Prevalence of Influenza A Viruses in Ducks Sampled in Northwestern Minnesota and Evidence for Predominance of H3N8 and H4N6 Subtypes in Mallards, 2007-2016.

Long-term comprehensive studies of avian influenza virus subtypes in ducks not only contribute to understanding variations and patterns of subtype diversity, but also can be important in defining seasonal and temporal risks associated with transmission of potentially highly pathogenic H5 and H7 subtypes to domestic poultry. We analyzed influenza A virus (IAV) surveillance data from dabbling ducks collected at an important migratory stopover site in northwestern Minnesota from 2007-2016 and identified prevalence and subtype diversity throughout this period. In total, 13,228 cloacal and oropharyngeal swabs from waterfowl were tested over the 10-year period; the majority of these waterfowl were mallards sampled from late August through late September ( = 9133). From these, 1768 IAVs were isolated (19.4% mean annual prevalence, ranging from 11.0% in 2007 to 32.8% in 2011), and both hemagglutinin (HA) and neuraminidase were identified for 1588. Although subtype diversity and prevalence varied by year, H3 and H4 HA subtypes predominated in all years, accounting for 65.7% of the observed HA subtype diversity. The mechanisms driving this consistent pattern of subtype diversity and predominance are not understood but may include factors at the host, population, and virus level.