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

Walia, Rasna R.; Anderson, Tavis K.; Vincent, Amy L.

doi:10.1111/irv.12559

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

Journal Article · 29 January 2019 · Influenza and Other Respiratory Viruses

DOI: https://doi.org/10.1111/irv.12559 · OSTI ID:1625884

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National Animal Disease Center USDA‐ARS Ames IA (United States). Virus and Prion Research Unit; DOE/OSTI
National Animal Disease Center USDA‐ARS Ames IA (United States). Virus and Prion Research Unit

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.

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Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 1625884

Journal Information:: Influenza and Other Respiratory Viruses, Journal Name: Influenza and Other Respiratory Viruses Journal Issue: 3 Vol. 13; ISSN 1750-2640

Country of Publication:: United States

Language:: English

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Effect of strain-specific maternally-derived antibodies on influenza A virus infection dynamics in nursery pigs Chamba Pardo, Fabian Orlando; Wayne, Spencer; Culhane, Marie Rene PLOS ONE, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pone.0210700	journal	January 2019
Bordetella bronchiseptica Colonization Limits Efficacy, but Not Immunogenicity, of Live-Attenuated Influenza Virus Vaccine and Enhances Pathogenesis After Influenza Challenge Hughes, Holly R.; Brockmeier, Susan L.; Loving, Crystal L. Frontiers in Immunology, Vol. 9 https://doi.org/10.3389/fimmu.2018.02255	journal	October 2018
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Influenza A Virus Field Surveillance at a Swine-Human Interface Rambo-Martin, Benjamin L.; Keller, Matthew W.; Wilson, Malania M. mSphere, Vol. 5, Issue 1 https://doi.org/10.1128/msphere.00822-19	journal	February 2020
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