Isolation and characterization of avian influenza viruses in Northern California

Recent human infections with avian influenza viruses (AIV) highlight the need for continued surveillance of AIV in waterfowl. California’s Sacramento Valley is an important wintering site for waterfowl from which avian influenza viruses may be isolated. To determine host correlates of AIV infection and better understand the risk posed by AIV circulating in California, we collected cloacal swabs from 2,066 hunter-killed ducks across four hunting seasons at different locations in the Sacramento Valley. We determined that Northern shovelers have a higher AIV infection rate than other waterfowl species from which we commonly sampled and that the relationship between sex and AIV infection is a poorly understood factor that needs to be investigated on a species level. Additionally, we detected three viruses of the subtype H7N3. Whole genome sequencing of these viruses revealed genetic markers that have been correlated with increased pathogenesis in mammals. All three H7N3 viruses were capable of replication in mammalian cells at levels similar to a human seasonal H1N1 virus. Additionally, at least one of these H7N3 viruses is able to cause disease in mice similarly to a human seasonal H1N1 virus. These results provide insights into host factors of AIV susceptibility that can help guide future surveillance efforts as well as evidence of novel subtype H7N3 with mammalian adaptations that could pose a risk to public health and therefore should be monitored closely.