Tangential flow ultrafiltration and whole segment amplification to improve avian influenza virus detection in California wetlands

Migratory waterfowl, including geese and ducks, are considered the primary reservoir of avian influenza virus (AIv). The US Department of Agriculture (USDA) surveillance efforts of waterfowl for AIv have been discontinued in the contiguous United States. Consequently, the utilization of new approaches to identify AIvs waterfowl roosting, feeding and nesting environments, is important from a food security perspective. In order to better inform commercial poultry operations in the Central Valley of California, University of California, Davis and the University of Delaware have developed a web application that utilizes various remote sensing technologies to identify waterfowl location and densities. Specifically, by using historic NEXt generation RADar (NEXRAD) data stored on the app, we identified wetlands with high waterfowl density for water sampling via tangential flow ultrafiltration coupled with multi-segment PCR for AIv detection. Our data demonstrate that a combination of filtration, M-RTPCR, and sequencing vastly outperformed standard M-segment qPCR methods producing whole genome segment sequences that provided a detailed characterization of the AIv environmental reservoir. Utilizing a combination of remote sensing and targeted filtration of wetlands coupled to M-RTPCR and sequencing has the potential to be a novel, superior, and cost-effective surveillance approach for AIv.