Environmental sampling and next generation sequencing for influenza A virus surveillance in swine (IAV-S)

Current surveillance systems for IAV-S can be costly and labour-intensive, underscoring the necessity for a non-invasive, population-based approach to enhance pandemic preparedness. We collected swine oral fluids and environmental samples including room-level and human breathing zone air samples and surface swabs in a swine barn from May 2018 to February 2019. All samples were analyzed by real-time polymerase chain reaction (RT-PCR) for the detection of the matrix segment of influenza A virus. A subset of these samples were analyzed using high-throughput sequencing (HTS) to investigate the utility of environmental samples to conduct whole genome analyses of IAV-S.