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Genotype patterns of contemporary reassorted H3N2 virus in U.S. swine

Pravina Kitikoon, Martha I. Nelson, Mary Lea Killian, Tavis K. Anderson, Leo Koster, Marie R. Culhane, Amy L. Vincent
Journal of general virology 2013 v.94 no.Pt 6 pp. 1236-1241
Influenza A virus, antigenic variation, cross reaction, genotype, humans, mutation, phylogeny, swine, vertebrate viruses, United States
To understand the evolution of swine-origin H3N2v influenza viruses that have infected 320 humans in the USA since August 2011, we performed a phylogenetic analysis at a whole genome scale of North American swine influenza viruses (n = 200). All viral isolates evolved from the prototypical North American H3 cluster 4 (c4), with evidence for further diversification into subclusters. At least ten distinct reassorted H3N2/pandemic H1N1 (rH3N2p) genotypes were identified in swine. Genotype 1 (G1) was most frequently detected in swine and all human H3N2v viruses clustered within a single G1 clade. These data suggest that the genetic requirements for transmission to humans may be restricted to a specific subset of swine viruses. Mutations at putative antigenic sites as well as reduced serological cross-reactivity among the H3 subclusters suggest antigenic drift of these contemporary viruses.