title: Avian influenza at both ends of a migratory flyway: characterizing viral genomic diversity to optimize surveillance plans for North America.
abstract: Although continental populations of avian influenza viruses are genetically distinct, transcontinental reassortment in low pathogenic avian influenza (LPAI) viruses has been detected in migratory birds. Thus, genomic analyses of LPAI viruses could serve as an approach to prioritize species and regions targeted by North American surveillance activities for foreign origin highly pathogenic avian influenza (HPAI). To assess the applicability of this approach, we conducted a phylogenetic and population genetic analysis of 68 viral genomes isolated from the northern pintail (Anas acuta) at opposite ends of the Pacific migratory flyway in North America. We found limited evidence for Asian LPAI lineages on wintering areas used by northern pintails in California in contrast to a higher frequency on breeding locales of Alaska. Our results indicate that the number of Asian LPAI lineages observed in Alaskan northern pintails, and the nucleotide composition of LPAI lineages, is not maintained through fall migration. Accordingly, our data indicate that surveillance of Pacific Flyway northern pintails to detect foreign avian influenza viruses would be most effective in Alaska. North American surveillance plans could be optimized through an analysis of LPAI genomics from species that demonstrate evolutionary linkages with European or Asian lineages and in regions that have overlapping migratory flyways with areas of HPAI outbreaks.
authors.affiliation: Alaska Science Center, U.S. Geological Survey Anchorage, AK, USA.
authors.forename: John M
authors.initials: JM
authors.lastname: Pearce
authors.affiliation: Alaska Science Center, U.S. Geological Survey Anchorage, AK, USA.
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Ramey
authors.affiliation: Alaska Science Center, U.S. Geological Survey Anchorage, AK, USA.
authors.forename: Paul L
authors.initials: PL
authors.lastname: Flint
authors.affiliation: Alaska Science Center, U.S. Geological Survey Anchorage, AK, USA.
authors.forename: Anson V
authors.initials: AV
authors.lastname: Koehler
authors.affiliation: Western Ecological Research Center, U.S. Geological Survey Dixon, CA, USA.
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Fleskes
authors.affiliation: National Wildlife Health Center, U.S. Geological Survey Madison, WI, USA.
authors.forename: J Christian
authors.initials: JC
authors.lastname: Franson
authors.affiliation: National Wildlife Health Center, U.S. Geological Survey Madison, WI, USA.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Hall
authors.affiliation: Alaska Science Center, U.S. Geological Survey Anchorage, AK, USA.
authors.forename: Dirk V
authors.initials: DV
authors.lastname: Derksen
authors.affiliation: National Wildlife Health Center, U.S. Geological Survey Madison, WI, USA.
authors.forename: Hon S
authors.initials: HS
authors.lastname: Ip
keywords: avian influenza; genetic; low pathogenic; migration; northern pintail; virus; waterfowl