Ecological shifts in avian influenza viruses following HPAIV introductions in southwestern Alaska, 2011-2024

Southwestern Alaska wetlands are critical staging habitats for migratory waterfowl that breed in western North America and East Asia. Since 2011, samples originating from hunter-harvested waterfowl and environmental feces have been collected annually in and around Izembek National Wildlife Refuge, Alaska to assess the occurrence, evolution, and spread of avian influenza viruses (AIVs). Viruses from wild birds inhabiting this region have consistently been detected, and frequent intercontinental viral dispersal has been observed. In 2014 and 2022, H5 subtype highly pathogenic avian influenza viruses (HPAIVs) were detected in the Pacific Flyway of North America, which may have been influenced by the genetic and antigenic diversity of low pathogenicity avian influenza viruses (LPAIVs) circulating among migratory birds at the time. Conversely, the introduction of HPAIVs may have altered the ecology of co-circulating LPAIVs among wild aquatic bird hosts. To assess these ecological interactions, we examined long-term patterns in LPAIV and HPAIV occurrence and diversity, focusing on changes associated with HPAI introduction events. During 14 years of surveillance for AIVs, virus prevalence peaked during periods of HPAIV introduction. Reassortment between HPAIVs and LPAIVs generated novel HPAIV genotypes and one LPAIV incorporating a HPAIV gene segment. The proportion of Eurasian-lineage gene segments increased following introduction of HPAIVs in 2022. This long-term dataset highlights the changing ecology of LPAIVs and HPAIVs among wild birds at one of North America's most consistently sampled active surveillance sites for AIVs.