Antigenic and genetic diversity of H1 and H3 influenza A viruses in swine in Brazil

BackgroundInfluenza A virus (IAV) circulates within human and swine populations, and pigs are considered intermediate hosts for the generation of IAV with pandemic potential. Surveillance and characterization of IAVs circulating in pig populations are crucial to strain match vaccines to control IAV transmission in pigs and quantify pandemic potential to humans. MethodsHere, we characterized the genetic and antigenic diversity of IAVs circulating in Brazilian swine between 2010-2018. Phylogenetic maximum-likelihood trees were generated for 84 Brazilian hemagglutinin (HA) gene segments. Hemagglutination inhibition (HI) assay data was used with antigenic cartography to quantify the antigenic differences among representative H1 and H3 swine viruses and relative cross-reactivity between these viruses and human seasonal vaccine strains. ResultsWe identified two genetic lineages of H1 viruses derived from separate human-to-swine transmission events (H1 1B lineage, clades 1B.2.3 and 1B.2.4), an H3 lineage that has diversified into two genetic clades (H3 1990.5.1 and 1990.5.2), and HA genes associated with the 2009 H1N1 pandemic. There was limited cross-reactivity between circulating swine lineages and significant antigenic variation within lineage. ConclusionsThe antigenic diversity among endemic IAV in swine indicates a need for regional strain-specific vaccination strategies in Brazil. Our data supports the need for systematic genomic surveillance and characterization in Brazil to improve the efficacy of swine vaccines and quantify the pandemic potential of endemic swine influenza A viruses.