Abstract
We surveyed the genetic diversity among avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States. These isolates represented 29 type A influenza virus hemagglutinin (HA) and neuraminidase (NA) subtype combinations, with up to 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of the largest data set of AIV genomes compiled to date, we were able to document a remarkably high rate of genome reassortment, with no clear pattern of gene segment association and occasional inter-hemisphere gene segment migration and reassortment. 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.
Highlights
Low pathogenic (LP), antigenically diverse influenza A viruses are widely distributed in wild avian species around the world
Strains of poultry-adapted H5 or H7 avian influenza viruses (AIV) evolve into highly pathogenic (HP) AIV usually through acquisition of an insertional mutation resulting in a polybasic amino acid cleavage site within the HA [15,25]
It is thought that the natural reservoir of influenza A viruses is the wild bird population
Summary
Low pathogenic (LP), antigenically diverse influenza A viruses are widely distributed in wild avian species around the world They are maintained by asymptomatic infections, most frequently documented in aquatic birds of the orders Anseriformes and Charadriformes. Despite the recent expansion of AIV surveillance [7,8,10,34,35] and genomic data [5,36,37,38], fundamental questions remain concerning the ecology and evolution of these viruses Prominent among these are: (i) the structure of genetic diversity of AIV in wild birds, including the role played by inter-hemispheric migration, (ii) the frequency and pattern of segment reassortment, and (iii) the evolutionary processes that determine the antigenic structure of AIV, maintained as discrete HA and NA subtypes.
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