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

Influenza A virus (IAV) is one of the most frequently detected respiratory pathogens in swine. A passive surveillance system in the United States (U.S.) provides aggregated 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 how fine-scale variation affects IAV transmission, we conducted active surveillance on sow farms and linked nurseries from 4 U.S. production flows for up to 14 months. 85 complete HA sequences and 62 whole genomes with associated epidemiological information were generated. We conducted phylodynamic analyses and detected six genetic clades from four HA lineages: H1 1A classical swine, H1 1B human-seasonal, and H3 2010.1 and 1990.4. The H1 1B and H3 1990.4 showed evidence of transmission from sow farm to nursery. The H1 1A and H3 2010.1 viruses were detected in nurseries without a linked sow farm detection. Seven separate human-to-swine transmission events in the H1N1 pandemic clade (1A.3.3.2) in sow and nursery sites were identified. Nursery sites were infected with IAV that was both linked and unlinked to the sow farm. Control efforts may be impacted by subclinical IAV transmission in the breeding herd, the 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, thereby minimizing the opportunity for novel reassorted viruses to emerge and impact animal health.