Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016

BACKGROUND: Regular spatial and temporal analyses of the genetic diversity and evolutionary patterns of influenza A virus (IAV) in swine inform control efforts and improve animal health. Initiated in 2009, the USDA passively surveils IAV in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing the hemagglutinin (HA) and neuraminidase (NA) genes at a minimum, and sharing these data publicly. OBJECTIVES: In this study, our goal was to quantify and describe regional and national patterns in the genetic diversity and evolution of IAV in U.S. swine from 2010 to 2016. METHODS: A comprehensive phylogenetic and epidemiological analysis of publicly available HA and NA genes generated by the USDA surveillance system collected from January 2010 to December 2016 was conducted. RESULTS: The dominant subtypes and genetic clades detected during the study period were H1N1 (H1‐γ/1A.3.3.3, N1‐classical, 29%), H1N2 (H1‐δ1/1B.2.2, N2‐2002, 27%), and H3N2 (H3‐IV‐A, N2‐2002, 15%), but many other minor clades were also maintained. Year‐round circulation was observed, with a primary epidemic peak in October‐November and a secondary epidemic peak in March‐April. Partitioning these data into 5 spatial zones revealed that genetic diversity varied regionally and was not correlated with aggregated national patterns of HA/NA diversity. CONCLUSIONS: These data suggest that vaccine composition and control efforts should consider IAV diversity within swine production regions in addition to aggregated national patterns.