Influenza A viruses can infect swine, humans, dogs, cats, horses, marine mammals, and many avian species. Influenza A viruses from all host species are classified into subtypes based on the hemagglutinin (HA) and neuraminidase (NA) genes, for example H3N2 or H1N1. Along with the HA and NA genes, influenza A viruses contain 6 additional genes necessary for virus infection and replication. Prior to the introduction of the 2009 pandemic H1N1 virus from human to pigs, four distinct clusters of the HA gene from H1 swine influenza viruses (SIV) co-circulated along with H3N2 viruses in the U.S. Viruses from the classical H1N1 SIV lineage evolved over time to form α-, β-, and γ-clusters based on the genetic makeup of the HA gene. SIV with HA genes most similar to human seasonal H1 viruses emerged in pigs in 2003 to form the δ-cluster. All four HA cluster gene types can be found with neuraminidase genes of either the N1 or N2 subtype. Limited sequence information was available regarding the 6 genes that make up the triple reassortant internal gene (TRIG) cassette in contemporary H1 SIV. In addition, information regarding the antigenic relatedness of the H1 viruses necessary for vaccine development and diagnostic reagent updates were in need due to the dynamic and variable nature of H1 SIV. We characterized 12 H1 isolates from 2008 by sequencing and phylogenetic analysis of all eight gene segments and by serologic cross-reactivity in the hemagglutination inhibition (HI) assay. This study provides information on the level of diversity of each gene segment in 2008 U.S. isolates as well as information necessary to make informed vaccine strain selection and diagnostic reagent updates. This data also revealed that the 2008 viruses characterized from U.S. swine were genetically distinct from the 2009 human pandemic H1N1.

Contact: Amy L. Vincent, DVM PhD; 2823 Virus and Prion Diseases Research Unit, USDA-ARS, National Animal Disease Center, 1920 Dayton Avenue, Ames, IA 50010 USA: email: [email protected], phone: 515-337-7557""