Influenza a Virus Detection at the Human–Swine Interface in US Midwest Swine Farms

Abstract

This study evaluated influenza A virus (IAV) detection and genetic diversity over time, specifically at the human–swine interface in breeding and nursery farms. Active surveillance was performed monthly in five swine farms in the Midwest United States targeting the employees, the prewean piglets at sow farms, and the same cohort of piglets in downstream nurseries. In addition, information was collected at enrollment for each employee and farm to assess production management practices, IAV vaccination status, diagnostic procedures, and biosecurity. Farm employee and swine samples were screened by IAV reverse transcription real-time polymerase chain reaction (RT-rtPCR), followed by IAV subtyping RT-rtPCR and whole genome sequencing on PCR-positive samples. This study showed higher positivity of IAV RNA detection in nursery pigs compared to prewean pigs, and more whole genome sequences were also obtained in the nursery phase. Surveillance of farm employees revealed two detections of H3N2 representing the 2022–2023 human IAV season, confirming the presence of influenza in farm employees while present at work, and thus highlighting the importance of biosecurity measures at the human–swine interface. This study highlights the importance of routine active surveillance to understand the dynamics of IAV at the farm level in both farm employees and swine.