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United States Department of Agriculture

Agricultural Research Service

Title: The evolutionary genetics and emergence of avian influenza viruses in wild birds

item Dugan, Vivien
item Chen, Rubing
item Spiro, David
item Sengamalay, Naomi
item Zaborsky, Jennifer
item Ghedin, Elodie
item Nolting, Jacqueling
item Swayne, David
item Runstadler, Jonathan
item Happ, George
item Senne, David
item Wang, Ruixue
item Slemons, Richard
item Holmes, Edward
item Taubenberger, Jeffery

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/5/2008
Publication Date: 5/1/2008
Citation: Dugan, V.G., Chen, R., Spiro, D.J., Sengamalay, N., Zaborsky, J., Ghedin, E., Nolting, J., Swayne, D.E., Runstadler, J., Happ, G.M., Senne, D.A., Wang, R., Slemons, R.D., Holmes, E.C., Taubenberger, J.K. 2008. The evolutionary genetics and emergence of avian influenza viruses in wild birds. PLoS Pathogens [serial online]. 4(5):e1000076. Available:

Interpretive Summary: One hundred sixty seven avian influenza viruses (AIV) were obtained from 14 species of wild birds in four locations across North America in a multi-institutional study. The viruses were sequenced and a high rate of exchange of genetic material was identified between the viruses. This indicates, AIV form transient gene configurations with continual reshuffling of genetic material through reassortment as compared to influenza viruses in mammals which form a limited number of gene configurations.

Technical Abstract: We surveyed the genetic diversity of avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes sampled from 14 bird species in four locations across North America. This revealed 29 combinations of hemagglutinin (HA) and neuraminidase (NA) subtypes, with 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of all available AIV genomes, the largest undertaken to date, we were able to document a remarkably high rate of genome reassortment, with no clear pattern of segment association. From this, we propose that AIV in wild birds forms transient ‘genome constellations’, continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted influenza A viruses. Low pathogenic (LP) influenza A viruses are widely distributed in wild avian species, with asymptomatic infections most common in waterfowl of the orders Anseriformes and Ciconiiformes. Wild birds are thought to represent major natural reservoirs for influenza A viruses and at least 105 species of wild birds, mostly juveniles, have been identified as harboring influenza A viruses. Avian influenza A viruses (AIV) possess antigenically diverse hemagglutinin (HA) and neuraminidase (NA) subtypes, and all known HA (H1-H16) and NA (N1-N9) subtypes, in at least 103 of the possible 144 combinations, have been found in wild birds.

Last Modified: 10/20/2017
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