Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades

Authors: THOMAS, MEGAN - Iowa State University; JANZEN, GARRETT - Oak Ridge Institute For Science And Education (ORISE); MARKIN, ALEXEY - Iowa State University; SHARMA, ADITI - Iowa State University; HEWITT, KELLY - Iowa State University; LI, GANWU - Iowa State University; Baker, Amy; GAUGER, PHILLIP - Iowa State University; Anderson, Tavis

Submitted to: Veterinary Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/11/2025
Publication Date: 8/15/2025
Citation: Thomas, M.N., Janzen, G.M., Markin, A., Sharma, A., Hewitt, K., Li, G., Baker, A.L., Gauger, P.C., Anderson, T.K. 2025. Active surveillance for influenza A virus in swine reveals within-farm reassortment and cocirculation of distinct subtypes and genetic clades. Veterinary Microbiology. https://doi.org/10.1016/j.vetmic.2025.110681.
DOI: https://doi.org/10.1016/j.vetmic.2025.110681

Interpretive Summary: The United States has a passive surveillance system for influenza A virus (IAV) in swine that has been used to measure and determine changes in genetic diversity at a national level. Despite the utility of these data for determining general trends in IAV diversity, they may not directly apply to farm-level intervention efforts as information is aggregated to a state level. Specifically, the primary prevention strategy for IAV in swine is vaccination using strains that match the diversity currently circulating in that farm. In this study, we used farm-level active surveillance to quantify genetic diversity, characterize transmission, and identify farm-specific factors that affect IAV detection and diversity. This study highlighted how the connectivity between the multiple stages in modern swine production influenced the detection, persistence, and diversity of IAV in pigs within the farm. There were 3 to 5 distinct genetic groups of viruses co-circulating within a single farm. Mixing of the gene segments of these strains through reassortment formed novel combinations. Farm-level management factors and the transmission of human seasonal IAV to swine via agricultural workers also impacted the frequency and observed genetic diversity of IAV within a farm. These data suggest that active surveillance of multiple stages of swine production (mother pigs, piglets, growing pigs) provides an approach that can detect significant changes in the diversity of IAV. Vaccines matched to the genetic diversity of IAV on farms can best be achieved through a combination of active surveillance and sampling of clinically ill pigs in the passive surveillance system.

Technical Abstract: Influenza A virus (IAV) is one of the three most frequently detected causes of respiratory disease in swine. A passive IAV in swine surveillance system in the United States (U.S.) provides aggregated national metrics to quantify spatial and temporal changes in genetic diversity. However, swine production is not homogenous: production systems vary in size and management strategies that affect the transmission and evolution of IAV. To assess the impact of fine-scale variation in swine production on IAV transmission, we conducted active surveillance on sow farms and linked nurseries from 4 U.S. production systems for up to 14 monthly collections. From IAV-positive samples, we obtained 85 complete HA sequences, and of these, we successfully assembled 62 whole genomes with associated epidemiological information. To infer transmission and evolution, we conducted Bayesian phylodynamic analyses and detected six genetic clades from four HA lineages: the H1 1A classical swine, the H1 1B human-seasonal, and the H3 2010.1 and 1990.4 lineages. The 1B and H3 1990.4 strains showed evidence of transmission from sow farm to nursery. In contrast, 1A and H3 2010.1 viruses were detected in nurseries without detection in a linked sow farm. We also detected seven separate human-to-swine transmission events in the H1N1 pandemic clade (1A.3.3.2) in sow and nursery sites. Our data demonstrated that nursery sites were infected with IAV that was both linked and unlinked to the sow farm. These data suggest that control efforts may be impacted by subclinical IAV transmission in the breeding herd, mixing of sow farm sources at the nursery, regional spread of new strains, and human-to-swine transmission. Regular surveillance activities within production systems provide the ability to match vaccine components to circulating diversity, minimizing the opportunity for novel reassorted viruses to emerge and impact animal health.