title: Long-term surveillance of H7 influenza viruses in American wild aquatic birds: are the H7N3 influenza viruses in wild birds the precursors of highly pathogenic strains in domestic poultry?
abstract: The emergence of influenza A virus (IAV) in domestic avian species and associated transmissions to mammals is unpredictable. In the Americas, the H7 IAVs are of particular concern, and there have been four separate outbreaks of highly pathogenic (HP) H7N3 in domestic poultry in North and South America between 2002 and 2012, with occasional spillover into humans. Here, we use long-term IAV surveillance in North American shorebirds at Delaware Bay, USA, from 1985 to 2012 and in ducks in Alberta, Canada, from 1976 to 2012 to determine which hemagglutinin (HA)-neuraminidase (NA) combinations predominated in Anseriformes (ducks) and Charadriiformes (shorebirds) and whether there is concordance between peaks of H7 prevalence and transmission in wild aquatic birds and the emergence of H7 IAVs in poultry and humans. Whole-genome sequencing supported phylogenetic and genomic constellation analyses to determine whether HP IAVs emerge in the context of specific internal gene segment sequences. Phylogenetic analysis of whole-genome sequences of the H7N3 influenza viruses from wild birds and HP H7N3 outbreaks in the Americas indicate that each HP outbreak was an independent emergence event and that the low pathogenic (LP) avian influenza precursors were most likely from dabbling ducks. The different polybasic cleavage sites in the four HP outbreaks support independent origins. At the 95% nucleotide percent identity-level phylogenetic analysis showed that the wild duck HA, PB1, and M sequences clustered with the poultry and human outbreak sequences. The genomic constellation analysis strongly suggests that gene segments/virus flow from wild birds to domestic poultry.
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Krauss
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.
authors.forename: Karla M
authors.initials: KM
authors.lastname: Stucker
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.|Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
authors.forename: Seth A
authors.initials: SA
authors.lastname: Schobel
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: Danner
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Friedman
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Knowles
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: Ghazi
authors.initials: G
authors.lastname: Kayali
authors.affiliation: Conserve Wildlife Foundation of New Jersey, Bordentown, NJ 08505, USA.
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: Niles
authors.affiliation: Endangered and Nongame Species, New Jersey Division of Fish and Wildlife, Trenton, NJ 08332, USA.
authors.forename: Amanda D
authors.initials: AD
authors.lastname: Dey
authors.affiliation: Environment Canada, Canadian Wildlife Service, Edmonton T6B 1K5, AB, Canada.
authors.forename: Garnet
authors.initials: G
authors.lastname: Raven
authors.affiliation: Environment Canada, Canadian Wildlife Service, Edmonton T6B 1K5, AB, Canada.
authors.forename: Paul
authors.initials: P
authors.lastname: Pryor
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.
authors.forename: Xudong
authors.initials: X
authors.lastname: Lin
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.
authors.forename: Suman R
authors.initials: SR
authors.lastname: Das
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.affiliation: J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.affiliation: St. Jude Children's Research Hospital, Department of Infectious Diseases, Memphis, TN 38105, USA.
authors.forename: Robert G
authors.initials: RG
authors.lastname: Webster
mesh_terms: D000416:Alberta / Q000453:epidemiology; D000818:Animals; D000829:Animals, Domestic; D000835:Animals, Wild; D046090:Anseriformes; D001715:Bird Diseases / Q000453:epidemiology*; D001717:Birds; D046091:Charadriiformes; D003691:Delaware / Q000453:epidemiology; D004196:Disease Outbreaks / Q000662:veterinary*; D004372:Ducks; D062665:Epidemiological Monitoring; D006801:Humans; D057920:Influenza A Virus, H7N3 Subtype / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology*; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology*; D017422:Sequence Analysis, DNA