Abstract
Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008–2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006–2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.
Highlights
Epidemiological surveillance of avian influenza viruses (AIVs) has revealed a huge and dynamic virus reservoir in wild birds, especially in ducks
The extensive AIV genome sequences accumulated during recent decades has made it possible to study the patterns of intracontinental virus distribution in North America
Current attempts to characterize AIV genetic structure and fully understand virus ecology are limited by the under-representation of sequence information from viruses across spatial, temporal, and host species scales, especially in the American portion of the Central flyway and the Canadian portion of the Atlantic flyway [7]
Summary
Epidemiological surveillance of avian influenza viruses (AIVs) has revealed a huge and dynamic virus reservoir in wild birds, especially in ducks. The extensive AIV genome sequences accumulated during recent decades has made it possible to study the patterns of intracontinental virus distribution in North America. A large-scale statistical phylogeographic investigation of AIVs demonstrated a strong link between AIV phylogeny, spatial distance and migratory flyway [7] Another recent large-scale analysis did not find that flyway separation affected the distribution of AIVs over long periods [8], supporting extensive movement of viruses between regions in North America. Comparison of 161 Alaskan dabbling duck AIV genomes from 2005 to 2008 detected inter-species transmission of viruses between Northern Pintail (Anas acuta), Mallard (A. platyrhynchos), American Greenwinged Teal (A. carolinensis) and Northern Shoveler (A. clypeata) during all sampling years [10]. Mallards in Alaska carry intercontinental AIV reassortants but, unlike Northern Pintails that move between Alaska and Asia, these are due to secondary infection from other bird species [15]
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