Submitted to: Journal of General Virology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/19/2010
Publication Date: 4/1/2011
Citation: Lorusso, A., Vincent, A.L., Harland, M.L., Alt, D., Bayles, D.O., Swenson, S.L., Gramer, M.R., Russel, C.A., Smith, D.J., Lager, K.M., Lewis, N.S. 2011. Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008. Journal of General Virology. 92(Pt 4):919-930. Interpretive Summary: 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 alpha-, beta-, and gamma-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 delta-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 analysis of all eight gene segments and by serum antibody 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 study also revealed that the 2008 viruses characterized from U.S. swine were genetically distinct from the 2009 human pandemic H1N1, suggesting the 6 gene segments related to North American swine viruses found in the pandemic virus were not circulating in the U.S. swine population for some time prior to the pandemic.
Technical Abstract: Swine play an important role in the evolution of influenza A viruses. Prior to the introduction of the 2009 pandemic H1N1 virus from humans into pigs, four phylogenetic clusters of the hemagglutinin (HA) gene from H1 influenza viruses could be found in U.S. swine. Viruses from the classical H1N1 swine lineage evolved to form alpha-, beta-, and gamma-clusters whereas viruses with HA genes most similar to human seasonal H1 viruses emerged in 2003 to form the delata-cluster. Limited sequence information was available regarding the six genes that make up the triple reassortant internal gene (TRIG) cassette in contemporary H1 influenza viruses of swine. In addition, information regarding the antigenic relatedness of the H1 viruses was lacking due to the dynamic and variable nature of swine lineage H1. We characterized twelve 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. Based on genetic analysis, each of the four previously described phylogenetic clusters of H1 influenza viruses of swine were represented in the 2008 panel. Additionally, it was demonstrated that the delta-cluster HA were sub-divided into sub-clusters delta1 and delta2. Genetic diversity was demonstrated in all gene segments, but most notably in the HA gene. The genetic evolution of the NA gene was compatible to that of the HA gene. The gene segments from the 2009 pandemic H1N1 formed clusters separate from North American swine lineage viruses, suggesting progenitors of the pandemic virus were not present in U.S. pigs immediately prior to 2009. Serologic cross-reactivity paired with antigenic cartography demonstrated that the viruses in the different phylogenetic clusters are also antigenically divergent.