title: Potential T cell epitopes within swine-origin triple reassortant influenza A (H3N2) variant virus which emerged in 2011: an immunoinformatics study.
abstract: An immuno-informatics study was conducted to determine possible pre-existing T cellular immunity to the recently emerged swine-origin triple reassortant H3N2 variant (S-OtrH3N2v-2011) which acquired the matrix gene of influenza A (H1N1)pdm09. Given the genetic origin of S-OtrH3N2v-2011, our study focused on the hemagglutinin (HA) and matrix1 (M1) proteins to identify common and conserved T cell epitopes. We compared HA CD4+ T cell epitopes of S-OtrH3N2v-2011 with seasonal H3N2 (1968-2011)-HA proteins. M1 CD4+ and CD8+ T cell epitopes of S-OtrH3N2v-2011 were compared with the M1 proteins of seasonal H1N1 (1977-2009) and A (H1N1)pdm09 (2009-2011) subtypes. The results revealed a high conservancy of epitopes localized particularly on HA2 and the entire M1 protein. The overall cross reactivity of predicted CD4+ T cell epitopes with previously experimentally defined (Immuno Epitope Database) CD4+ T epitopes of HA and M1 proteins was ∼51%. CD8+ T cell cross-reactivity of ∼74% was documented for M1 protein. Analysis suggests possible pre-existing CD4+ T cell immunity to S-OtrH3N2v-2011 in the human population.
authors.affiliation: Ontario Agency for Health Protection and Promotion, Toronto, Ontario, Canada; Mount Sinai Hospital, Toronto, Ontario, Canada.
authors.forename: Venkata R
authors.initials: VR
authors.lastname: Duvvuri
authors.forename: Alex
authors.initials: A
authors.lastname: Marchand-Austin
authors.forename: Alireza
authors.initials: A
authors.lastname: Eshaghi
authors.forename: Samir N
authors.initials: SN
authors.lastname: Patel
authors.forename: Donald E
authors.initials: DE
authors.lastname: Low
authors.forename: Jonathan B
authors.initials: JB
authors.lastname: Gubbay
mesh_terms: D000595:Amino Acid Sequence; D015496:CD4-Positive T-Lymphocytes / Q000276:immunology; D019295:Computational Biology; D017124:Conserved Sequence; D003429:Cross Reactions / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000276:immunology*; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics / Q000276:immunology*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics / Q000276:immunology*; D016865:Reassortant Viruses / Q000235:genetics / Q000276:immunology*; D017386:Sequence Homology, Amino Acid; D014763:Viral Matrix Proteins / Q000235:genetics / Q000276:immunology*
chemical_list: D018984:Epitopes, T-Lymphocyte; D019267:Hemagglutinin Glycoproteins, Influenza Virus; C488936:M1 protein, Influenza A virus; D014763:Viral Matrix Proteins