Location: Virus and Prion ResearchTitle: Regional Patterns of Genetic Diversity in Swine Influenza A Viruses in The United States From 2010 to 2016
Submitted to: Influenza and Other Respiratory Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2018
Publication Date: 4/6/2018
Citation: Walia, R.R., Anderson, T.K., Vincent, A.L. 2018. Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016. Influenza and Other Respiratory Viruses. https://doi.org/10.1111/irv.12559.
Interpretive Summary: Understanding the genetic diversity and patterns of influenza A viruses (IAV) evolution in the swine population is critical for controlling this important pathogen. This study quantified the genetic diversity of swine IAV collected from 2010-2016 at regional and national levels. Seasonal patterns of transmission of swine IAV were observed, and genetic diversity within certain regions was different than the overall national pattern. Minor variants were underreported in the global dataset, but when considered in a regional context, were important long-term components of observed diversity. The identification of these patterns demonstrates the importance of a robust surveillance system for swine IAV that includes representation from all swine production regions to inform control measures taken against IAV. Timely vaccine updates that reflect regional patterns of genetic diversity may help reduce infection and transmission and improve animal health and wellbeing. Our study has the potential to inform vaccine development to better control transmission of swine IAV within swine hosts and between swine and humans.
Technical Abstract: To inform intervention efforts and improve animal health, regular spatial and temporal analysis of the genetic diversity and evolutionary patterns of influenza A virus (IAV) in swine is required. Initiated in 2009, the USDA passively surveils IAV in U.S. swine, with a focus on subtyping clinical respiratory submissions, sequencing the hemagglutinin (HA), matrix (M), and neuraminidase (NA) genes, and sharing these data in public databases. To understand regional and national patterns of IAV in U.S. swine, we characterized genetic diversity by comprehensive phylogenetic analysis of publicly available HA, NA, and M genes generated from the USDA surveillance system collected from January 2010 to December 2016. Viral isolates were categorized into established genetic HA and NA clades: the dominant subtypes and clades detected during the study period were H1N1 (H1-gamma, N1-classical, 29%), H1N2 (H1-delta1, N2-2002, 27%), and H3N2 (H3-IV-A, N2-2002, 15%) and the vast majority of M genes were of H1N1pdm09 origin. Year-round circulation of all subtypes 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 across the United States and within region diversity was not correlated with a national summary of HA/NA diversity. These data suggest that regional and zonal patterns should be considered in addition to the aggregated national measures of genetic diversity for vaccine composition and control efforts, and that these patterns of swine IAV genetic diversity are likely driven by local ecological and/or immunological factors.