The genomic evolution of H1 influenza A viruses from swine detected in the United States between 2009 and 2016.

ABSTRACT: Transmission of influenza A virus (IAV) from humans to swine occurs with relative frequency and is a critical contributor to swine IAV diversity. Subsequent to the introduction of these human seasonal lineages, there is often reassortment with endemic viruses and antigenic drift. To address whether particular genome constellations contributed to viral persistence following the introduction of the 2009 H1N1 human pandemic virus to swine in the USA, we collated and analysed 616 whole genomes of swine H1 isolates. For each gene, sequences were aligned, the best-known maximum likelihood phylogeny was inferred, and each virus was assigned a clade based upon its evolutionary history. A time-scaled Bayesian approach was implemented for the haemagglutinin (HA) gene to determine the patterns of gen

SUBMITTER: Gao S 

PROVIDER: S-EPMC5817270 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature