Sources and sinks of influenza A virus genomic diversity in swine from 2009 to 2022 in the United States

Abstract

Influenza A virus (IAV) in swine in the U.S. is surveilled to monitor genetic evolution to inform intervention efforts and aid pandemic preparedness. We describe data from the U.S. Department of Agriculture National Surveillance Plan for Influenza A Virus in Pigs from 2009 to 2022. Clinical respiratory cases were subtyped followed by sequencing of hemagglutinin (HA) and neuraminidase (NA), and a subset of viruses were whole genome sequenced. Phylogenetic analysis identified geographic and temporal IAV reassortment hotspots. Regions acting as IAV genomic diversity sources or sinks were quantified, and dissemination was qualified and modeled. The dominant IAV clades were H1N2 (1B.2.1), H3N2 (1990.4.a), and H1N1 (H1-1A.3.3.3-c3). Internal genes were classified as triple-reassortant (T) or pandemic 2009 (P), and three genome constellations represented 73.5% of detections across the last two years. In some years, the distribution of IAV diversity was so narrowly distributed that it presented a statistical signal associated with local adaptation. We also demonstrated that the source of most IAV genomic diversity was in Midwest states (IL, MO, IA), and while this was correlated with swine inventory, the emergence and persistence of diversity was tied to swine transport across the U.S. The continued regional detection of unique HA, NA, and genome constellations provides support for targeted interventions to improve animal health and enhance pandemic preparedness. ImportanceVariation in the genetic diversity of influenza A virus (IAV) in swine through time and between regions impacts control efforts. This study quantified the genomic diversity of swine IAV collected from 2009-2022 at regional and national levels and modeled sources and sinks of that diversity. Seasonal patterns of IAV transmission were observed, and some locations contributed disproportionately to the emergence of genomic diversity. Minor groups of viruses had the potential to disseminate across the U.S. with animal movement. The identification of these patterns demonstrates the importance of a robust surveillance system to inform vaccine updates that reflect regional patterns of genetic diversity. We show how preemptive interventions in swine IAV diversity hubs could reduce reassortment and the emergence of novel genomic diversity, and how these efforts are likely to reduce the transmission of swine IAV within swine and between swine and humans.