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 informs control efforts and improves animal health. Initiated in 2009, the USDA passively surveils IAV in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing at minimum the hemagglutinin (HA) and neuraminidase (NA) genes, 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. This article is protected by copyright. All rights reserved.