Identification of SARS-CoV-2 CTL epitopes for development of a multivalent subunit vaccine for COVID-19. 2021

Clayton Fernando Rencilin, and Joseph Christina Rosy, and Manikandan Mohan, and Richard Coico, and Krishnan Sundar
Department of Biotechnology, School of Bio and Chemical Engineering, Kalasalingam Academy of Research and Education, Krishnankoil 626126, Tamil Nadu, India.

An immunoinformatics-based approach was used to identify potential multivalent subunit CTL vaccine candidates for SARS-CoV-2. Criteria for computational screening included antigen processing, antigenicity, allergenicity, and toxicity. A total of 2604 epitopes were found to be strong binders to MHC class I molecules when analyzed using IEDB tools. Further testing for antigen processing yielded 826 peptides of which 451 were 9-mers that were analyzed for potential antigenicity. Antigenic properties were predicted for 102 of the 451 peptides. Further assessment for potential allergenicity and toxicity narrowed the number of candidate CTL epitopes to 50 peptide sequences, 45 of which were present in all strains of SARS-CoV-2 that were tested. The predicted CTL epitopes were then tested to eliminate those with MHC class II binding potential, a property that could induce hyperinflammatory responses mediated by TH2 cells in immunized hosts. Eighteen of the 50 epitopes did not show class II binding potential. To our knowledge this is the first comprehensive analysis on the proteome of SARS-CoV-2 for prediction of CTL epitopes lacking binding properties that could stimulate unwanted TH2 responses. Future studies will be needed to assess these epitopes as multivalent subunit vaccine candidates which stimulate protective CTL responses against SARS-COV-2.

UI MeSH Term Description Entries
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000071497 Immunogenicity, Vaccine The capacity of VACCINES to stimulate the ADAPTIVE IMMUNE RESPONSE to produce antibodies and antigen-specific T-CELL responses. It is typically measured in vaccinated individuals in observational studies setting. Antigenicity, Vaccine,Vaccine Antigenicity,Vaccine Immunogenicity
D000086382 COVID-19 A viral disorder generally characterized by high FEVER; COUGH; DYSPNEA; CHILLS; PERSISTENT TREMOR; MUSCLE PAIN; HEADACHE; SORE THROAT; a new loss of taste and/or smell (see AGEUSIA and ANOSMIA) and other symptoms of a VIRAL PNEUMONIA. In severe cases, a myriad of coagulopathy associated symptoms often correlating with COVID-19 severity is seen (e.g., BLOOD COAGULATION; THROMBOSIS; ACUTE RESPIRATORY DISTRESS SYNDROME; SEIZURES; HEART ATTACK; STROKE; multiple CEREBRAL INFARCTIONS; KIDNEY FAILURE; catastrophic ANTIPHOSPHOLIPID ANTIBODY SYNDROME and/or DISSEMINATED INTRAVASCULAR COAGULATION). In younger patients, rare inflammatory syndromes are sometimes associated with COVID-19 (e.g., atypical KAWASAKI SYNDROME; TOXIC SHOCK SYNDROME; pediatric multisystem inflammatory disease; and CYTOKINE STORM SYNDROME). A coronavirus, SARS-CoV-2, in the genus BETACORONAVIRUS is the causative agent. 2019 Novel Coronavirus Disease,2019 Novel Coronavirus Infection,2019-nCoV Disease,2019-nCoV Infection,COVID-19 Pandemic,COVID-19 Pandemics,COVID-19 Virus Disease,COVID-19 Virus Infection,Coronavirus Disease 2019,Coronavirus Disease-19,SARS Coronavirus 2 Infection,SARS-CoV-2 Infection,Severe Acute Respiratory Syndrome Coronavirus 2 Infection,COVID19,2019 nCoV Disease,2019 nCoV Infection,2019-nCoV Diseases,2019-nCoV Infections,COVID 19,COVID 19 Pandemic,COVID 19 Virus Disease,COVID 19 Virus Infection,COVID-19 Virus Diseases,COVID-19 Virus Infections,Coronavirus Disease 19,Disease 2019, Coronavirus,Disease, 2019-nCoV,Disease, COVID-19 Virus,Infection, 2019-nCoV,Infection, COVID-19 Virus,Infection, SARS-CoV-2,Pandemic, COVID-19,SARS CoV 2 Infection,SARS-CoV-2 Infections,Virus Disease, COVID-19,Virus Infection, COVID-19
D000086663 COVID-19 Vaccines Vaccines or candidate vaccines containing SARS-CoV-2 component antigens, genetic materials, or inactivated SARS-CoV-2 virus, and designed to prevent COVID-19. 2019 Novel Coronavirus Vaccine,2019 Novel Coronavirus Vaccines,2019-nCoV Vaccine,2019-nCoV Vaccines,COVID 19 Vaccine,COVID-19 Vaccine,COVID-19 Virus Vaccine,COVID-19 Virus Vaccines,COVID19 Vaccine,COVID19 Vaccines,COVID19 Virus Vaccine,COVID19 Virus Vaccines,Coronavirus Disease 2019 Vaccine,Coronavirus Disease 2019 Vaccines,Coronavirus Disease 2019 Virus Vaccine,Coronavirus Disease 2019 Virus Vaccines,Coronavirus Disease-19 Vaccine,Coronavirus Disease-19 Vaccines,SARS Coronavirus 2 Vaccines,SARS-CoV-2 Vaccine,SARS-CoV-2 Vaccines,SARS2 Vaccine,SARS2 Vaccines,2019 nCoV Vaccine,2019 nCoV Vaccines,COVID 19 Vaccines,COVID 19 Virus Vaccine,COVID 19 Virus Vaccines,Coronavirus Disease 19 Vaccine,Coronavirus Disease 19 Vaccines,SARS CoV 2 Vaccine,SARS CoV 2 Vaccines,Vaccine, 2019-nCoV,Vaccine, COVID 19,Vaccine, COVID-19,Vaccine, COVID-19 Virus,Vaccine, COVID19,Vaccine, COVID19 Virus,Vaccine, Coronavirus Disease-19,Vaccine, SARS-CoV-2,Vaccine, SARS2,Vaccines, 2019-nCoV,Vaccines, COVID-19,Vaccines, COVID-19 Virus,Vaccines, COVID19,Vaccines, COVID19 Virus,Vaccines, Coronavirus Disease-19,Vaccines, SARS-CoV-2,Vaccines, SARS2,Virus Vaccine, COVID-19,Virus Vaccine, COVID19,Virus Vaccines, COVID-19,Virus Vaccines, COVID19
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000949 Histocompatibility Antigens Class II Large, transmembrane, non-covalently linked glycoproteins (alpha and beta). Both chains can be polymorphic although there is more structural variation in the beta chains. The class II antigens in humans are called HLA-D ANTIGENS and are coded by a gene on chromosome 6. In mice, two genes named IA and IE on chromosome 17 code for the H-2 antigens. The antigens are found on B-lymphocytes, macrophages, epidermal cells, and sperm and are thought to mediate the competence of and cellular cooperation in the immune response. The term IA antigens used to refer only to the proteins encoded by the IA genes in the mouse, but is now used as a generic term for any class II histocompatibility antigen. Antigens, Immune Response,Class II Antigens,Class II Histocompatibility Antigen,Class II Major Histocompatibility Antigen,Ia Antigens,Ia-Like Antigen,Ia-Like Antigens,Immune Response Antigens,Immune-Associated Antigens,Immune-Response-Associated Antigens,MHC Class II Molecule,MHC II Peptide,Class II Antigen,Class II Histocompatibility Antigens,Class II MHC Proteins,Class II Major Histocompatibility Antigens,Class II Major Histocompatibility Molecules,I-A Antigen,I-A-Antigen,IA Antigen,MHC Class II Molecules,MHC II Peptides,MHC-II Molecules,Antigen, Class II,Antigen, I-A,Antigen, IA,Antigen, Ia-Like,Antigens, Class II,Antigens, Ia,Antigens, Ia-Like,Antigens, Immune-Associated,Antigens, Immune-Response-Associated,I A Antigen,II Peptide, MHC,Ia Like Antigen,Ia Like Antigens,Immune Associated Antigens,Immune Response Associated Antigens,MHC II Molecules,Molecules, MHC-II,Peptide, MHC II,Peptides, MHC II
D013602 T-Lymphocytes, Cytotoxic Immunized T-lymphocytes which can directly destroy appropriate target cells. These cytotoxic lymphocytes may be generated in vitro in mixed lymphocyte cultures (MLC), in vivo during a graft-versus-host (GVH) reaction, or after immunization with an allograft, tumor cell or virally transformed or chemically modified target cell. The lytic phenomenon is sometimes referred to as cell-mediated lympholysis (CML). These CD8-positive cells are distinct from NATURAL KILLER CELLS and NATURAL KILLER T-CELLS. There are two effector phenotypes: TC1 and TC2. Cell-Mediated Lympholytic Cells,Cytotoxic T Cells,Cytotoxic T Lymphocyte,Cytotoxic T-Lymphocytes,TC1 Cell,TC1 Cells,TC2 Cell,TC2 Cells,Cell Mediated Lympholytic Cells,Cell, Cell-Mediated Lympholytic,Cell, TC1,Cell, TC2,Cell-Mediated Lympholytic Cell,Cytotoxic T Cell,Cytotoxic T Lymphocytes,Cytotoxic T-Lymphocyte,Lymphocyte, Cytotoxic T,Lympholytic Cell, Cell-Mediated,Lympholytic Cells, Cell-Mediated,T Cell, Cytotoxic,T Lymphocyte, Cytotoxic,T Lymphocytes, Cytotoxic,T-Lymphocyte, Cytotoxic
D015395 Histocompatibility Antigens Class I Membrane glycoproteins consisting of an alpha subunit and a BETA 2-MICROGLOBULIN beta subunit. In humans, highly polymorphic genes on CHROMOSOME 6 encode the alpha subunits of class I antigens and play an important role in determining the serological specificity of the surface antigen. Class I antigens are found on most nucleated cells and are generally detected by their reactivity with alloantisera. These antigens are recognized during GRAFT REJECTION and restrict cell-mediated lysis of virus-infected cells. Class I Antigen,Class I Antigens,Class I Histocompatibility Antigen,Class I MHC Protein,Class I Major Histocompatibility Antigen,MHC Class I Molecule,MHC-I Peptide,Class I Histocompatibility Antigens,Class I Human Antigens,Class I MHC Proteins,Class I Major Histocompatibility Antigens,Class I Major Histocompatibility Molecules,Human Class I Antigens,MHC Class I Molecules,MHC-I Molecules,MHC-I Peptides,Antigen, Class I,Antigens, Class I,I Antigen, Class,MHC I Molecules,MHC I Peptide,MHC I Peptides,Molecules, MHC-I,Peptide, MHC-I,Peptides, MHC-I
D017778 Vaccines, Combined Two or more vaccines in a single dosage form. Bivalent Vaccine,Bivalent Vaccines,Combined Vaccine,Combined Vaccines,Decavalent Vaccine,Decavalent Vaccines,Heptavalent Vaccine,Heptavalent Vaccines,Hexavalent Vaccine,Hexavalent Vaccines,Multivalent Vaccine,Multivalent Vaccines,Nonavalent Vaccine,Nonavalent Vaccines,Octavalent Vaccine,Octavalent Vaccines,Pentavalent Vaccine,Pentavalent Vaccines,Polyvalent Vaccine,Polyvalent Vaccines,Quadrivalent Vaccine,Quadrivalent Vaccines,Tetravalent Vaccine,Tetravalent Vaccines,Vaccines, Multivalent,Vaccines, Polyvalent,Vaccines, Combination,Combination Vaccines,Vaccine, Bivalent,Vaccine, Combined,Vaccine, Decavalent,Vaccine, Heptavalent,Vaccine, Hexavalent,Vaccine, Multivalent,Vaccine, Nonavalent,Vaccine, Octavalent,Vaccine, Pentavalent,Vaccine, Polyvalent,Vaccine, Quadrivalent,Vaccine, Tetravalent,Vaccines, Bivalent,Vaccines, Decavalent,Vaccines, Heptavalent,Vaccines, Hexavalent,Vaccines, Nonavalent,Vaccines, Octavalent,Vaccines, Pentavalent,Vaccines, Quadrivalent,Vaccines, Tetravalent
D062105 Molecular Docking Simulation A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein. Molecular Docking,Molecular Docking Simulations,Molecular Docking Analysis,Analysis, Molecular Docking,Docking Analysis, Molecular,Docking Simulation, Molecular,Docking, Molecular,Molecular Docking Analyses,Molecular Dockings,Simulation, Molecular Docking

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