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.
Keywords: genetic diversity; influenza A virus; molecular epidemiology; regional diversity; seasonality; swine.
Published 2018. This article is a U.S. Government work and is in the public domain in the USA. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.