Regional Patterns of Genetic Diversity in Swine Influenza A Viruses in the United States from 2010 to 2016

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.

Walia RR, Anderson TK, Vincent AL; Regional Patterns of Genetic Diversity in Swine Influenza A Viruses in the United States from 2010 to 2016; Influenza Other Respir Viruses. 2018 Apr 6. doi: 10.1111/irv.12559. [Epub ahead of print] PMID: 29624873 DOI: 10.1111/irv.12559
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