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

Abstract

Influenza A virus (IAV) is one of the three most frequently detected respiratory pathogens 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, 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.