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof); a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the Spike protein (or a portion thereof) comprises one or more proline substitutions.
- the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof); a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the composition further comprises a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
- the composition further comprises a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15.
- the conserved protein or antigen is conserved among human and animal coronaviruses.
- the portion of the coronavirus spike (S) protein is derived from a full-length spike glycoprotein. In some embodiments, the portion of the coronavirus spike (S) protein is derived from a partial spike glycoprotein. In some embodiments, the portion of the coronavirus spike (S) protein is receptor-binding domain (RBD).
- the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD).
- the present invention also includes a pre-emptive pan-coronavirus vaccine composition, the composition comprising one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise one or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- a conserved coronavirus Spike protein or a portion thereof
- a conserved coronavirus NSP2 protein or a portion thereof
- a conserved coronavirus NSP3 protein or a portion thereof
- the one or more large sequence coronavirus proteins comprises two or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the one or more large sequence coronavirus proteins comprises three or more of: a conserved coronavirus Spike protein(or a portion thereof); a conserved coronavirus NSP2 protein(or a portion thereof); a conserved coronavirus NSP3 protein(or a portion thereof); a conserved coronavirus NSP14 protein(or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the one or more large sequence coronavirus proteins comprises four or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the one or more large sequence coronavirus proteins comprises: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof).
- the large coronavirus sequences are highly conserved among human and animal coronaviruses.
- the Spike (S) protein further comprises at least one proline substitution.
- the Spike (S) protein comprises a receptor-binding domain (RBD).
- the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD).
- the composition further comprises a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
- the composition further comprises a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15.
- the present invention also features a pre-emptive pan-coronavirus vaccine composition, the composition comprising, or comprising a sequence encoding one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
- the present invention also features a method of preventing infection or reinfection by one or more coronavirus variants or subvariants in a subject, said method comprising administering a therapeutically effective amount of a composition according to the present invention.
- FIG.1A shows a dendrogram showing the evolution of SARS-CoV-2 lineages based on PANGO and Nextstrain nomenclature (top panel). Phylogenetic analysis performed between 712,000 human SARS-CoV-2 genome sequences to show degree of genetic similarity among different SARS-CoV-2 lineages evolved between December 2019 and April 2021(bottom panel).
- FIG.1B shows phylogenetic analysis performed among VOCs of SARS-CoV-2, CoVs strains from human and other species showed minimum genetic distance between the first SARSCoV2 isolate WuhanHu1 reported from the Wuhan Seafood market with different VOCs, followed by bat strains hCoV-19-bat-Yunnan-RmYN02, hCoV-19-bat-Yunnan-RaTG13, and bat-CoV-19-ZXC21 (top panel). Genetic distances based on Maximum Composite Likelihood model among the human, bat, pangolin, civet cat and camel genome sequences.
- FIG. 2A and 2B shows identification of SARS-CoV-2 CD8+ T cell epitopes specific to spike glycoprotein possessing non-synonymous mutations from VOCs.
- FIG. 2A shows twenty-six, spike glycoprotein specific epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern.
- FIG. 2A and 2B shows identification of SARS-CoV-2 CD8+ T cell epitopes specific to spike glycoprotein possessing non-synonymous mutations from VOCs.
- FIG. 2A shows twenty-six, spike glycoprotein specific epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern.
- FIG. 2B and 2C show the SARS-CoV-2-derived CD8+ T cell epitopes are screened based on their presence among most frequently observed HLA-A alleles in global population (HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*23:01).
- MHC-I binding affinity and high degree of immunogenicity showed high PPC value of 91.48%, average number of epitope hits / HLA combinations recognized by the population is 21.3, and minimum number of epitope hits / HLA combinations recognized by 90% of the population (pc90) is 5.06.
- FIG. 3A, 3B, and 3C shows the identification of SARS-CoV-2 CD4+ T cell epitopes specific to spike glycoprotein possessing non-synonymous mutations from VOCs.
- FIG. 3A shows Nineteen spike glycoprotein specific CD4+ T cell epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern.
- 3B and 3C shows the SARS-CoV-2-derived CD4+ T cell epitopes are screened based on their presence among most frequently observed HLA-DR alleles in global population (HLA-DRB1*01:01, HLA-DRB1*11:01, HLA-DRB1*15:01, HLA-DRB1*03:01, HLADRB1*04:01).
- MHC-I binding affinity and high degree of immunogenicity showed high PPC value of 86.39%, average number of epitope hits / HLA combinations recognized by the population is 13.69, and minimum number of epitope hits / HLA combinations recognized by 90% of the population (pc90) is 2.87.
- FIG.4A and 4B shows the docking of SARS-CoV-2 Spike glycoprotein-derived B cell epitopes to human ACE2 receptors.
- FIG.4A shows eight spike glycoprotein specific B cell epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern.
- FIG.4B shows molecular docking of 8 B-cell epitopes, identified from the SARS-CoV-2 Spike glycoprotein, with ACE2 receptors. B cell epitope peptides are shown in ball and stick structures whereas the ACE2 receptor protein is shown as a template. [0035] FIG.
- FIG.5A shows experimental evidence showing immunization with pool of CD8+ T cell, CD4+ T cell, and B cell peptides to provide protection against all the current SARS-CoV-2 variants of concerns in triple transgenic h-ACE2-HLA-A2/DR mice.
- Viral titration (FIG.5A), weight loss (FIG.5B), and survival (FIG.5C) data have been shown.
- FIG.6 shows non-limiting configurations of vaccine compositions described herein.
- FIG. 7A and 7B shows non-limiting examples of hybrid vaccine compositions described herein.
- the proteins may be covalently or non-covalently linked together for administration of the vaccine composition.
- Nsp may refer to Nsp1, Nsp2, Nsp3, Nsp5, Nsp6, Nsp7, Nsp8, Nsp9, Nsp10, Nsp12, Nsp13, Nsp14, Nsp15, Nsp16, or a combination thereof
- Spike protein may refer to a portion of the spike protein, or a spike protein with one or more mutations (e.g., a spike protein with two or six proline substitutions).
- FIG. 8 shows sequence-based variant effect predictor analysis to access the pathogenicity of mutations in VOCs.
- FIG.9A, 9B, and 9C show screening of COVID-19 patients based on SARS-CoV-2 variants and subsequent evaluation of IFN- ⁇ CD8 + and CD4 + T cell responses for conserved CD8 + , and CD4 + T cell “asymptomatic” epitopes:
- FIG.9B shows ELISpot images and bar diagrams showing average frequencies of IFN- ⁇ producing cell spots from immune cells from PBMCs (1 x 10 6 cells per well) of COVID-19 infected with highly pathogenic SARS-CoV-2 variants of concern Beta (B.1.351) (left panel) and Omicron (B.1.1.529) (right panel).
- Cells were stimulated for 48 hours with 10mM of 16 immunodominant CD8 + T cell peptides derived from SARS-CoV-2 structural (Spike, Envelope, Membrane) and nonstructural (orf1ab, ORF6, ORF7b, ORF8a, ORF10) proteins.
- FIG.9B shows ELISpot images and bar diagrams showing average frequencies of IFN- ⁇ producing cell spots from immune cells from PBMCs (1 x 10 6 cells per well) of COVID-19 infected with highly pathogenic SARS-CoV-2 variants of concern Beta (B.1.351) (left panel) and Omicron (B.1.1
- FIG. 9C shows ELISpot images and bar diagrams showing average frequencies of IFN- ⁇ producing cell spots from immune cells from PBMCs (1 x 10 6 cells per well) of COVID-19 infected with SARS-CoV-2 variants of concern Alpha (B.1.1.7) (left panel) and Omicron (B.1.1.529) (right panel).
- Cells were stimulated for 48 hours with 10mM of 6 immunodominant CD4 + T cell peptides derived from SARS-CoV-2 structural (Spike, Membrane, Nucleocapsid) and nonstructural (ORF1a, ORF6, ORF8a) proteins.
- the bar diagrams show the average/mean numbers (+ SD) of IFN- ⁇ -spot forming cells (SFCs) after CD8 + T cell peptide-stimulation PBMCs of Asymptomatic and Symptomatic COVID-19 patients. Dotted lines represent an arbitrary threshold set to evaluate the relative magnitude of the response. A strong response is defined for mean SFCs > 25 per 1 x 10 6 stimulated PBMCs. Results were considered statistically significant at P ⁇ 0.05. [0040] FIG.
- FIG. 10A shows an experimental scheme of vaccination and challenge triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice.
- the pool of peptides comprised 25 ⁇ g of each of the 16 CD8 + T cell peptides, 6 CD4 + T cell peptides, and 7 B-cell peptides.
- the final composition of peptides was mixed with 25 ⁇ g of CpG and 25 ⁇ g of Alum. Mock-vaccinated mice were used as controls (Mock).
- mice Fourteen days following the second immunization, mice were intranasally challenged with each of the six different SARS-CoV-2 variants of concern (WA/USA2020, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529)).
- Vaccinated and mock-vaccinated mice were followed 14 days post-challenge for COVID-like symptoms, weight loss, survival, and virus replication.
- FIG. 10B shows the percent weight change recorded daily for 14 days p.i. in vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants.
- FIG.10C shows kaplan-Meir survival plots for vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants.
- FIG. 10D shows virus replication in vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants detected in throat swabs on Days 2, 4, 6, 8, 10, and 14, The indicated P values are calculated using the unpaired t-test, comparing results obtained in vaccinated VERSUS mock-vaccinated mice.
- FIG.11A, 11B, 11C, and 11D shows histopathology and immunohistochemistry of the lungs from in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice vaccinated and mock-vaccinated mice.
- FIG.11A shows representative images of hematoxylin and Eosin (H & E) staining of the lungs harvested on day 14 p.i. from vaccinated (left panels) and mock-vaccinated (right panels) mice.
- FIG.11B shows a representative immunohistochemistry (IHC) sections of the lungs were harvested on Day 14 p.i.
- FIG.11C Fluorescence microscopy images showing infiltration of CD8 + T cells (FIG.11C) and of CD4 + T cells (FIG.11D) in the lungs from vaccinated (left panels) and mock-vaccinated (right panels) mice. Lung sections were co-stained using DAPI (blue) and mAb specific to CD8 + T cells (Pink) (magnification, 20x). The white arrows point to CD8 + and CD4 + T cells infiltrating the infected lungs.
- FIG.11C Fluorescence microscopy images showing infiltration of CD8 + T cells (FIG.11C) and of CD4 + T cells (FIG.11D) in the lungs from vaccinated (left panels) and mock-vaccinated (right panels) mice. Lung sections were co-stained using DAPI (blue) and mAb specific to CD8 + T cells (Pink) (magnification, 20x). The white arrows point to CD8 + and CD4 + T
- 12A, 12B, 12C, and 12D shows the effect of Pan-Coronavirus immunization on CD8 + and CD4 + T cell function and memory response: FACS plots and bar graphs showing the (FIG. 12A) expression of CD8 + T cell function markers, (FIG. 12B) CD4 + T cell function associated markers, (FIG.
- CD8 + T effector memory response CD44 + CD62L-
- CD8 + T resident memory CD103 + CD69 +
- FIG.12D CD4 + T effector memory response (CD44 + CD62L-), and CD4 + resident memory (CD103 + CD69 + ) response in the lung of vaccinated and mock-vaccinated groups of mice infected with multiple SARS-CoV-2 variants. Bars represent means ⁇ SEM. Data were analyzed by student's t-test. Results were considered statistically significant at P ⁇ 0.05.
- FIG.13A, 13B, 13C, 13D, 13E, and 13F shows Immunogenicity of conserved SARS-CoV-2 CD8 + T cell epitopes in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice: ELISpot images and bar diagrams showing average frequencies of IFN- producing cell spots from mononuclear cells from lung tissue (1 x 10 6 cells per well) of vaccinated and mock-vaccinated mice challenged with (FIG. 13A) WA/USA2020, (FIG. 13B) Alpha (B.1.1.7), (FIG. 13C) Beta (B.1.351), (FIG. 13D) Gamma (P.1), (FIG.
- FIG.14A, 14B, 14C, 14D, 14E, and 14F show The magnitude of the IFN CD4 T cell responses for 6 conserved SARS-CoV-2 CD4 + T cell epitopes in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice: ELISpot images and bar diagrams showing average frequencies of IFN- producing cell spots from mononuclear cells from lung tissue (1 x 10 6 cells per well) of vaccinated and mock-vaccinated mice challenged with (FIG. 14A) WA/USA2020, (FIG. 14B) Alpha (B.1.1.7), (FIG. 14C) Beta (B.1.351), (FIG.
- FIG. 14D Gamma (P.1), (FIG. 14E) Delta (B.1.617.2), and (FIG. 14F) Omicron (B.1.1.529).
- Cells were stimulated for 48 hours with 10mM of 6 immunodominant CD4 + T cell peptides derived from SARS-CoV-2 structural (Spike, Envelope, Membrane) and nonstructural (orf1ab, ORF6, ORF7b, ORF8a, ORF10) proteins.
- the bar diagrams show the average/mean numbers (+ SD) of IFN- ⁇ -spot forming cells (SFCs) after CD8 + T cell peptide stimulation in lung tissues of vaccinated and mock-vaccinated mice.
- FIG.15A, 15B, 15C, and 15D show the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from K18-hACE2 single transgenic mice infected with SARS-CoV-2.
- FIG. 15D shows the average body weight change p.i. normalized to the body weight on the day of infection.
- FIG. 15B shows the maximum percent body weight change on day 7 p.i.
- FIG. 15C Shows the percentage survival detected in CXCL-9, CXCL-10, and CXCL-11 treated vs. untreated mice up to day 13 p.i.
- FIG. 16A and 16B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on disease outcome detected from HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice immunized with SARS-CoV-2 vaccine.
- FIG. 16A FIG.
- 16B shows a prototype of the multi-epitope Coronavirus vaccine consisting of highly conserved and immunogenic 16 CD8 + T cell epitopes, 6 CD4 + T cell epitopes, and 8 B cell epitopes (SEQ ID NO: 36).
- FIG.17A, 17B, 17C, and 17D shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice immunized with multi-epitope Coronavirus vaccine and challenged with SARS-CoV-2-USA-WA1/2020 variant.
- FIG.17A Data showing average percent weight change each day p.i. normalized to the body weight on the day of infection is shown in the right panel.
- the bar graph (left panel) shows the percent weight change at day 7 p.i. Bars represent means ⁇ SEM.
- FIG.17B Shows the percentage survival detected in mice groups of, CoV-Vacc, CoV-Vacc + CXCL-9, CoV-Vacc + CXCL-10, CoV-Vacc + CXCL-11, and mock vaccinated group up to 14 days p.i.
- FIG. 17C Viral titration data showing viral RNA copy number in the lungs for each group at days 4 and 8 p.i.
- FIG. 18A and 18B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD4 + T cells in the lung and spleen of immunized HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice.
- FIG. 19A and 19B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD8 + T cells in the lung and spleen of immunized hACE2-HLA-A2/DR triple transgenic mice.
- Graphs on the right panel show the difference in response to different chemokine treatments on the percentage of CD4 + T cells in the spleen of mice. Bars represent means ⁇ SEM.
- FIG. 20A and 20B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD4 + T cells and CD8 + T cells in the lung of immunized hACE2-HLA-A2/DR triple transgenic mice.
- Graphs depict the differences in response to various treatments on the percentage of CD4 + T cells present in the lungs of mice shown in the right panel. Bars represent the means ⁇ SEM. Student’s ttest was used to analyze the data.
- FIG. 22 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters
- FIG. 23 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 23 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 24 shows RT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 25 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 26A and 26B shows Anti SARS-CoV-2 Spike specific IgG measured in the serum of immunized hamsters with mRNA-LNP 2 proline versus 6 proline vaccine at 1ug and 10ug.
- FIG.26A show an endpoint titer is statistically significant increase in spike specific IgG antibody in the serum of hamsters immunized with Spike 2 proline (1ug) compared to Spike 6 proline (1ug). (blood was collected at day 27 after the first immunization (FIG.21).
- FIG.26B shows endpoint titer has no statistical significant difference in spike specific IgG antibody in the serum of hamsters immunized with Spike 2 proline (10ug) compared to Spike 6 proline (10ug) (blood was collected at day 27 after the first immunization) (FIG.21). Plates were coated with 100ng of Spike (S1+S2) from Sino biological [0057] FIG.
- FIG. 27 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 28 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 28 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 29 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 30 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 30 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
- FIG. 31A, 31B, and 31C shows an experimental schematic to determine the efficacy of mRNA-LNP vaccine against the SARS-CoV-2 variants of concern (Delta (B.1.617.2) FIG. 31A) and Omicron (B.1.1.529) FIG.31C) in golden hamster
- FIG. 32 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 32 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 33 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 34 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 34 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 35 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- FIG. 36 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters.
- TERMS [0067] Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which a disclosed invention belongs.
- the technology described herein is related to the herein described compositions, methods, and respective component(s) thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not ("comprising").
- Suitable methods and materials for the practice and/or testing of embodiments of the disclosure are described below. Such methods and materials are illustrative only and are not intended to be limiting. Other methods and materials similar or equivalent to those described herein can be used.
- the term "immunological response" to a composition or vaccine refers to the development in the host of a cellular and/or antibody-mediated immune response to a composition or vaccine of interest.
- an "immunological response” includes but is not limited to one or more of the following effects: the production of antibodies, B cells, helper T cells, and/or cytotoxic T cells, directed specifically to an antigen or antigens included in the composition or vaccine of interest.
- the host may display either a therapeutic or protective immunological response, so resistance to new infection will be enhanced and/or the clinical severity of the disease reduced. Such protection will be demonstrated by either a reduction or lack of symptoms normally displayed by an infected host, a quicker recovery time and/or a lowered viral titer in the infected host.
- the term “variant” refers to a substantially similar sequence.
- a variant comprises a deletion and/or addition and/or change of one or more nucleotides at one or more sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide.
- a "native" polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or an amino acid sequence, respectively.
- Variants of a particular polynucleotide of the disclosure can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide.
- "Variant" protein is intended to mean a protein derived from the native protein by deletion or addition of one or more amino acids at one or more sites in the native protein and/or substitution of one or more amino acids at one or more sites in the native protein.
- Variant proteins encompassed by the present disclosure are biologically active; that is they have the ability to elicit an immune response.
- the terms “treat” or “treatment” or “treating” refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow the development of the disease, such as slow down the development of a disorder, or reducing at least one adverse effect or symptom of a condition, disease or disorder, e.g., any disorder characterized by insufficient or undesired organ or tissue function.
- Treatment is generally “effective” if one or more symptoms or clinical markers are reduced as that term is defined herein.
- a treatment is “effective” if the progression of a disease is reduced or halted.
- treatment includes not just the improvement of symptoms or decrease of markers of the disease, but also a cessation or slowing of progress or worsening of a symptom that would be expected in absence of treatment.
- Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of disease, stabilized (e.g., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable.
- Treatment can also mean prolonging survival as compared to expected survival if not receiving treatment.
- “Treatment” also includes ameliorating a disease, lessening the severity of its complications, preventing it from manifesting, preventing it from recurring, merely preventing it from worsening, mitigating an inflammatory response included therein, or a therapeutic effort to affect any of the aforementioned, even if such therapeutic effort is ultimately unsuccessful.
- the term “carrier,” or “pharmaceutically acceptable carrier,” or “pharmaceutically acceptable vehicle” refers to any appropriate or useful carrier or vehicle for introducing a composition to a subject.
- Pharmaceutically acceptable carriers or vehicles may be conventional but are not limited to conventional vehicles. For example, E. W. Martin, Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA, 15th Edition (1975) and D. B.
- Carriers e.g., pharmaceutical carriers, pharmaceutical vehicles, pharmaceutical compositions, pharmaceutical molecules, etc.
- Carriers are materials generally known to deliver molecules, proteins, cells and/or drugs and/or other appropriate material into the body.
- the nature of the carrier will depend on the nature of the composition being delivered as well as the particular mode of administration being employed.
- pharmaceutical compositions administered may contain minor amounts of non- toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like.
- Patents that describe pharmaceutical carriers include, but are not limited to: U.S. Patent No. 6,667,371; U.S. Patent No. 6,613,355; U.S. Patent No.6,596,296; U.S. Patent No.6,413,536; U.S. Patent No.5,968,543; U.S. Patent No.4,079, 038; U.S. Patent No.4,093,709; U.S. Patent No.4,131,648; U.S. Patent No.4,138,344; U.S. Patent No.4,180,646; U.S. Patent No.4,304,767; U.S. Patent No.4,946,931, the disclosures of which are incorporated in their entirety by reference herein.
- the carrier may, for example, be solid, liquid (e.g., a solution), foam, a gel, the like, or a combination thereof.
- the carrier comprises a biological matrix (e.g., biological fibers, etc.).
- the carrier comprises a synthetic matrix (e.g., synthetic fibers, etc.).
- a portion of the carrier may comprise a biological matrix and a portion may comprise synthetic matrix.
- coronavirus may refer to a group of related viruses such as but not limited to severe acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
- a “subject” is an individual and includes, but is not limited to, a mammal (e.g., a human, horse, pig, rabbit, dog, sheep, goat, non-human primate, cow, cat, guinea pig, or rodent), a fish, a bird, a reptile, or an amphibian. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included.
- a “patient” is a subject afflicted with a disease or disorder.
- administering refers to methods of providing a pharmaceutical preparation to a subject. Such methods are well known to those skilled in the art and include, but are not limited to, administering the compositions orally, parenterally (e.g., intravenously, and subcutaneously), by intramuscular injection, by intraperitoneal injection, intrathecally, transdermally, extracorporeally, topically or the like.
- parenterally e.g., intravenously, and subcutaneously
- intramuscular injection e.g., intravenously, and subcutaneously
- intrathecally e.g., transdermally, extracorporeally, topically or the like.
- a composition can also be administered by topical intranasal administration (intranasally) or administration by inhalant.
- topical intranasal administration means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism (device) or droplet mechanism (device), or through aerosolization of the composition.
- Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism.
- an inhaler can be a spraying device or a droplet device for delivering a composition comprising the vaccine composition, in a pharmaceutically acceptable carrier, to the nasal passages and the upper and/or lower respiratory tracts of a subject. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intratracheal intubation.
- a composition can also be administered by buccal delivery or by sublingual delivery.
- buccal delivery may refer to a method of administration in which the compound is delivered through the mucosal membranes lining the cheeks.
- the vaccine composition is placed between the gum and the cheek of a patient.
- sublingual delivery may refer to a method of administration in which the compound is delivered through the mucosal membrane under the tongue.
- the vaccine composition is administered under the tongue of a patient.
- Parenteral administration of the composition if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, for example, U.S. Pat. No.3,610,795, which is incorporated by reference herein.
- the present invention also provides methods of testing said vaccines, e.g., using particular animal models and clinical trials.
- the vaccine compositions herein can induce efficient and powerful protection against the coronavirus disease or infection, e.g., by inducing the production of antibodies (Abs), CD4+ T helper (Th1) cells, and CD+8 cytotoxic T-cells (CTL).
- the vaccine compositions, e.g., the antigens, herein feature multiple epitopes, which helps provide multiple opportunities for the body to develop an immune response for preventing an infection.
- the epitopes are conserved epitopes, e.g., epitopes that are highly conserved among human coronaviruses and/or animal coronaviruses (e.g., coronaviruses isolated from animals susceptible to coronavirus infections).
- the vaccines herein may be designed to be effective against past, current, and future coronavirus outbreaks
- the term “conserved” refers to an epitope that is among the most highly conserved epitopes identified in a sequence alignment and analysis for its particular epitopes type (e.g., B cell, CD4 T cell, CD8 T cell).
- the conserved epitopes may be the 5 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 10 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 15 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 20 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 25 most highly conserved epitopes identified (for the particular type of epitope).
- the conserved epitopes may be the 30 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 40 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 50 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 50% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 60% most highly conserved epitopes identified (for the particular type of epitope).
- the conserved epitopes may be the 70% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 80% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 90% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 95% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 99% most highly conserved epitopes identified (for the particular type of epitope). The present invention is not limited to the aforementioned thresholds.
- one or more of the conserved epitopes are derived from one or more SARS-CoV-2 human strains or variants in current circulation; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; and/or one or more coronaviruses that cause the common cold.
- SARS-CoV-2 human strains and variants in current circulation may include the original SARS-CoV-2 strain (SARS-CoV-2 isolate Wuhan-Hu-1), and several variants of SARS-CoV-2 including but not limited to Spain variant B.1.177; Australia variant B.1.160, England variant B.1.1.7; South Africa variant B.1.351; Brazil variant P.1; California variant B.1.427/B.1.429; Scotland variant B.1.258; Belgium/Netherlands variant B.1.221; Norway/France variant B.1.367; Norway/Denmark.UK variant B.1.1.277; Sweden variant B.1.1.302; North America, Europe, Asia, Africa, and Australia variant B.1.525; a New York variant B.1.526; variant B.1.525; variant B.1.526, variant S:677H; variant S:677P; B.1.617.2-Delta, variant B.1.1.529-Omicron (BA.1); sub-variant Omicron (BA.1); sub-variant Omicron (BA
- the present invention is not limited to the aforementioned variants of SARS-CoV-2 and encompasses variants identified in the future.
- the one or more coronaviruses that cause the common cold may include but are not limited to strains 229E (alpha coronavirus), NL63 (alpha coronavirus), OC43 (beta coronavirus), HKU1 (beta coronavirus).
- coronaviruses may be used for determining conserved epitopes (including human SARS-CoVs as well as animal CoVs (e.g., bats, pangolins, civet cats, minks, camels, etc.)) that meet the criteria to be classified as “variants of concern” or “variants of interest.” Coronavirus variants that appear to meet one or more of the undermentioned criteria may be labeled "variants of interest” or "variants under investigation” pending verification and validation of these properties.
- conserved epitopes including human SARS-CoVs as well as animal CoVs (e.g., bats, pangolins, civet cats, minks, camels, etc.)
- coronaviruses may be used for determining conserved epitopes (including human SARS-CoVs as well as animal CoVs (e.g., bats, pangolins, civet cats, minks, camels, etc.)
- the criteria may include increased transmissibility, increased morbidity, increased mortality, increased risk of “long COVID”, ability to evade detection by diagnostic tests, decreased susceptibility to antiviral drugs (if and when such drugs are available), decreased susceptibility to neutralizing antibodies, either therapeutic (e.g., convalescent plasma or monoclonal antibodies) or in laboratory experiments, ability to evade natural immunity (e.g., causing reinfections), ability to infect vaccinated individuals, Increased risk of particular conditions such as multisystem inflammatory syndrome or longhaul COVID or Increased affinity for particular demographic or clinical groups, such as children or immunocompromised individuals.
- variants of interest are renamed “variant of concern” by monitoring organizations, such as the CDC.
- the present invention may feature a multi-epitope, pan-coronavirus vaccine composition, the composition comprising at least two of: a) one or more conserved coronavirus B-cell target epitopes selected from SEQ ID NO: 23-31,or a combination thereof; b) one or more conserved coronavirus CD4+ T cell target epitopes selected from SEQ ID NO: 17-22, or a combination thereof; or c) one or more conserved coronavirus CD8+ T cell target epitopes selected from SEQ ID NO: 1-16, or a combination thereof.
- at least one epitope is derived from a non-spike protein, wherein the composition induces immunity to only the epitopes
- Table 1 Shows non-limiting examples of conserved coronavirus epitopes.
- the composition comprises 1-16 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 2-16 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 2-10 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 2-15 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 2-5 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 5-10 CD8 + T cell target epitopes. In certain embodiments, the composition comprises 5-15 CD8 + T cell target epitopes. [0090] In certain embodiments, the composition comprises 1-6 CD4 + T cell target epitopes.
- the composition comprises 2-6 CD4 + T cell target epitopes. In certain embodiments, the composition comprises 3-6 CD4 + T cell target epitopes. In certain embodiments, the composition comprises 4-6 CD4 + T cell target epitopes. In certain embodiments, the composition comprises 5-6 CD4 + T cell target epitopes. In certain embodiments, the composition comprises 2-5 CD4 + T cell target epitopes. In certain embodiments, the composition comprises 3-5 CD4 + T cell target epitopes. [0091] In certain embodiments, the composition comprises 1-9 of the aforementioned B cell target epitopes. In certain embodiments, the composition comprises 2-9 B cell target epitopes. In certain embodiments, the composition comprises 2-5 B cell target epitopes.
- the composition comprises 5-9 B cell target epitopes.
- the epitopes may be each separated by a linker.
- the linker allows for an enzyme to cleave between the target epitopes.
- the present invention is not limited to particular linkers or particular lengths of linkers.
- one or more epitopes may be separated by a linker 2 amino acids in length.
- one or more epitopes may be separated by a linker 3 amino acids in length.
- one or more epitopes may be separated by a linker 4 amino acids in length.
- one or more epitopes may be separated by a linker 5 amino acids in length.
- one or more epitopes may be separated by a linker 6 amino acids in length. In certain embodiments, one or more epitopes may be separated by a linker 7 amino acids in length. In certain embodiments, one or more epitopes may be separated by a linker 8 amino acids in length. In certain embodiments, one or more epitopes may be separated by a linker 9 amino acids in length. In certain embodiments, one or more epitopes may be separated by a linker 10 amino acids in length. In certain embodiments, one or more epitopes may be separated by a linker from 2 to 10 amino acids in length. [0093] Linkers are well known to one of ordinary skill in the art.
- Non-limiting examples of linkers include AAY, KK, and GPGPG.
- one or more CD8+ T cell epitopes are separated by AAY.
- one or more CD4+ T cell epitopes are separated by GPGPG.
- one or more B cell epitopes are separated by KK.
- KK is a linker between a CD4+ T cell epitope and a B cell epitope.
- KK is a linker between a CD8+ T cell epitope and a B cell epitope.
- KK is a linker between a CD8+ T cell epitope and a CD4+ T cell epitope.
- AAY is a linker between a CD4 T cell epitope and a B cell epitope. In certain embodiments, AAY is a linker between a CD8+ T cell epitope and a B cell epitope. In certain embodiments, AAY is a linker between a CD8+ T cell epitope and a CD4+ T cell epitope. In certain embodiments, GPGPG is a linker between a CD4+ T cell epitope and a B cell epitope. In certain embodiments, GPGPG is a linker between a CD8+ T cell epitope and a B cell epitope.
- GPGPG is a linker between a CD8+ T cell epitope and a CD4+ T cell epitope.
- the target epitopes may be derived from structural proteins, non-structural proteins, or a combination thereof.
- structural proteins may include spike proteins (S), envelope proteins (E), membrane proteins (M), or nucleoproteins (N).
- the target epitopes are derived from at least one SARS-CoV-2 protein.
- the SARS-CoV-2 proteins may include ORF1ab protein, Spike glycoprotein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein, and ORF10 protein.
- the ORF1ab protein provides nonstructural proteins (Nsp) such as Nsp1, Nsp2, Nsp3 (Papain-like protease), Nsp4, Nsp5 (3C-like protease), Nsp6, Nsp7, Nsp8, Nsp9, Nsp10, Nsp11, Nsp12 (RNA polymerase), Nsp13 (5’ RNA triphosphatase enzyme), Nsp14 (guanosineN7-methyltransferase), Nsp15 (endoribonuclease), and Nsp16 (2′-O-ribose-methyltransferase).
- Nsp nonstructural proteins
- the antigen or antigens are operatively linked to a promoter.
- the antigen or antigens are operatively linked to a generic promoter.
- the antigen or antigens are operatively linked to a CMV promoter.
- the antigen or antigens are operatively linked to a CAG, EFIA, EFS, CBh, SFFV, MSCV, mPGK, hPGK, SV40, UBC, or other appropriate promoter.
- the antigen or antigens are operatively linked to a tissue-specific promoter (e.g., a lung-specific promoter).
- a tissue-specific promoter e.g., a lung-specific promoter
- the antigen or antigens may be operatively linked to a SpB promoter or a CD144 promoter.
- Table 2 shows non-limiting examples of a portion of a promoter that may be used in accordance with the present invention.
- the vaccine composition comprises a molecular adjuvant and/or one or more T Cell enhancement compositions.
- the adjuvant and/or enhancement compositions may help improve the immunogenicity and/or long-term memory of the vaccine composition.
- molecular adjuvants include CpG, such as a CpG polymer, and flagellin.
- the vaccine composition comprises a T cell attracting chemokine. The T cell attracting chemokine helps pull the T cells from the circulation to the appropriate tissues, e.g., the lungs, heart, kidney, and brain.
- Non-limiting examples of T cell attracting chemokines include CCL5, CXCL9, CXCL10, CXCL11, CCL25, CCL28, CXCL14, CXCL17, or a combination thereof.
- the vaccine composition comprises a composition that promotes T cell proliferation.
- Non-limiting examples of compositions that promote T cell proliferation include IL-7, IL-15, IL-2, or a combination thereof.
- the vaccine composition comprises a composition that promotes T cell homing in the lungs.
- Non-limiting examples of compositions that promote T cell homing include CCL25, CCL28, CXCL14, CXCL17 or a combination thereof.
- Table 3 example of vaccine compositions described herein. The present invention is not limited to the examples in Table 3.
- the present invention features a pan-coronavirus vaccine composition.
- the composition comprising one or more conserved large sequences, each of the one or more conserved large sequences comprise at least one of: one or more conserved coronavirus B-cell target epitopes, one or more conserved coronavirus CD4+ T cell target epitopes, and/or one or more conserved coronavirus CD8+ T cell target epitopes.
- the present invention may also feature a pan-coronavirus vaccine composition.
- composition comprising two or more conserved large sequences, each of the two or more conserved large sequences comprise at least one of: one or more conserved coronavirus B-cell target epitopes, one or more conserved coronavirus CD4+ T cell target epitopes, and/or one or more conserved coronavirus CD8+ T cell target epitopes.
- at least one large sequence is derived from a non-spike protein.
- the conserved large sequences may be the 3 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 4 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 5 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 6 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 7 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 8 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 9 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 10 most highly conserved sequences identified.
- the conserved large sequences may be the 15 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 20 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 25 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 30 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 40 most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 50 most highly conserved sequences identified. In some embodiments, the conserved sequences may be the 50% most highly conserved large sequences identified. In some embodiments, the conserved large sequences may be the 60% most highly conserved sequences identified.
- the large conserved sequences may be the 70% most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 80% most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 90% most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 95% most highly conserved sequences identified. In some embodiments, the conserved large sequences may be the 99% most highly conserved sequences identified. The present invention is not limited to the aforementioned thresholds.
- the non-spike protein is ORF1ab protein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein and ORF10 protein.
- the present invention may further feature a pan-coronavirus vaccine composition, the composition comprising one or more large sequences, wherein each of the one or more large sequences comprise conserved regions of a coronavirus.
- the portion of the coronavirus spike (S) protein is highly conserved among human and animal coronaviruses.
- the portion of the coronavirus spike (S) protein may be derived from one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold.
- the one or more large sequences are highly conserved among human and animal coronaviruses.
- the one or more large sequences are derived from at least one of SARS-CoV-2 proteins.
- the one or more large sequences are derived from one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold.
- the conserved large sequences may be selected from Variants of Concern or Variants of Interest.
- the one or more SARS-CoV-2 human strains or variants in current circulation are selected from: variant B.1.177; variant B.1.160, variant B.1.1.7; variant B.1.351; variant P.1; variant B.1.427/B.1.429; variant B.1.258; variant B.1.221; variant B.1.367; variant B.1.1.277; variant B.1.1.302; variant B.1.525; variant B.1.526, variant S:677H; variant S:677P; variant B.1.1.529-Omicron (BA.1); variant B.1.1.529-Omicron (BA.2); and variant B.1.617.2-Delta).
- the one or more coronaviruses that cause the common cold are selected from: 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus, and HKU1 beta coronavirus.
- the one or more large sequences are derived from a whole protein sequence expressed by SARS-CoV-2. In some embodiments, the one or more large sequences are derived from a partial protein sequence expressed by SARS-CoV-2. In other embodiments, the one or more large conserved sequences is derived from a full-length spike glycoprotein. In some embodiments, the one or more large conserved sequences is derived from a partial spike glycoprotein.
- the spike (S) protein comprises at least one proline substitution, or at least two proline substitution, or at least, four proline substitution, or at least six proline substitution.
- the spike (S) protein may comprise two consecutive proline substitutions at amino acid positions 986 and 987.
- the proline substitutions may comprise K986P and V987P mutations.
- the spike (S) protein is receptor-binding domain (RBD).
- the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD).
- Table 4 Shows non-limiting examples of a portion of a coronavirus spike (S) protein that may be used in accordance with the present invention.
- the large sequences are derived from structural proteins, non-structural proteins, or a combination thereof.
- the one or more large sequences comprises Spike glycoprotein (S) or a portion thereof, Nucleoprotein or a portion thereof, Membrane protein or a portion thereof, and ORF1a/b or a portion thereof.
- the one or more large sequences comprises Spike glycoprotein (S) or a portion thereof, Nucleoprotein or a portion thereof, and ORF1a/b or a portion thereof.
- the one or more large sequences is selected from the group consisting of: ORF1ab protein, Spike glycoprotein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein an ORF10 protein.
- the ORF1ab protein comprises nonstructural protein (Nsp) 1, Nsp2, Nsp3, Nsp4, Nsp5, Nsp6, Nsp7, Nsp8, Nsp9, Nsp10, Nsp11, Nsp12, Nsp13, Nsp14, Nsp15 and Nsp16.
- Table 5 shows non-limiting examples of large sequences that may be used in vaccine compositions described herein. [00117] Table 5:
- the one or more of the large sequences comprises a T-cell epitope restricted to a large number of human class 1 and class 2 HLA haplotypes and are not restricted to HLA-0201 for class 1 or HLA-DR for class 2.
- the one or more large sequences are separated by a linker.
- the linker may be 2 to 10 amino acids in length.
- the one or more large sequences are operatively linked to a generic promoter.
- the generic promoter is a CMV or a CAG promoter.
- Table 6 and FIG. 6 shows examples of vaccine compositions described herein. The present invention is not limited to the examples in Table 6.
- the vaccine compositions described herein are used to prevent a coronavirus disease in a subject. In other embodiments, the vaccine compositions described herein are used to prevent a coronavirus infection prophylactically in a subject. In further embodiments, the vaccine compositions described herein elicits an immune response in a subject.
- Additional sequences and details about methods to select sequences can be found in U.S. Application No. PCT/US21/27355, U.S. Application No. PCT/US21/27340, U.S. Application No. PCT/US21/27341 the specifications of which are hereby incorporated in their entirety by reference.
- EXAMPLES [00124] The following is a non-limiting example of the present invention.
- EXAMPLE 1 Genome-Wide B Cell, CD4+, and CD8+ T Cell Epitopes That Are Highly conserveed between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines.
- the identified epitopes 1) recalled B-cells and CD4+ and CD8+ T cells from both COVID-19 patients and healthy individuals who were never exposed to SARS-CoV-2, and 2) induced strong B-cell and T-cell responses in humanized HLA-DR1/HLA-A*02:01 double-transgenic mice.
- the findings pave the way to develop a preemptive multi epitope pan-coronavirus vaccine (as shown below) to protect against past, current, and future outbreaks.
- SARS-CoV-2 isolate Wuhan-Hu-1 and EU2 (B1.160) (0.0001); followed by VOCs CAL20C (0.0003), 20B (B.1.1.302) (0.0003), B.1.1.7 (0.0004), P.1 (0.0005), 20C (0.0005), and B.1.367 (0.0005).
- SL-CoVs isolate from bats namely: Bat-CoV-YN02 (0.0511), and Bat-CoV-RaTG13 (0.0402) showed genetic similarity with the SARS-CoV-2 (FIG. 1B), showing an evolutionary convergence of SARS-CoV-2 from the bat strains.
- HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*23:01 63-65
- FIG. 2A and 2B were focused on.
- a total of 26 potential CD8+ T cell epitopes specific to the spike glycoprotein region possessing all the 36 non-synonymous mutations were identified.
- Immunization with pool of CD8 + T cell, CD4 + T cell, and B cell peptides provide protection against all the current SARS-CoV-2 variants of concerns:
- the inventors have immunized a group of triple transgenic h-ACE2-HLA-A2/DR mice with pool of CD8 + T cell, CD4 + T cell, and B cell peptides on Day 0 and Day 14.
- a second group of triple transgenic mice were left non-immunized. Following 14 days of the two doses of immunization, on Day 28 of the experiment mice were challenged with Washington, Alpha, Beta, Gamma, Delta, and Omicron variants of SARS-CoV-2.
- inclusion of epitopes specific to these mutations in a vaccine will aid in protecting a larger mass of the population who otherwise are prone to hospitalization and mortality when being infected by VOCs Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.1, B.1.617.2), and Omicron (BA.1, BA.2) that possess S:D614G/ S:K417N/S:E484K.
- SARS-CoV-2-Wuhan-Hu-1 MN908947.3 protein sequence as a reference against all the SARS-CoV-2 VOCs, common cold, and animal CoV strains. The sequences were aligned using ClustalW algorithm in MEGA X.
- SARS-CoV-2 CD8+ and CD4+ T Cell Epitope Prediction Epitope prediction was performed considering the spike glycoprotein (YP_009724390.1) for the reference SARS-CoV-2 isolate, Wuhan-Hu-1.
- the reference spike protein sequence was substituted with all the non-synonymous mutations reported on the 17 VOCs to screen CD8 + T cell (FIG.2A) and CD4 + T cell (FIG.3A) epitopes.
- the tools used for CD8+ T cell-based epitope prediction were SYFPEITHI, MHC-I binding predictions, and Class I Immunogenicity. Of these, the latter two were hosted on the IEDB platform.
- Multiple databases and algorithms were used for the prediction of CD4 + T cell epitopes, namely SYFPEITHI, MHC-II Binding Predictions, Tepitool, and TEPITOPEpan.
- HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*23:01 the 5 most frequent HLA-A class I alleles (HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*23:01) with nearly 91.48% coverage of the world population, regardless of race and ethnicity (FIG. 2B and 2C) were selected, using a phenotypic frequency cutoff ⁇ 6%.
- HLA-DRB1*11:01, HLA-DRB1*15:01, HLA-DRB1*03:01, HLA-DRB1*04:01 alleles with population coverage of 86.39% (FIG.3B and 3C).
- NetMHC SARS-CoV-2 protein sequence was analyzed against all the aforementioned MHC-I and MHC-II alleles. Epitopes with 9mer length for MHC-I and 15mer length for MHC-II were predicted. Subsequently, the peptides were analyzed for binding stability to the respective HLA allotype.
- SARS-CoV-2 B Cell Epitope Prediction Linear B cell epitope predictions were carried out on the spike glycoprotein (S), the primary target of B cell immune responses for SARS-CoV. The spike glycoprotein sequence was substituted with non-synonymous mutations reported on 17 VOCs. The BepiPred 2.0 algorithm embedded in the B cell prediction analysis tool hosted on IEDB platform was used. For each protein, the epitope probability score for each amino acid and the probability of exposure was retrieved.
- B cell epitopes were predicted using a cutoff of 0.55 (corresponding to a specificity greater than 0.81 and sensitivity below 0.3) and considering sequences having more than 5 amino acid residues. This screening process resulted in 8 B-cell peptides (FIG. 4A). These epitopes represent all the major non-synonymous mutations reported among the VOCs. One B-cell epitope (S 439-482 ) was observed to possess the maximum number of VOC-specific mutations.
- the GISAID database recorded 1,581,990 human-SARS-CoV-2 genome sequences and the number of genome sequences continues to grow daily.
- 712,000 human-SARS-CoV-2 genome sequences representing six continents were extrapolated from the GISAID database as on April 1, 2021.
- Population coverage calculation (PPC) was carried out using the Population Coverage software hosted on IEDB platform.
- EXAMPLE 2 Cross-Protection Induced by Highly conserveed Human B, CD4+, and CD8+ T Cell Epitopes-Based Coronavirus Vaccine against Severe Infection, Disease, and Death Caused by Multiple SARS-CoV-2 Variants of Concern.
- the present invention features a multi-epitope-based Coronavirus vaccine that incorporated B, CD4 + , and CD8 + T cell epitopes conserved among all known SARS-CoV-2 VOCs and selectively recognized by CD8 + and CD4 + T-cells from asymptomatic COVID-19 patients irrespective of VOC infection.
- pan-Coronavirus vaccine (i) is safe; (ii) induces high frequencies of lung-resident functional CD8 + and CD4 + TEM and TRM cells; and (iii) provides robust protection against virus replication and COVID19related lung pathology and death caused by six SARSCoV2 VOCs: Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), Delta (lineage B.1.617.2) and Omicron (B.1.1.529).
- CD8 + T cell epitopes were screened for their conservancy against variants namely h-CoV-2/Wuhan (MN908947.3), h-CoV-2/WA/USA2020 (OQ294668.1), h-CoV-2/Alpha(B1.1.7) (OL689430.1), h-CoV-2/Beta(B 1.351) (MZ314998), h-CoV-2/Gamma(P.1) (MZ427312.1), h-CoV-2/Delta(B.1.617.2) (OK091006.1), and h-CoV-2/Omicron(B.1.1.529) (OM570283.1) (33).
- PBMCs Fresh PBMCs were isolated from SYMP and ASYMP COVID-19 patients, on average within 4 days after reporting their first symptoms. PBMCs were then stimulated in vitro for 72 hours using each of the 16 CD8 + T cell epitopes or each of the 6 CD4 + T cell epitopes. Numbers of responding IFN- ⁇ -producing CD8 + and CD4 + T cells (quantified in ELISpot assay as the number of IFN- ⁇ -spot forming cells, or “SFCs”) were subsequently determined.
- ASYMP COVID-19 patients showed significantly higher frequencies of SARS-CoV-2 epitope-specific IFN- ⁇ -producing CD8 + T cells (mean SFCs > 25 per 1 x 10 6 pulmonary immune cells), irrespective of infection with Beta (P ⁇ 0.5, FIG.9B) or Omicron (P ⁇ 0.5, FIG.9B) variants.
- severely ill or hospitalized symptomatic COVID-19 patients showed significantly lower frequencies of SARS-CoV-2 epitope-specific IFN- ⁇ -producing CD8 + T cells (P ⁇ 0.5, FIG.9B) or Omicron (P ⁇ 0., FIG. 9B) variants.
- a pan-Coronavirus vaccine composed of a mixture of conserved “asymptomatic” CD4 + and CD8 + T cell epitopes provides robust protection against infection and disease caused by six SARS-CoV-2 variants of concern:
- a prototype pan-Coronavirus vaccine composed of a mixture of 6 conserved “asymptomatic” CD4 + T cell epitopes and 16 conserved “asymptomatic” CD4 + and CD8 + T cell epitopes was used, previously this vaccine was identified to span the whole SARS-CoV-2 genome.
- CD4 + and CD8 + T cell epitopes that show immunodominance selectively in SYMP COVID-19 patients infected with various SARS-CoV-2 VOCs was focused mainly on.
- a pool of peptides comprising 25 ⁇ g each of 16 CD8 + T cell peptides (ORF1ab 2210 ⁇ 2218 , ORF1ab 3013 ⁇ 3021 , ORF1ab 4283 ⁇ 4291 , ORF1ab 6749-6757 , ORF6 3-11 , ORF7b 26 ⁇ 34 , ORF8a 73 ⁇ 81 , ORF10 3 ⁇ 11 , ORF10 5 ⁇ 13 , S 958 ⁇ 966 , S 1000 ⁇ 1008 , S 1220 ⁇ 1228 , E 20 ⁇ 28 , E 26 ⁇ 34 , M 52 ⁇ 60 , and M 89 ⁇ 97 ), 6 CD4 + T cell epitopes (ORF1a 1350 ⁇ 1365 , ORF6 12 ⁇ 26 , ORF8b 1 ⁇ 15 , S 1 ⁇ 13 , M 176 ⁇ 190 , and N 388 ⁇ 403 ), and 7 B-cell peptides selected from the Spike protein, were mixed with cpG1826
- mice that received the pan-Coronavirus vaccine showed significant protection from weight loss (FIG.10B) and death (FIG.10C) following infection with each of the six SARS-CoV-2 variants of concern: WA/USA2020, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529). All mice immunized with the conserved pan-Coronavirus vaccine survived infection with SARS-CoV-2 variants of concern.
- pan-Coronavirus vaccine showed significant protection from virus replication for most of SARS-CoV-2 variants and confirms a plausible anti-viral effect following immunization with asymptomatic B, CD4 + and CD8 + T cell epitopes carefully selected as being highly conserved from multiple SARS-CoV-2 variants.
- SARS-CoV-2 Nucleocapsid Antibody-based Immunohistochemistry (IHC) staining was further performed on lung tissues obtained from vaccinated and mock-vaccinated groups of mice infected with SARS-CoV-2 variants. Significantly lower antibody staining was detected in the lung tissues of the vaccinated compared mock-vaccinated group of mice following infection with each of the six SARS-CoV-2 variants of concern.
- IHC Immunohistochemistry
- Increased frequencies of lung-resident functional CD8 + and CD4 + T EM and T RM cells induced by the Pan-Coronavirus vaccine are associated with protection against multiple SARS-CoV-2 variants: To determine whether increased frequencies of lung-resident functional CD8 + and CD4 + T cells induced by the pan-Coronavirus vaccine are associated with protection against multiple SARS-CoV-2 variants, flow cytometry was used and the frequencies of IFN- ⁇ CD8 + T cells and CD69 CD8 + T cells were compared (FIG.12A), IFN- ⁇ CD4 + T cells and CD69 CD4 + T cells (FIG.12B) in cell suspensions from the lungs of vaccinated versus mock-vaccinated groups of mice.
- the nine B-cell epitopes were screened for their conservancy against variants namely h-CoV-2/Wuhan (MN908947.3), h-CoV-2/WA/USA2020 (OQ294668.1), h-CoV-2/Alpha(B1.1.7) (OL689430.1), h-CoV-2/Beta(B 1.351) (MZ314998), h-CoV-2/Gamma(P.1) (MZ427312.1), h-CoV-2/Delta(B.1.617.2) (OK091006.1), and h-CoV-2/Omicron(B.1.1.529) (OM570283.1).
- the peptide binding IgG level was significantly higher for all nine “universal” B cell epitopes in COVID-19 patients as well as in vaccinated triple transgenic mice, irrespective of SARS-CoV-2 variant. Reduced peptide binding IgG level was observed for severely ill COVID-19 patients and in mock-vaccinated triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice.
- Viruses SARS-CoV-2 viruses specific to six variants, namely (i) SARS-CoV-2-USA/WA/2020 (Batch Number: G2027B); (ii) Alpha (B.1.1.7) (isolate England/204820464/2020 Batch Number: C2108K); (iii) Beta (B.1.351) (isolate South Africa/KRISP-EC-K005321/2020; Batch Number: C2108F), (iv) Gamma (P.1) (isolate hCoV-19/Japan/TY7-503/2021; Batch Number: G2126A), (v) Delta (B.1.617.2) (isolate h-CoV-19/USA/MA29189; Batch number: G87167), and Omicron (BA.1.529) (isolate h-CoV-19/USA/FL17829; Batch number: G76172) were procured from Microbiologics (St.
- mice were subcutaneously immunized with a pool of conserved Pan-Coronavirus peptides.
- the peptide pool administered per mouse comprised 25 ⁇ g each of the 9-mer long 16 CD8 + T cell peptides (ORF1ab 2210 ⁇ 2218 , ORF1ab 3013 ⁇ 3021 , ORF1ab 4283 ⁇ 4291 , ORF1ab 6749-6757 , ORF6 3-11 , ORF7b 26 ⁇ 34 , ORF8a 73 ⁇ 81 , ORF10 3 ⁇ 11 , ORF10 5 ⁇ 13 , S 958 ⁇ 966 , S 1000 ⁇ 1008 , S 1220 ⁇ 1228 , E 20 ⁇ 28 , E 26 ⁇ 34 , M 52 ⁇ 60 , and M 89 ⁇ 97 ), 15 ⁇ mer long 6 CD4 + T cell epitopes (ORF1a 1350 ⁇ 1365 , ORF6 12 ⁇ 26 , ORF8b 1 ⁇ 15 , S 1 ⁇ 13 , M 176 ⁇ 190
- SARS-CoV-2 positivity was defined by a positive RT-PCR on nasopharyngeal swab samples. All the subjects were genotyped by PCR for class I HLA-A*02:01 and class II HLA ⁇ DRB1*01:01 among the 682 patients (and after excluding a few for which the given amount of blood was insufficient – i.e., less than 6ml), we ended up with 210 that were genotyped for HLA-A*02:01 + or/and HLA ⁇ DRB1*01:01 + .
- Severity 5 patients who died from COVID-19 complications
- Severity 4 infected COVID-19 patients with severe disease that were admitted to the intensive care unit (ICU) and required ventilation support
- Severity 3 infected COVID-19 patients with severe disease that required enrollment in ICU, but without ventilation support
- Severity 2 infected COVID-19 patients with moderate symptoms that involved a regular hospital admission
- Severity 1 infected COVID-19 patients with mild symptoms
- Severity 0 infected individuals with no symptoms.
- EXAMPLE 3 A Multi-Epitope/CXCL11 Prime/Pull Coronavirus Mucosal Vaccine Boosts the Frequency and the Function of Lung-Resident CD4+ and CD8+ Memory T Cells and Protects against COVID-19-like Symptoms and Death Caused by SARS-CoV-2 infection.
- the present invention features a pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope//CXCL11 prime/pull mucosal Coronavirus vaccine.
- This prime/pull vaccine strategy comprises intranasal delivery of a lung-tropic adeno-associated virus type 9 (AAV-9) vector that incorporates highly conserved human B, CD4+ CD8+ cell epitopes of SARS-CoV-2 (prime) and pulling the primed B and T cells into the lungs using the T cell attracting chemokine, CXCL-11 (pull).
- AAV-9 lung-tropic adeno-associated virus type 9
- SARS-CoV-2-infected and CXCL-11-treated K18-hACE2 mice presented significant protection against weight loss (FIG.15B and FIG.15D) and death (FIG.15C) compared to the SARS-CoV-2-infected untreated control K18-hACE2 mice (P ⁇ 0.05).
- SARS-CoV-2-infected and CXCL-9-treated K18-hACE2 mice did not show significant improvement in weight loss (FIG.15B and FIG.15D) and death (FIG.15C) compared to the SARS-CoV-2-infected untreated control K18-hACE2 mice (P > 0.05).
- a multi-epitope/CXCL11 prime/pull Coronavirus vaccine protects against COVID19-like symptoms in HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice following infection with SARS-CoV-2: Since treatment with the CXCL-11, but not CXCL-9 and CXCL-10 chemokines, appeared to improve COVID-19-like symptoms and survivals of K18-hACE2 mice following infection with SARS-CoV-2, next it was determined whether CXCL-11 treatment would also improve the protection induced by a multi-epitope coronavirus vaccine.
- the prime/pull Coronavirus vaccination consists of (i) first priming of SARSCoV2specific B cells, CD4 T cells, and CD8 T cells in HLA DR 0101/HLA A 0201/hACE2 triple transgenic mice using the engineered lung-tropic AAV9 multi-epitope Coronavirus vaccine co-expressing the recently identified immunodominant B, CD4 +, and CD8 + T cell epitopes (i.e., CoV-Vacc) and delivered intranasally followed by (ii) Pulling the “primed” B cells, CD4 + T cells, and CD8 + T cells into the lungs using mouse CXCL-9, CXCL-10, or CXCL-11 T-cell attracting chemokines delivered intranasally (nose drops).
- first priming of SARSCoV2specific B cells, CD4 T cells, and CD8 T cells in HLA DR 0101/HLA A 0201/hACE2 triple transgenic mice using the engineered lung-tropic AAV9 multi-epitope Coronavirus
- mice were intranasally challenged with 1 x 10 4 pfu of SARS-CoV-2 (USA-WA1/2020). Subsequently, all vaccinated groups received additional treatment with CXCL-9, CXCL-10, or CXCL-11 on days 30, 32, and 34 post-immunization. All animals were then monitored for up to day 14 post-infection (p.i.), for weight loss, virus replication in the lungs, and death. On day 14 p.i., mice were euthanized, and lungs were collected for lung inflammation using H & E staining.
- HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice that received the same multi-epitope CoV-Vacc bearing human CD4 + and CD8 + T cell epitopes without chemokine treatment (CoV Vacc alone) as well as in mock-vaccinated mice (Mock).
- chemokine treatment CoV Vacc alone
- mock-vaccinated mice Mock
- CoV-Vacc multi-epitope Coronavirus vaccine
- Vaccinated HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic were subsequently left untreated (control) or treated intranasally on days 10, 12, and 14 post-vaccination and on days 22, 24, and 26 post-vaccination with the CXCL-9, CXCL-10, or CXCL-11 T-cell-attracting chemokine.
- Vaccinated/chemokine-treated and Vaccinated/untreated mice were euthanized on day 27 post-vaccine and the frequencies of the three major lung-resident memory CD4 + and CD8 + T cells expressing CXCR3, CD103, CD62L, and CD44 among total lung cells (i.e.
- T EM effector memory
- T RM resident memory
- T CM central memory
- CXCR3 + CD4 + T cells did not show significant variation for mice immunized with CoV Vacc + CXCL-9, CoV Vacc + CXCL-10, or CoV Vacc + CXCL-11, compared to mice immunized only with Vacc or mock group of mice.
- FIG. 19A a higher magnitude in the frequency of total CD8 + T cells in lung immune cells was shown to be observed in the immunized mice.
- the mice immunized with CoV-Vacc showed a significant increase in CXCR3 + CD8 + T cells, CD44 + CD62L-CD8 + T cells, and CD44 + CD62L + CD8 + T cells when compared to the mock group.
- CD103 + CD8 + T cells showed a decrease in the CoV-Vacc + CXCL-11 group compared to the immunized and mock groups.
- these results demonstrate that the protection induced by the multiepitope//CXCL11 prime/pull Coronavirus vaccine in SARS-CoV-2 infected HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice are associated with high frequencies of lung-resident memory CD4 + and CD8 + T EM , T CM, and T RM cells.
- HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice that received the same multi-epitope CoV-Vacc bearing human CD4 + and CD8 + T cell epitopes without chemokine treatment (CoV Vacc alone) as well as in mock-vaccinated mice (Mock).
- chemokine treatment CoV Vacc alone
- mock-vaccinated mice Mock.
- CoV-Vacc multi-epitope Coronavirus vaccine
- Vaccinated HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic were subsequently left untreated (control) or treated intranasally on days 10, 12, and 14 post-vaccination and on days 22, 24, and 26 post-vaccination with the CXCL-9, CXCL-10, or CXCL-11 T-cell-attracting chemokine.
- Vaccinated/chemokine-treated and Vaccinated/untreated mice were euthanized on day 27 post-vaccine immune cells were harvested for the frequency and the function of major lung-memory CD4 + and CD8 + T cells determined by FACS.
- FIG.20A A significant increase in the percentage of tetramer + CD4 + T cells was found among immunized and CXCL11-treated mice compared to all other mice groups. Similarly, we found a significant increase in Granzyme B + CD4 + T cells, IFN- ⁇ + CD4 + T cells, and TNF- ⁇ + CD4 + T cells in mice immunized with the CoV-Vacc and treated with the chemokine CXCL11. In FIG.20B, a slight increase in magnitude in the percentage of tetramer + CD8 + T cells in the lungs of immunized and CXCL11-treated mice compared to all other mice groups.
- mice Female K18-hACE2 transgenic mice (8-9 weeks old) were purchased from the Jackson Laboratory (Bar Harbor, ME). K18-hACE2 mice breeding was conducted in the UCI animal facility where female mice were used at 8-9 weeks. In addition, female HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice (8-9 weeks old) were used. The HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mouse colony was established here at the UCI by cross-breeding K18-hACE2 mice (51) with double transgenic HLA-DR*0101/HLA-A*0201 mice (17).
- mice received sterile PBS (mock). Mice were treated intranasally with CXCL-9, CXCL-10, and CXCL-11 (2.4 ⁇ g in 20 ⁇ l of sterile PBS/mice). murine MIG (CXCL-9), IP-10 (CXCL-10) and I-TAC (CXCL-11) were obtained (PEPROTECH, USA). [00199] As used herein, the term “about” refers to plus or minus 10% of the referenced number. [00200]
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Abstract
Pan-coronavirus vaccines for inducing efficient, powerful and long-lasting protection against all Coronaviruses infections and diseases, comprising multiple highly conserved large sequences which may comprise one or more conserved B, CD4 and CDS T cell epitopes that help provide multiple targets for the body to develop an immune response for preventing a Coronavirus infection and/or disease. In certain embodiments, the large sequences are conserved proteins or large sequences, e.g., sequences that are highly conserved among human coronaviruses and/or animal coronaviruses (e.g., coronaviruses isolated from animals susceptible to coronavirus infections).
Description
SARSCOV2 MULTIANTIGEN UNIVERSAL VACCINES CROSS-REFERENCES TO RELATED APPLICATIONS [0001] This application claims benefit of U.S. Provisional Application No.63/349,904 filed June 7, 2022, U.S Provisional Application No. 63/349,799 filed June 7, 2022, and U.S. Provisional Application No. 63/451,302 filed March 10, 2023, the specifications of which are incorporated herein in their entirety by reference. [0002] This application also claims benefit of U.S. Application No. 18/046,862 filed October 14, 2022, U.S. Application No. 18/046,875 filed October 14, 2022, and U.S. Application No. 18/046,462 filed October 13, 2022, the specifications of which are incorporated herein in their entirety by reference. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT [0003] This invention was made with government support under Grant No. AI158060 awarded by National Institute of Health. The government has certain rights in the invention. REFERENCE TO A SEQUENCE LISTING [0004] The contents of the electronic sequence listing (name of the file UCI 22_10 PCT.xml; Size: 592,890,311 bytes; and Date of Creation: June 7, 2023) is herein incorporated by reference in its entirety. FIELD OF THE INVENTION [0005] The present invention relates to vaccines, for example, viral vaccines, such as those directed to coronaviruses, e.g., pan-coronavirus vaccines. BACKGROUND OF THE INVENTION [0006] While the Wuhan Hu1 variant of SARS-CoV-2 is the ancestral reference virus, Alpha (B.1.1.7), Beta (B.1.351), Gamma or P1 (B.1.1.28.1), and Delta (lineage B.1.617.2) variants of concern (VOCs) subsequently emerged in Brazil, India, and South Africa vaccines from 2020 to 2022. The most recent SARS CoV-2 variants, including multiple heavily mutated Omicron (B.1.1.529) sub-variants, have prolonged the COVID-19 pandemic. These new variants emerged since December 2020 at a much higher rate, consistent with the accumulation of two mutations per month, and strong selective pressure on the immunologically important SARS-CoV-2 genes. The Alpha, Beta, Gamma, Delta, and Omicron Variants are defined as Variants of Concern (VOC) based on their high transmissibility associated with increased hospitalizations and deaths. This is a result of reduced neutralization by antibodies generated by previous variants and/or by the first-generation COVID-19 vaccines, together with failures of treatments and diagnostics. Dr. Peter Marks, Director/CBER (Center for Biologics Evaluation and Research) for the FDA recently outlined the need for a next-generation vaccine that will protect from multiple SARS-CoV-2 VOCs. [0007] Besides SARS CoV-2 variants, two additional Coronaviruses from the severe acute respiratory syndrome (SARS) like betacoronavirus (sarbecovirus) lineage, SARS coronavirus (SARS-CoV) and MERS-CoV, have caused epidemics and pandemics in humans over the past 20 years. In addition, the discovery of diverse Sarbecoviruses in bats together with the constant “jumping” of these zoonotic viruses
from bats to intermediate animals raises the possibility of another COVID pandemic in the future. Hence, there is an urgent need to develop a pre-emptive universal pan-Coronavirus vaccine to protect against all SARS-CoV-2 variants, SARS-CoV, MERS-CoV, and other zoonotic Sarbecoviruses with the potential to jump from animals into humans. [0008] The Spike protein is a surface predominant antigen of SARS-CoV-2 that is involved in the docking and penetration of the virus into the target host cells. As such, the Spike protein is the main target of the first-generation COVID-19 subunit vaccines aiming mainly at inducing neutralizing antibodies. Nearly 56% of the 10 billion doses of first-generation COVID-19 vaccines are based on the Spike antigen alone, while the remaining 44% of the COVID-19 vaccines were based on whole virion inactivated (WVI) vaccines. Both the Spike-based COVID-19 sub-unit vaccines and the whole virion-inactivated vaccines were successful. However, because the Spike protein is the most mutated SARS-CoV-2 antigen, these first-generation vaccines lead to immune evasion by many new variants and subvariants, such as the Omicron XBB1.5 sub-variant. Therefore, the second-generation COVID-19 vaccines should be focused not only on the highly variable Spike protein but also on other highly conserved structural and non-structural SARS-CoV-2 antigens capable of inducing protection mediated by not only neutralizing antibodies but also by cross-reactive CD4+ and CD8+ T cells.. BRIEF SUMMARY OF THE INVENTION [0009] It is an objective of the present invention to provide compositions and methods featuring a universal pre-emptive coronavirus vaccine as specified in the independent claims. Embodiments of the invention are given in the dependent claims. Embodiments of the present invention can be freely combined with each other if they are not mutually exclusive. [0010] For example, the present invention features a universal pre-emptive pan-Coronavirus vaccine composition, wherein the composition comprising at least two of: (i) one or more conserved coronavirus B-cell target epitopes selected from SEQ ID NO: 23-31, or a combination thereof; (ii) one or more conserved coronavirus CD4+ T cell target epitopes selected from SEQ ID NO: 17-22, or a combination thereof; and (iii) one or more conserved coronavirus CD8+ T cell target epitopes selected from SEQ ID NO: 1-16, or a combination thereof. An at least one epitope of the composition is derived from a non-spike protein. [0011] In some embodiments, the target epitopes are derived from a SARS-CoV-2 protein selected from a group consisting of: ORF1ab protein, Spike glycoprotein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein and ORF10 protein. [0012] In some embodiments, one or more of the one or more epitopes may be part of one or more large sequences. The one or more large sequences are highly conserved among human and animal Coronaviruses. In some embodiments, at least one large sequence is a whole protein sequence expressed by SARS-CoV-2, a partial protein sequence expressed by SARS-CoV-2, or a combination thereof.
[0013] In some embodiments, the large sequences are selected from Variants of Concern or Variants of Interest. In some embodiments, the one or more large sequences are derived from a whole protein sequence expressed by SARS-CoV-2. In some embodiments, the one or more large sequences are derived from a partial protein sequence expressed by SARS-CoV-2. In some embodiments, the one or more large sequences is derived from a full-length spike glycoprotein. In some embodiments, the one or more large sequences is derived from a partial spike glycoprotein. In some embodiments, the one or more large sequences comprises Spike glycoprotein (S) or a portion thereof, Nucleoprotein or a portion thereof, and protein encoded by ORF1a/b or a portion thereof. [0014] Referring to the embodiments herein, the one or more conserved epitopes may be derived from one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold. past, current, and future coronavirus outbreaks. [0015] Referring to the embodiments herein, the one or more large sequences may be derived from one or more of: one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold. past, current, and future coronavirus outbreaks. [0016] In some embodiments, the one or more SARS-CoV-2 human strains or variants in current circulation are selected from: strain B.1.177; strain B.1.160, strain B.1.1.7; strain B.1.351; strain P.1; strain B.1.427/B.1.429; strain B.1.258; strain B.1.221; strain B.1.367; strain B.1.1.277; strain B.1.1.302; strain B.1.525; strain B.1.526, strain S:677H; strain S:677P; strain B.1.1.529-Omicron (BA.1); strain B.1.1.529-Omicron (BA.2); and strain B.1.617.2-Delta. [0017] In some embodiments, the one or more coronaviruses that cause the common cold are selected from: 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus, and HKU1 beta coronavirus. [0018] In some embodiments, the vaccine composition protects against disease caused by one or more coronavirus variants or coronavirus subvariants. In some embodiments, the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants wherein the coronavirus variants comprise alpha, beta, gamma, delta, and omicron. In some embodiments, the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus. In some embodiments, the vaccine composition protects against infection and reinfection of coronavirus variants or coronavirus subvariants. In some embodiments, the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants, wherein the coronavirus variants comprise alpha, beta,
gamma, delta, and omicron. In some embodiments, the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus. In some embodiments, the vaccine composition protects against infection or reinfection of one or more coronavirus variants or coronavirus subvariant. In some embodiments, the vaccine composition protects against infection or reinfection of multiple coronavirus variants or coronavirus subvariants. In some embodiments, the vaccine composition protects against infection or re-infection caused by one coronavirus variants or coronavirus subvariants. In some embodiments, the vaccine composition induces strong and long-lasting protection mediated by antibodies (Abs), CD4+ T helper (Th1) cells, and/or CD8+ cytotoxic T-cells (CTL). In some embodiments, the composition protects against Sarbecoviruses, wherein sarbecoviruses comprise SARS-CoV1 or SARS-CoV2. [0019] Referring to the embodiments herein, the composition may further comprise a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof. [0020] Referring to the embodiments herein, the composition may further comprise a composition that promotes T cell proliferation, wherein the composition that promotes T cell proliferation is IL-7 or IL-15. [0021] One of the unique and inventive technical features of the present invention is the use of highly conserved epitopes. Without wishing to limit the invention to any theory or mechanism, it is believed that the technical feature of the present invention advantageously provides for a universal vaccine composition that will protect from future human outbreaks and deter future zoonosis. None of the presently known prior references or work has the unique inventive technical feature of the present invention. [0022] The present invention also includes a pre-emptive pan-coronavirus vaccine composition comprising: at least two conserved coronavirus antigens selected from: (i) a conserved coronavirus Spike protein; (ii) a conserved coronavirus NSP2 protein; (iii) a conserved coronavirus NSP3 protein; (iv) a conserved coronavirus NSP14 protein; and (v) a conserved coronavirus Nucleoprotein. The aforementioned proteins or antigens may refer to portions of a particular entire protein. Thus, the present invention also includes a pre-emptive pan-coronavirus vaccine composition comprising: at least two conserved coronavirus antigens selected from: (i) a conserved coronavirus Spike protein or a portion thereof; (ii) a conserved coronavirus NSP2 protein or a portion thereof; (iii) a conserved coronavirus NSP3 protein or a portion thereof; (iv) a conserved coronavirus NSP14 protein or a portion thereof; and (v) a conserved coronavirus Nucleoprotein or a portion thereof. [0023] In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP2 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion
thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the Spike protein (or a portion thereof) comprises one or more proline substitutions. In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP3 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof). In some embodiments, the composition
comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the composition comprises a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof); a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the Spike protein (or a portion thereof) comprises one or more proline substitutions. In some embodiments, the composition comprises a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); and a conserved coronavirus NSP14 protein (or a portion thereof); a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). [0024] In some embodiments, the composition further comprises a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof. In some embodiments, the composition further comprises a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15. In some embodiments, the conserved protein or antigen is conserved among human and animal coronaviruses. In some embodiments, the portion of the coronavirus spike (S) protein is derived from a full-length spike glycoprotein. In some embodiments, the portion of the coronavirus spike (S) protein is derived from a partial spike glycoprotein. In some embodiments, the portion of the coronavirus spike (S) protein is receptor-binding domain (RBD). In some embodiments, the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD). [0025] The present invention also includes a pre-emptive pan-coronavirus vaccine composition, the composition comprising one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise one or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). [0026] In some embodiments, the one or more large sequence coronavirus proteins comprises two or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the one or more large sequence coronavirus proteins comprises three or more of: a conserved coronavirus Spike protein(or a portion thereof); a conserved coronavirus NSP2 protein(or a portion thereof); a conserved coronavirus NSP3 protein(or a portion thereof); a conserved coronavirus NSP14 protein(or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the one or more large sequence coronavirus proteins comprises four or more of: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus
NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); or a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the one or more large sequence coronavirus proteins comprises: a conserved coronavirus Spike protein (or a portion thereof); a conserved coronavirus NSP2 protein (or a portion thereof); a conserved coronavirus NSP3 protein (or a portion thereof); a conserved coronavirus NSP14 protein (or a portion thereof); and a conserved coronavirus nucleoprotein (nucleocapsid) (or a portion thereof). In some embodiments, the large coronavirus sequences are highly conserved among human and animal coronaviruses. In some embodiments, the Spike (S) protein further comprises at least one proline substitution. In some embodiments, the Spike (S) protein comprises a receptor-binding domain (RBD). In some embodiments, the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD). In some embodiments, the composition further comprises a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof. In some embodiments, the composition further comprises a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15. [0027] The present invention also features a pre-emptive pan-coronavirus vaccine composition, the composition comprising, or comprising a sequence encoding one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein. [0028] The present invention also features a method of preventing infection or reinfection by one or more coronavirus variants or subvariants in a subject, said method comprising administering a therapeutically effective amount of a composition according to the present invention. [0029] Any feature or combination of features described herein are included within the scope of the present invention provided that the features included in any such combination are not mutually inconsistent as will be apparent from the context, this specification, and the knowledge of one of ordinary skill in the art. Additional advantages and aspects of the present invention are apparent in the following detailed description and claims. BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWING(S) [0030] The features and advantages of the present invention will become apparent from a consideration of the following detailed description presented in connection with the accompanying drawings in which: [0031] FIG. 1A and 1B shows the evolution of emerging SARS-CoV-2 Variants of Concerns and their genetic similarity with other human and animal coronaviruses: FIG.1A shows a dendrogram showing the evolution of SARS-CoV-2 lineages based on PANGO and Nextstrain nomenclature (top panel). Phylogenetic analysis performed between 712,000 human SARS-CoV-2 genome sequences to show degree of genetic similarity among different SARS-CoV-2 lineages evolved between December 2019 and April 2021(bottom panel). FIG.1B shows phylogenetic analysis performed among VOCs of SARS-CoV-2, CoVs strains from human and other species showed minimum genetic distance between the first
SARSCoV2 isolate WuhanHu1 reported from the Wuhan Seafood market with different VOCs, followed by bat strains hCoV-19-bat-Yunnan-RmYN02, hCoV-19-bat-Yunnan-RaTG13, and bat-CoV-19-ZXC21 (top panel). Genetic distances based on Maximum Composite Likelihood model among the human, bat, pangolin, civet cat and camel genome sequences. Results indicate least genetic distance among SARS-CoV-2 isolated Wuhan-Hu-1 with VOCs EU2, CAL20C, 20B, B.1.17, P.1, and 20C B.1.367 (bottom panel). [0032] FIG. 2A and 2B shows identification of SARS-CoV-2 CD8+ T cell epitopes specific to spike glycoprotein possessing non-synonymous mutations from VOCs. FIG. 2A shows twenty-six, spike glycoprotein specific epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern. FIG. 2B and 2C show the SARS-CoV-2-derived CD8+ T cell epitopes are screened based on their presence among most frequently observed HLA-A alleles in global population (HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*11:01, HLA-A*23:01). MHC-I binding affinity and high degree of immunogenicity showed high PPC value of 91.48%, average number of epitope hits / HLA combinations recognized by the population is 21.3, and minimum number of epitope hits / HLA combinations recognized by 90% of the population (pc90) is 5.06. [0033] FIG. 3A, 3B, and 3C shows the identification of SARS-CoV-2 CD4+ T cell epitopes specific to spike glycoprotein possessing non-synonymous mutations from VOCs. FIG. 3A shows Nineteen spike glycoprotein specific CD4+ T cell epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern. FIG. 3B and 3C shows the SARS-CoV-2-derived CD4+ T cell epitopes are screened based on their presence among most frequently observed HLA-DR alleles in global population (HLA-DRB1*01:01, HLA-DRB1*11:01, HLA-DRB1*15:01, HLA-DRB1*03:01, HLADRB1*04:01). MHC-I binding affinity and high degree of immunogenicity showed high PPC value of 86.39%, average number of epitope hits / HLA combinations recognized by the population is 13.69, and minimum number of epitope hits / HLA combinations recognized by 90% of the population (pc90) is 2.87. [0034] FIG.4A and 4B shows the docking of SARS-CoV-2 Spike glycoprotein-derived B cell epitopes to human ACE2 receptors. FIG.4A shows eight spike glycoprotein specific B cell epitopes were predicted. The spike glycoprotein is substituted with all the known non-synonymous mutations reported in context to the 17 SARS-CoV-2 specific variants of concern. FIG.4B shows molecular docking of 8 B-cell epitopes, identified from the SARS-CoV-2 Spike glycoprotein, with ACE2 receptors. B cell epitope peptides are shown in ball and stick structures whereas the ACE2 receptor protein is shown as a template. [0035] FIG. 5A, 5B, and 5C shows experimental evidence showing immunization with pool of CD8+ T cell, CD4+ T cell, and B cell peptides to provide protection against all the current SARS-CoV-2 variants of concerns in triple transgenic h-ACE2-HLA-A2/DR mice. Viral titration (FIG.5A), weight loss (FIG.5B), and survival (FIG.5C) data have been shown. [0036] FIG.6 shows non-limiting configurations of vaccine compositions described herein. [0037] FIG. 7A and 7B shows non-limiting examples of hybrid vaccine compositions described herein. The proteins may be covalently or non-covalently linked together for administration of the vaccine composition. Note: “Nsp” may refer to Nsp1, Nsp2, Nsp3, Nsp5, Nsp6, Nsp7, Nsp8, Nsp9, Nsp10, Nsp12,
Nsp13, Nsp14, Nsp15, Nsp16, or a combination thereof, Spike protein may refer to a portion of the spike protein, or a spike protein with one or more mutations (e.g., a spike protein with two or six proline substitutions). [0038] FIG. 8 shows sequence-based variant effect predictor analysis to access the pathogenicity of mutations in VOCs. [0039] FIG.9A, 9B, and 9C show screening of COVID-19 patients based on SARS-CoV-2 variants and subsequent evaluation of IFN-ɣ CD8+ and CD4+ T cell responses for conserved CD8+, and CD4+ T cell “asymptomatic” epitopes: FIG. 9A shows an experimental plan of the screening process of COVID-19 patients (n = 210) into Asymptomatic and Symptomatic categories based on clinical parameters. Blood and nasopharyngeal swabs were collected from all the subjects and a qRT-PCR assay was performed. Six novel nonsynonymous mutations (Δ69-70, Δ242-244, N501Y, E484K, L452R, and T478K) were used to identify the haplotypes unique to different SARS-CoV-2 variants of concern (Omicron (B.1.1.529 (BA.1)), Omicron (B.1.1.529 (BA.2)), Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Epsilon (B.1.427/B.1.429)) and variants of interest (Eta (B.1.525), R.1, Zeta (P.2), Iota (B.1.526) and B.1.2/501Y or B.1.1.165). FIG.9B shows ELISpot images and bar diagrams showing average frequencies of IFN-ɣ producing cell spots from immune cells from PBMCs (1 x 106 cells per well) of COVID-19 infected with highly pathogenic SARS-CoV-2 variants of concern Beta (B.1.351) (left panel) and Omicron (B.1.1.529) (right panel). Cells were stimulated for 48 hours with 10mM of 16 immunodominant CD8+ T cell peptides derived from SARS-CoV-2 structural (Spike, Envelope, Membrane) and nonstructural (orf1ab, ORF6, ORF7b, ORF8a, ORF10) proteins. FIG. 9C shows ELISpot images and bar diagrams showing average frequencies of IFN-ɣ producing cell spots from immune cells from PBMCs (1 x 106 cells per well) of COVID-19 infected with SARS-CoV-2 variants of concern Alpha (B.1.1.7) (left panel) and Omicron (B.1.1.529) (right panel). Cells were stimulated for 48 hours with 10mM of 6 immunodominant CD4+ T cell peptides derived from SARS-CoV-2 structural (Spike, Membrane, Nucleocapsid) and nonstructural (ORF1a, ORF6, ORF8a) proteins. The bar diagrams show the average/mean numbers (+ SD) of IFN-ɣ-spot forming cells (SFCs) after CD8+ T cell peptide-stimulation PBMCs of Asymptomatic and Symptomatic COVID-19 patients. Dotted lines represent an arbitrary threshold set to evaluate the relative magnitude of the response. A strong response is defined for mean SFCs > 25 per 1 x 106 stimulated PBMCs. Results were considered statistically significant at P < 0.05. [0040] FIG. 10A, 10B, 10C, and 10D shows protection induced against six SARS-CoV-2 variants of concern in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice following immunization with a pan-Coronavirus vaccine incorporating conserved human B, CD4+, and CD8+ T cell “asymptomatic” epitopes: FIG. 10A shows an experimental scheme of vaccination and challenge triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice. Triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice (7-8-week-old, n = 60) were immunized subcutaneously on Days 0 and 14 with a multi-epitope pan-Coronavirus vaccine consisting of a pool of conserved B, CD4+ T cell and CD8+ T cell human epitope peptides. The pool of peptides comprised 25μg of each of the 16 CD8+ T cell peptides, 6 CD4+ T cell peptides, and 7 B-cell peptides. The final composition of peptides was mixed with 25μg of CpG and 25μg of Alum. Mock-vaccinated mice were used as controls (Mock). Fourteen days following the second immunization, mice were intranasally challenged with each of the six different SARS-CoV-2 variants of
concern (WA/USA2020, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529)). Vaccinated and mock-vaccinated mice were followed 14 days post-challenge for COVID-like symptoms, weight loss, survival, and virus replication. FIG. 10B shows the percent weight change recorded daily for 14 days p.i. in vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants. FIG.10C shows kaplan-Meir survival plots for vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants. FIG. 10D shows virus replication in vaccinated and mock-vaccinated mice following the challenge with each of the six different SARS-CoV-2 variants detected in throat swabs on Days 2, 4, 6, 8, 10, and 14, The indicated P values are calculated using the unpaired t-test, comparing results obtained in vaccinated VERSUS mock-vaccinated mice. [0041] FIG.11A, 11B, 11C, and 11D shows histopathology and immunohistochemistry of the lungs from in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice vaccinated and mock-vaccinated mice. FIG.11A shows representative images of hematoxylin and Eosin (H & E) staining of the lungs harvested on day 14 p.i. from vaccinated (left panels) and mock-vaccinated (right panels) mice. FIG.11B shows a representative immunohistochemistry (IHC) sections of the lungs were harvested on Day 14 p.i. from vaccinated (left panels) and mock-vaccinated (right panels) mice and stained with SARS-CoV-2 Nucleocapsid antibody. Black arrows point to the antibody staining. Fluorescence microscopy images showing infiltration of CD8+ T cells (FIG.11C) and of CD4+ T cells (FIG.11D) in the lungs from vaccinated (left panels) and mock-vaccinated (right panels) mice. Lung sections were co-stained using DAPI (blue) and mAb specific to CD8+ T cells (Pink) (magnification, 20x). The white arrows point to CD8+ and CD4+ T cells infiltrating the infected lungs. [0042] FIG. 12A, 12B, 12C, and 12D shows the effect of Pan-Coronavirus immunization on CD8+ and CD4+ T cell function and memory response: FACS plots and bar graphs showing the (FIG. 12A) expression of CD8+ T cell function markers, (FIG. 12B) CD4+ T cell function associated markers, (FIG. 12C) CD8+ T effector memory response (CD44+CD62L-), and CD8+ T resident memory (CD103+CD69+) response, and (FIG.12D) CD4+ T effector memory response (CD44+CD62L-), and CD4+ resident memory (CD103+CD69+) response in the lung of vaccinated and mock-vaccinated groups of mice infected with multiple SARS-CoV-2 variants. Bars represent means ± SEM. Data were analyzed by student's t-test. Results were considered statistically significant at P < 0.05. [0043] FIG.13A, 13B, 13C, 13D, 13E, and 13F shows Immunogenicity of conserved SARS-CoV-2 CD8+ T cell epitopes in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice: ELISpot images and bar diagrams showing average frequencies of IFN- producing cell spots from mononuclear cells from lung tissue (1 x 106 cells per well) of vaccinated and mock-vaccinated mice challenged with (FIG. 13A) WA/USA2020, (FIG. 13B) Alpha (B.1.1.7), (FIG. 13C) Beta (B.1.351), (FIG. 13D) Gamma (P.1), (FIG. 13E) Delta (B.1.617.2), and (FIG.13F) Omicron (B.1.1.529). The cells were stimulated for 48 hours with 10mM of 16 immunodominant CD8+ T cell peptides. The bar diagrams show the average/mean numbers (+ SD) of IFN-ɣ-spot forming cells (SFCs) after CD8+ T cell peptide stimulation in lung tissues of vaccinated and mock-vaccinated mice. Dotted lines represent an arbitrary threshold set to evaluate the relative magnitude of the response. A strong response is defined for mean SFCs > 25 per 1 x 106 stimulated PBMCs. Results were considered statistically significant at P < 0.05.
[0044] FIG.14A, 14B, 14C, 14D, 14E, and 14F show The magnitude of the IFN CD4 T cell responses for 6 conserved SARS-CoV-2 CD4+ T cell epitopes in triple transgenic HLA-A*02:01/HLA-DRB1*01:01-hACE-2 mice: ELISpot images and bar diagrams showing average frequencies of IFN- producing cell spots from mononuclear cells from lung tissue (1 x 106 cells per well) of vaccinated and mock-vaccinated mice challenged with (FIG. 14A) WA/USA2020, (FIG. 14B) Alpha (B.1.1.7), (FIG. 14C) Beta (B.1.351), (FIG. 14D) Gamma (P.1), (FIG. 14E) Delta (B.1.617.2), and (FIG. 14F) Omicron (B.1.1.529). Cells were stimulated for 48 hours with 10mM of 6 immunodominant CD4+ T cell peptides derived from SARS-CoV-2 structural (Spike, Envelope, Membrane) and nonstructural (orf1ab, ORF6, ORF7b, ORF8a, ORF10) proteins. The bar diagrams show the average/mean numbers (+ SD) of IFN-ɣ-spot forming cells (SFCs) after CD8+ T cell peptide stimulation in lung tissues of vaccinated and mock-vaccinated mice. The dotted lines represent an arbitrary threshold set to evaluate the relative magnitude of the response. A strong response is defined for mean SFCs > 25 per 1 x 106 stimulated PBMCs. Results were considered statistically significant at P ≤ 0.05. [0045] FIG.15A, 15B, 15C, and 15D show the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from K18-hACE2 single transgenic mice infected with SARS-CoV-2. (FIG.15A) Experimental plan to study the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from K18-hACE2 single transgenic mice following infection with SARS-CoV-2 (Washington USA-WA1/2020 variant).8-9 week-old male and female K18-hACE2 mice (n = 20) were infected intranasally with 1 x 104 pfu of the SARS-CoV-2-USA-WA1/2020 variant. Mice were subsequently treated intranasally with CXCL-9 (n = 4), CXCL-10 (n = 4), and CXCL-11 (n = 4) on days 3, 5, 7, and 9 post-infection (p.i). As a control mice (n = 4) were left untreated.15D shows the average body weight change p.i. normalized to the body weight on the day of infection. FIG. 15B shows the maximum percent body weight change on day 7 p.i. (FIG.15C) Shows the percentage survival detected in CXCL-9, CXCL-10, and CXCL-11 treated vs. untreated mice up to day 13 p.i. [0046] FIG. 16A and 16B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on disease outcome detected from HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice immunized with SARS-CoV-2 vaccine. (FIG. 16A) FIG. 16B shows a prototype of the multi-epitope Coronavirus vaccine consisting of highly conserved and immunogenic 16 CD8+ T cell epitopes, 6 CD4+ T cell epitopes, and 8 B cell epitopes (SEQ ID NO: 36). Experimental plan to study the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice immunized with multi-epitope Coronavirus vaccine (CoV-Vacc).8-9 week-old male and female HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice were intranasally immunized with CoV-Vacc; 2x1010 VP per mice on day 0 (n = 28). As a control mice (n = 7) were left unimmunized. The immunized mice were subsequently treated intranasally with 2.4 μg of; CXCL-9 (n = 7), CXCL-10 (n = 7), and CXCL-11 (n = 7) on days 10,12,14,22,24,26 post-immunization. On day 27 two mice per group were euthanized, and lung tissues were collected. The immune cell response was evaluated by flow cytometry. The remaining mice (n = 25) were intranasally infected with 1x104 pfu of SARS-CoV-2 (USA-WA1/2020) on day 28 post-immunization. Three mice groups were subsequently treated intranasally with CXCL-9 (n = 5), CXCL-10 (n = 5), and CXCL-11 (n = 5) on days 30, 32, and 34 post-immunization. disease monitoring, weighing, and survival were monitored
in the mice up to day 14 p.i. [0047] FIG.17A, 17B, 17C, and 17D shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11 chemokines on COVID-19-like symptoms detected from HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice immunized with multi-epitope Coronavirus vaccine and challenged with SARS-CoV-2-USA-WA1/2020 variant. (FIG.17A) Data showing average percent weight change each day p.i. normalized to the body weight on the day of infection is shown in the right panel. The bar graph (left panel) shows the percent weight change at day 7 p.i. Bars represent means ± SEM. (FIG.17B) Shows the percentage survival detected in mice groups of, CoV-Vacc, CoV-Vacc + CXCL-9, CoV-Vacc + CXCL-10, CoV-Vacc + CXCL-11, and mock vaccinated group up to 14 days p.i. (FIG. 17C) Viral titration data showing viral RNA copy number in the lungs for each group at days 4 and 8 p.i. (FIG. 17D) Representative H & E staining images of the lungs at day 14 p.i. of SARS-CoV-2 infected mice treated with different chemokines at 4x, 10x, and 40x magnifications. [0048] FIG. 18A and 18B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD4+ T cells in the lung and spleen of immunized HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice. (FIG.18A) The left panel shows FACS plots for CD4+ T cells in the lungs of mice immunized with the multi-epitope Coronavirus vaccine (n = 7) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs depict the differences in response to various treatments on the percentage of CD4+ T cells present in the lungs of mice shown in the right panel. Bars represent the means ± SEM. Student’s t-test was used to analyze the data. (FIG. 18B) The left panel represents FACS plots for CD4+ T cells in the spleen of mice immunized with the multi-epitope Coronavirus vaccine (n = 7) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs on the right panel show the difference in response to different chemokine treatments on the percentage of CD4+ T cells in the spleen of mice. Bars represent means ± SEM. [0049] FIG. 19A and 19B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD8+ T cells in the lung and spleen of immunized hACE2-HLA-A2/DR triple transgenic mice. (FIG. 19A) The left panel shows FACS plots for CD8+ T cells in the lungs of mice immunized with the multi-epitope Coronavirus vaccine (n = 7) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs depict the differences in response to various treatments on the percentage of CD8+ T cells present in the lungs of mice shown in the right panel. Bars represent the means ± SEM. Student’s t-test was used to analyze the data. (FIG.19B) The left panel represents FACS plots for CD8+ T cells in the spleen of mice immunized with the multi-epitope Coronavirus vaccine (n = 7) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs on the right panel show the difference in response to different chemokine treatments on the percentage of CD4+ T cells in the spleen of mice. Bars represent means ± SEM. [0050] FIG. 20A and 20B shows the effect of treatment with CXCL-9, CXCL-10, and CXCL-11chemokines on CD4+ T cells and CD8+ T cells in the lung of immunized hACE2-HLA-A2/DR triple transgenic mice. (FIG. 20A) The left panel shows FACS plots for CD4+ T cells in the lungs of mice immunized with the multi-epitope Coronavirus vaccine (n = 5) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs depict the differences in response to various treatments on the percentage of CD4+ T cells present in the lungs of mice shown in the right panel. Bars represent the means ± SEM. Student’s
ttest was used to analyze the data. (FIG.20B) The left panel represents FACS plots for CD8 T cells in the lungs of mice immunized with the multi-epitope Coronavirus vaccine (n = 5) and treated with CXCL-9, CXCL-10, and CXCL-11. Graphs on the right panel show the difference in response to different chemokine treatments on the percentage of CD8+ T cells in the lungs of mice. Bars represent means ± SEM. [0051] FIG.21A, 21B, and 21C shows an experimental schematic (FIG.21A) to determine the efficacy of mRNA-LNP vaccine against the SARS-CoV-2 Delta (B.1.617.2) (FIG. 21B) and Omicron (B.1.1.529) (FIG.21C) variants in golden hamster. [0052] FIG. 22 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters [0053] FIG. 23 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0054] FIG. 24 shows RT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0055] FIG. 25 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0056] FIG. 26A and 26B shows Anti SARS-CoV-2 Spike specific IgG measured in the serum of immunized hamsters with mRNA-LNP 2 proline versus 6 proline vaccine at 1ug and 10ug. FIG.26A show an endpoint titer is statistically significant increase in spike specific IgG antibody in the serum of hamsters immunized with Spike 2 proline (1ug) compared to Spike 6 proline (1ug). (blood was collected at day 27 after the first immunization (FIG.21). FIG.26B shows endpoint titer has no statistical significant difference in spike specific IgG antibody in the serum of hamsters immunized with Spike 2 proline (10ug) compared to Spike 6 proline (10ug) (blood was collected at day 27 after the first immunization) (FIG.21). Plates were coated with 100ng of Spike (S1+S2) from Sino biological [0057] FIG. 27 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters. [0058] FIG. 28 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters. [0059] FIG. 29 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters. [0060] FIG. 30 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Omicron (B.1.1.529) variant in golden hamsters.
[0061] FIG. 31A, 31B, and 31C shows an experimental schematic to determine the efficacy of mRNA-LNP vaccine against the SARS-CoV-2 variants of concern (Delta (B.1.617.2) FIG. 31A) and Omicron (B.1.1.529) FIG.31C) in golden hamster [0062] FIG. 32 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0063] FIG. 33 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0064] FIG. 34 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0065] FIG. 35 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. [0066] FIG. 36 shows qRT-PCR data showing reduced viral copy number for hamsters immunized with different mRNA-LNP Pan-CoV-Vaccines against the SARS-CoV-2 Delta (B.1.617.2) variant in golden hamsters. TERMS [0067] Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which a disclosed invention belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. The term "comprising" means that other elements can also be present in addition to the defined elements presented. The use of "comprising" indicates inclusion rather than limitation. Stated another way, the term "comprising" means "including principally, but not necessarily solely." Furthermore, variations of the word "comprising," such as "comprise" and "comprises," have correspondingly the same meanings. In one respect, the technology described herein is related to the herein described compositions, methods, and respective component(s) thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not ("comprising"). [0068] Suitable methods and materials for the practice and/or testing of embodiments of the disclosure are described below. Such methods and materials are illustrative only and are not intended to be limiting. Other methods and materials similar or equivalent to those described herein can be used. For example, conventional methods well known in the art to which the disclosure pertains are described in various general and more specific references, including, for example, Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring Harbor Laboratory Press, 1989; Sambrook et al., Molecular Cloning: A Laboratory Manual, 3d ed., Cold Spring Harbor Press, 2001; Ausubel et al., Current Protocols in Molecular Biology, Greene Publishing Associates, 1992 (and Supplements to 2000); Ausubel et al.,
Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 4th ed., Wiley & Sons, 1999; Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1990; and Harlow and Lane, Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1999, Gene Expression Technology (Methods in Enzymology, Vol.185, edited by D. Goeddel, 1991. Academic Press, San Diego, Calif.), “Guide to Protein Purification” in Methods in Enzymology (M. P. Deutshcer, ed., (1990) Academic Press, Inc.); PCR Protocols: A Guide to Methods and Applications (Innis, et al.1990. Academic Press, San Diego, Calif.), Culture of Animal Cells: A Manual of Basic Technique, 2nd Ed. (R. I. Freshney.1987. Liss, Inc. New York, N.Y.), Gene Transfer and Expression Protocols, pp.109-128, ed. E. J. Murray, The Humana Press Inc., Clifton, N.J.), and the Ambion 1998 Catalog (Ambion, Austin, Tex.), the disclosures of which are incorporated in their entirety herein by reference. [0069] Although methods and materials similar or equivalent to those described herein can be used to practice or test the disclosed technology, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and are not intended to be limiting. [0070] As used herein, the term "immunological response" to a composition or vaccine refers to the development in the host of a cellular and/or antibody-mediated immune response to a composition or vaccine of interest. Usually, an "immunological response" includes but is not limited to one or more of the following effects: the production of antibodies, B cells, helper T cells, and/or cytotoxic T cells, directed specifically to an antigen or antigens included in the composition or vaccine of interest. The host may display either a therapeutic or protective immunological response, so resistance to new infection will be enhanced and/or the clinical severity of the disease reduced. Such protection will be demonstrated by either a reduction or lack of symptoms normally displayed by an infected host, a quicker recovery time and/or a lowered viral titer in the infected host. [0071] As used herein, the term "variant" refers to a substantially similar sequence. For polynucleotides, a variant comprises a deletion and/or addition and/or change of one or more nucleotides at one or more sites within the native polynucleotide and/or a substitution of one or more nucleotides at one or more sites in the native polynucleotide. As used herein, a "native" polynucleotide or polypeptide comprises a naturally occurring nucleotide sequence or an amino acid sequence, respectively. Variants of a particular polynucleotide of the disclosure (e.g., the reference polynucleotide) can also be evaluated by comparison of the percent sequence identity between the polypeptide encoded by a variant polynucleotide and the polypeptide encoded by the reference polynucleotide. "Variant" protein is intended to mean a protein derived from the native protein by deletion or addition of one or more amino acids at one or more sites in the native protein and/or substitution of one or more amino acids at one or more sites in the native protein. Variant proteins encompassed by the present disclosure are biologically active; that is they have the ability to elicit an immune response. [0072] As used herein, the terms "treat" or "treatment" or "treating" refers to both therapeutic treatment
and prophylactic or preventative measures, wherein the object is to prevent or slow the development of the disease, such as slow down the development of a disorder, or reducing at least one adverse effect or symptom of a condition, disease or disorder, e.g., any disorder characterized by insufficient or undesired organ or tissue function. Treatment is generally "effective" if one or more symptoms or clinical markers are reduced as that term is defined herein. Alternatively, a treatment is "effective" if the progression of a disease is reduced or halted. That is, "treatment" includes not just the improvement of symptoms or decrease of markers of the disease, but also a cessation or slowing of progress or worsening of a symptom that would be expected in absence of treatment. Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of disease, stabilized (e.g., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. "Treatment" can also mean prolonging survival as compared to expected survival if not receiving treatment. “Treatment” also includes ameliorating a disease, lessening the severity of its complications, preventing it from manifesting, preventing it from recurring, merely preventing it from worsening, mitigating an inflammatory response included therein, or a therapeutic effort to affect any of the aforementioned, even if such therapeutic effort is ultimately unsuccessful. [0073] As used herein, the term “carrier,” or “pharmaceutically acceptable carrier,” or “pharmaceutically acceptable vehicle” refers to any appropriate or useful carrier or vehicle for introducing a composition to a subject. Pharmaceutically acceptable carriers or vehicles may be conventional but are not limited to conventional vehicles. For example, E. W. Martin, Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA, 15th Edition (1975) and D. B. Troy, ed. Remington: The Science and Practice of Pharmacy, Lippincott Williams & Wilkins, Baltimore MD and Philadelphia, PA, 21st Edition (2006) describe compositions and formulations suitable for pharmaceutical delivery of one or more therapeutic compounds or molecules. Carriers (e.g., pharmaceutical carriers, pharmaceutical vehicles, pharmaceutical compositions, pharmaceutical molecules, etc.) are materials generally known to deliver molecules, proteins, cells and/or drugs and/or other appropriate material into the body. In general, the nature of the carrier will depend on the nature of the composition being delivered as well as the particular mode of administration being employed. In addition to biologically-neutral carriers, pharmaceutical compositions administered may contain minor amounts of non- toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like. Patents that describe pharmaceutical carriers include, but are not limited to: U.S. Patent No. 6,667,371; U.S. Patent No. 6,613,355; U.S. Patent No.6,596,296; U.S. Patent No.6,413,536; U.S. Patent No.5,968,543; U.S. Patent No.4,079, 038; U.S. Patent No.4,093,709; U.S. Patent No.4,131,648; U.S. Patent No.4,138,344; U.S. Patent No.4,180,646; U.S. Patent No.4,304,767; U.S. Patent No.4,946,931, the disclosures of which are incorporated in their entirety by reference herein. The carrier may, for example, be solid, liquid (e.g., a solution), foam, a gel, the like, or a combination thereof. In some embodiments, the carrier comprises a biological matrix (e.g., biological fibers, etc.). In some embodiments, the carrier comprises a synthetic matrix (e.g., synthetic fibers, etc.). In certain embodiments, a portion of the carrier may comprise a biological matrix and a portion may comprise synthetic matrix.
[0074] As used herein, coronavirus may refer to a group of related viruses such as but not limited to severe acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All the coronaviruses cause respiratory tract infection that range from mild to lethal in mammals. Several non-limiting examples of Coronavirus strains are described herein. [0075] A “subject” is an individual and includes, but is not limited to, a mammal (e.g., a human, horse, pig, rabbit, dog, sheep, goat, non-human primate, cow, cat, guinea pig, or rodent), a fish, a bird, a reptile, or an amphibian. The term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be included. A “patient” is a subject afflicted with a disease or disorder. The term “patient” includes human and veterinary subjects [0076] The terms “administering,” and “administration” refer to methods of providing a pharmaceutical preparation to a subject. Such methods are well known to those skilled in the art and include, but are not limited to, administering the compositions orally, parenterally (e.g., intravenously, and subcutaneously), by intramuscular injection, by intraperitoneal injection, intrathecally, transdermally, extracorporeally, topically or the like. [0077] A composition can also be administered by topical intranasal administration (intranasally) or administration by inhalant. As used herein, “topical intranasal administration” means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism (device) or droplet mechanism (device), or through aerosolization of the composition. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. As used herein, “an inhaler” can be a spraying device or a droplet device for delivering a composition comprising the vaccine composition, in a pharmaceutically acceptable carrier, to the nasal passages and the upper and/or lower respiratory tracts of a subject. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intratracheal intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disorder being treated, the particular composition used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein. [0078] A composition can also be administered by buccal delivery or by sublingual delivery. As used herein “buccal delivery” may refer to a method of administration in which the compound is delivered through the mucosal membranes lining the cheeks. In some embodiment, for a buccal delivery the vaccine composition is placed between the gum and the cheek of a patient. As used herein “sublingual delivery” may refer to a method of administration in which the compound is delivered through the mucosal membrane under the tongue. In some embodiments, for a sublingual delivery the vaccine composition is administered under the tongue of a patient. [0079] Parenteral administration of the composition, if used, is generally characterized by injection.
Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, for example, U.S. Pat. No.3,610,795, which is incorporated by reference herein. DETAILED DESCRIPTION OF THE INVENTION [0080] Before the present compounds, compositions, and/or methods are disclosed and described, it is to be understood that this invention is not limited to specific synthetic methods or to specific compositions, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. Embodiments of the present invention can be freely combined with each other if they are not mutually exclusive Multi-Epitope Vaccines: [0081] The present invention features preemptive multi-epitope pan-Coronavirus vaccines, methods of use, and methods of producing said vaccines, methods of preventing coronavirus infections, etc. The present invention also provides methods of testing said vaccines, e.g., using particular animal models and clinical trials. The vaccine compositions herein can induce efficient and powerful protection against the coronavirus disease or infection, e.g., by inducing the production of antibodies (Abs), CD4+ T helper (Th1) cells, and CD+8 cytotoxic T-cells (CTL). [0082] The vaccine compositions, e.g., the antigens, herein feature multiple epitopes, which helps provide multiple opportunities for the body to develop an immune response for preventing an infection. [0083] In certain embodiments, the epitopes are conserved epitopes, e.g., epitopes that are highly conserved among human coronaviruses and/or animal coronaviruses (e.g., coronaviruses isolated from animals susceptible to coronavirus infections). The vaccines herein may be designed to be effective against past, current, and future coronavirus outbreaks [0084] As used herein, the term “conserved” refers to an epitope that is among the most highly conserved epitopes identified in a sequence alignment and analysis for its particular epitopes type (e.g., B cell, CD4 T cell, CD8 T cell). For example, the conserved epitopes may be the 5 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 10 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 15 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 20 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 25 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 30 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 40 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved
epitopes may be the 50 most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 50% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 60% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 70% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 80% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 90% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 95% most highly conserved epitopes identified (for the particular type of epitope). In some embodiments, the conserved epitopes may be the 99% most highly conserved epitopes identified (for the particular type of epitope). The present invention is not limited to the aforementioned thresholds. [0085] In certain embodiments, one or more of the conserved epitopes are derived from one or more SARS-CoV-2 human strains or variants in current circulation; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; and/or one or more coronaviruses that cause the common cold. SARS-CoV-2 human strains and variants in current circulation may include the original SARS-CoV-2 strain (SARS-CoV-2 isolate Wuhan-Hu-1), and several variants of SARS-CoV-2 including but not limited to Spain variant B.1.177; Australia variant B.1.160, England variant B.1.1.7; South Africa variant B.1.351; Brazil variant P.1; California variant B.1.427/B.1.429; Scotland variant B.1.258; Belgium/Netherlands variant B.1.221; Norway/France variant B.1.367; Norway/Denmark.UK variant B.1.1.277; Sweden variant B.1.1.302; North America, Europe, Asia, Africa, and Australia variant B.1.525; a New York variant B.1.526; variant B.1.525; variant B.1.526, variant S:677H; variant S:677P; B.1.617.2-Delta, variant B.1.1.529-Omicron (BA.1); sub-variant Omicron (BA.1); sub-variant Omicron (BA.2); sub-variant Omicron (BA.3); sub-variant Omicron (BA.4); sub-variant Omicron (BA.5). The present invention is not limited to the aforementioned variants of SARS-CoV-2 and encompasses variants identified in the future. The one or more coronaviruses that cause the common cold may include but are not limited to strains 229E (alpha coronavirus), NL63 (alpha coronavirus), OC43 (beta coronavirus), HKU1 (beta coronavirus). [0086] Additionally, other coronaviruses may be used for determining conserved epitopes (including human SARS-CoVs as well as animal CoVs (e.g., bats, pangolins, civet cats, minks, camels, etc.)) that meet the criteria to be classified as “variants of concern” or “variants of interest.” Coronavirus variants that appear to meet one or more of the undermentioned criteria may be labeled "variants of interest" or "variants under investigation" pending verification and validation of these properties. In some embodiments, the criteria may include increased transmissibility, increased morbidity, increased mortality, increased risk of “long COVID”, ability to evade detection by diagnostic tests, decreased susceptibility to antiviral drugs (if and when such drugs are available), decreased susceptibility to neutralizing antibodies, either therapeutic (e.g., convalescent plasma or monoclonal antibodies) or in laboratory experiments, ability to evade natural immunity (e.g., causing reinfections), ability to infect vaccinated individuals,
Increased risk of particular conditions such as multisystem inflammatory syndrome or longhaul COVID or Increased affinity for particular demographic or clinical groups, such as children or immunocompromised individuals. Once validated, variants of interest are renamed “variant of concern” by monitoring organizations, such as the CDC. [0087] The present invention may feature a multi-epitope, pan-coronavirus vaccine composition, the composition comprising at least two of: a) one or more conserved coronavirus B-cell target epitopes selected from SEQ ID NO: 23-31,or a combination thereof; b) one or more conserved coronavirus CD4+ T cell target epitopes selected from SEQ ID NO: 17-22, or a combination thereof; or c) one or more conserved coronavirus CD8+ T cell target epitopes selected from SEQ ID NO: 1-16, or a combination thereof. In some embodiments, at least one epitope is derived from a non-spike protein, wherein the composition induces immunity to only the epitopes [0088] Table 1: Shows non-limiting examples of conserved coronavirus epitopes.
Claims
WHAT IS CLAIMED IS: 1. A universal pre-emptive pan-Coronavirus vaccine composition, the composition comprising at least two of: a. one or more conserved coronavirus B-cell target epitopes selected from SEQ ID NO: 23-31,or a combination thereof; b. one or more conserved coronavirus CD4+ T cell target epitopes selected from SEQ ID NO: 17-22, or a combination thereof; or c. one or more conserved coronavirus CD8+ T cell target epitopes selected from SEQ ID NO: 1-16, or a combination thereof; wherein at least one epitope of the composition is derived from a non-spike protein. 2. The composition of claim 1, wherein the one or more conserved epitopes are derived from one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold. past, current, and future coronavirus outbreaks. 3. The composition of claim 3, wherein the one or more SARS-CoV-2 human strains or variants in current circulation are selected from: variant B.1.177; variant B.1.160, variant B.1.1.7 (UK), variant P.1 (Japan/Brazil), variant B.1.351 (South Africa), variant B.1.427 (California), variant B.1.429 (California), variant B.1.258; variant B.1.221; variant B.1.367; variant B.1.1.277; variant B.1.1.302; variant B.1.525; variant B.1.526, variant S:677H; variant S:677P; B.1.617.2-Delta, variant B.1.1.529-Omicron (BA.1); sub-variant Omicron (BA.1); sub-variant Omicron (BA.
2); sub-variant Omicron (BA.
3); sub-variant Omicron (BA.4); sub-variant Omicron (BA.5).
4. The composition of claim 3, wherein the one or more coronaviruses that cause the common cold are selected from: 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus, and HKU1 beta coronavirus.
5. The composition of any on of claims 1-4, wherein the target epitopes are derived from a SARS-CoV-2 protein selected from a group consisting of: ORF1ab protein, Spike glycoprotein, ORF3a protein, Envelope protein, Membrane glycoprotein, ORF6 protein, ORF7a protein, ORF7b protein, ORF8 protein, Nucleocapsid protein and ORF10 protein.
6. The composition of any one of claims 1-5 further comprising a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
7. The composition of any one of claims 1-6 further comprising a composition that promotes T cell proliferation, wherein the composition that promotes T cell proliferation is IL-7 or IL-15.
8. The composition of any one of claims 1-7, wherein one or more of the epitopes are part of one or more large sequences.
9. The composition of claim 8, wherein the one or more large sequences are highly conserved
among human and animal Coronaviruses.
10. The composition of claim 8 or claim 9, wherein at least one large sequence is a whole protein sequence expressed by SARS-CoV-2, a partial protein sequence expressed by SARS-CoV-2, or a combination thereof.
11. The composition of any of claims 8-10, wherein the one or more large sequences are derived from one or more of: one or more of: one or more SARS-CoV-2 human strains or variants in current circulation; one or more SARS-CoV-2 variants identified in the future; one or more coronaviruses that has caused a previous human outbreak; one or more coronaviruses isolated from animals selected from a group consisting of bats, pangolins, civet cats, minks, camels, and other animal receptive to coronaviruses; or one or more coronaviruses that cause the common cold. past, current, and future coronavirus outbreaks.
12. The composition of claim 11, wherein the one or more SARS-CoV-2 human strains or variants in current circulation are selected from: strain B.1.177; strain B.1.160, strain B.1.1.7; strain B.1.351; strain P.1; strain B.1.427/B.1.429; strain B.1.258; strain B.1.221; strain B.1.367; strain B.1.1.277; strain B.1.1.302; strain B.1.525; strain B.1.526, strain S:677H; strain S:677P; strain B.1.1.529-Omicron (BA.1); strain B.1.1.529-Omicron (BA.2); and strain B.1.617.2-Delta.
13. The composition of claim 11, wherein the one or more coronaviruses that cause the common cold are selected from: 229E alpha coronavirus, NL63 alpha coronavirus, OC43 beta coronavirus, and HKU1 beta coronavirus.
14. The composition of any of claims 8-13, wherein the large sequences are selected from Variants of Concern or Variants of Interest.
15. The composition of any of claims 8-14, wherein the one or more large sequences are derived from a whole protein sequence expressed by SARS-CoV-2.
16. The composition of any of claims 8-14, wherein the one or more large sequences are derived from a partial protein sequence expressed by SARS-CoV-2.
17. The composition of any of claims 8-16, wherein the one or more large sequences is derived from a full-length spike glycoprotein.
18. The composition of any of claims 8-16, wherein the one or more large sequences is derived from a partial spike glycoprotein.
19. The composition of any of claims 8-18, wherein the one or more large sequences comprises Spike glycoprotein (S) or a portion thereof, Nucleoprotein or a portion thereof, and protein encoded by ORF1a/b or a portion thereof.
20. The composition of any of claims 1-19, wherein the vaccine composition protects against disease caused by one or more coronavirus variants or coronavirus subvariants.
21. The composition of claim 20, wherein the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants wherein the coronavirus variants comprise alpha, beta, gamma, delta, and omicron.
22. The composition of claim 20, wherein the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus.
23. The composition of any of claims 1-22, wherein the vaccine composition protects against
infection and reinfection of coronavirus variants or coronavirus subvariants.
24. The composition of claim 23, wherein the coronavirus variants or coronavirus subvariants comprise past or currently circulating coronavirus variants or coronavirus subvariants, wherein the coronavirus variants comprise alpha, beta, gamma, delta, and omicron.
25. The composition of claim 23, wherein the coronavirus variants or coronavirus subvariants comprise future variants or future subvariants of human and animal coronavirus.
26. The composition of claim 23, wherein the vaccine composition protects against infection or reinfection of one or more coronavirus variants or coronavirus subvariant.
27. The composition of claim 26, wherein the vaccine composition protects against infection or reinfection of multiple coronavirus variants or coronavirus subvariants.
28. The composition of claim 26, wherein the vaccine composition protects against infection or re-infection caused by one coronavirus variants or coronavirus subvariants.
29. The composition of any one of claims 1-28, wherein the vaccine composition induces strong and long-lasting protection mediated by antibodies (Abs), CD4+ T helper (Th1) cells, and/or CD8+ cytotoxic T-cells (CTL).
30. The composition of any one of claims 1-29, wherein the composition protects against Sarbecoviruses, wherein sarbecoviruses comprise SARS-CoV1 or SARS-CoV2.
31. A pre-emptive pan-coronavirus vaccine composition, the composition comprising, or comprising a sequence encoding: at least two conserved coronavirus antigens selected from: (i) a conserved coronavirus Spike protein; (ii) a conserved coronavirus NSP2 protein; (iii) a conserved coronavirus NSP3 protein; (iv) a conserved coronavirus NSP14 protein; and (v) a conserved coronavirus Nucleoprotein.
32. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; and a conserved coronavirus NSP2 protein.
33. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; and a conserved coronavirus NSP3 protein.
34. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; and a conserved coronavirus NSP14 protein.
35. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; and a conserved coronavirus Nucleoprotein.
36. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; and a conserved coronavirus NSP3 protein.
37. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; and a conserved coronavirus NSP14 protein.
38. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; and a conserved coronavirus Nucleoprotein.
39. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein.
40. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus Nucleoprotein.
41. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
42. The composition of any one of claims 31-41, wherein the Spike protein comprises one or more proline substitutions.
43. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; and a conserved coronavirus NSP3 protein.
44. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; and a conserved coronavirus NSP14 protein.
45. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; and a conserved coronavirus Nucleoprotein.
46. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein.
47. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP3 protein; and a conserved coronavirus Nucleoprotein.
48. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
49. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein.
50. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus Nucleoprotein.
51. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
52. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
53. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein.
54. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved
coronavirus NSP3 protein; and a conserved coronavirus Nucleoprotein.
55. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein; a conserved coronavirus Nucleoprotein.
56. The composition of any one of claims 31-41 wherein the Spike protein comprises one or more proline substitutions.
57. The composition of claim 31, wherein the at least two conserved coronavirus antigens are: a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; and a conserved coronavirus NSP14 protein; a conserved coronavirus Nucleoprotein.
58. The composition of any one of claims 31-57, wherein the composition further comprises a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
59. The composition of any of claims 31-58, wherein the composition further comprises a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15.
60. The composition of any of claims 31-59, wherein the conserved protein or antigen is conserved among human and animal coronaviruses.
61. The composition of any of claims 31-60, wherein the portion of the coronavirus spike (S) protein is derived from a full-length spike glycoprotein.
62. The composition of any of claims 31-60, wherein the portion of the coronavirus spike (S) protein is derived from a partial spike glycoprotein.
63. The composition of any of claims 31-60, wherein the portion of the coronavirus spike (S) protein is receptor-binding domain (RBD).
64. The composition of claim 63, wherein the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD).
65. The composition of any one of claims 31-64, wherein the composition comprises one of SEQ ID NO: 64-116.
66. A pre-emptive pan-coronavirus vaccine composition, the composition comprising, or comprising a sequence encoding one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise one or more of: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; or a conserved coronavirus Nucleoprotein.
67. The composition of claim 66, wherein the one or more large sequence coronavirus proteins comprises two or more of: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; or a conserved coronavirus Nucleoprotein.
68. The composition of claim 66, wherein the one or more large sequence coronavirus proteins comprises three or more of: a conserved coronavirus Spike protein; a conserved coronavirus
NSP2 protein; a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; or a conserved coronavirus Nucleoprotein.
69. The composition of claim 66, wherein the one or more large sequence coronavirus proteins comprises four or more of: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; or a conserved coronavirus Nucleoprotein.
70. The composition of claim 66, wherein the one or more large sequence coronavirus proteins comprises: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP3 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
71. The composition of any one of claims 66-70, wherein the large coronavirus sequences are highly conserved among human and animal coronaviruses.
72. The composition of any one of claims 66-71, wherein the Spike (S) protein further comprises at least one proline substitution.
73. The composition of any one of claims 66-72, wherein the Spike (S) protein comprises a receptor-binding domain (RBD).
74. The composition of any one of claims 66-72, wherein the RBD comprises a trimerized SARS-CoV-2 receptor-binding domain (RBD).
75. The composition of any one of claims 66-74, wherein the composition comprises one of SEQ ID NO: 64-116.
76. The composition of any of claims 66-75 further comprising a T cell attracting chemokine, wherein the T cell attracting chemokine is CCL5, CXCL9, CXCL10, CXCL11, or a combination thereof.
77. The composition of any of claims 66-76 further comprising a composition that promotes T cell proliferation and T-cell memory, wherein the composition that promotes T cell proliferation and memory is IL-7, IL-2, or IL-15.
78. A pre-emptive pan-coronavirus vaccine composition, the composition comprising, or comprising a sequence encoding one or more large sequence coronavirus proteins, wherein the one or more large sequence coronavirus proteins comprise: a conserved coronavirus Spike protein; a conserved coronavirus NSP2 protein; a conserved coronavirus NSP14 protein; and a conserved coronavirus Nucleoprotein.
79. A method of preventing infection or reinfection by one or more coronavirus variants or subvariants in a subject, said method comprising administering a therapeutically effective amount of a composition according to one of claims 1-78.
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| US18/046,875 US20230173060A1 (en) | 2020-04-14 | 2022-10-14 | Large sequence pan-coronavirus vaccine compositions |
| US18/046,875 | 2022-10-14 | ||
| US18/046,862 US20230146932A1 (en) | 2020-04-14 | 2022-10-14 | Multi-epitope pan-coronavirus vaccine compositions |
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| PCT/US2023/068080 WO2023240148A2 (en) | 2022-06-07 | 2023-06-07 | Hybrid flu-coronavirus vaccine |
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| JP2016508133A (en) * | 2012-12-18 | 2016-03-17 | アイカーン スクール オブ メディシン アット マウント サイナイ | Influenza virus vaccine and use thereof |
| WO2021211748A1 (en) * | 2020-04-14 | 2021-10-21 | The Regents Of The University Of California | Pan-coronavirus vaccine compositions |
| EP4185324A1 (en) * | 2020-07-21 | 2023-05-31 | Flugen, Inc. | Vaccine using m2/bm2-deficient influenza vectors |
| US20230330214A1 (en) * | 2020-10-02 | 2023-10-19 | Osaka University | Improved dna vaccine for sars-cov-2 |
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