Abstract
Duck hunting preserves (DHP) have resident populations of farm-raised mallard ducks, which create potential foci for the evolution of novel influenza A viruses (IAVs). Through an eleven-year (2003–2013) IAV surveillance project in seven DHPs in Maryland, USA, we frequently identified IAVs in the resident, free-flying mallard ducks (5.8% of cloacal samples were IAV-positive). The IAV population had high genetic diversity, including 12 HA subtypes and 9 NA subtypes. By sequencing the complete genomes of 290 viruses, we determined that genetically diverse IAVs were introduced annually into DHP ducks, predominantly from wild birds in the Anatidae family that inhabit the Atlantic and Mississippi flyways. The relatively low viral gene flow observed out of DHPs suggests that raised mallards do not sustain long-term viral persistence nor do they serve as important sources of new viruses in wild birds. Overall, our findings indicate that DHPs offer reliable samples of the diversity of IAV subtypes, and could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations, which would provide a cost-efficient strategy for long-term IAV monitoring. Such monitoring could allow for early identification and characterization of viruses that threaten bird species of high economic and environmental interest.
Highlights
The high genetic diversity of avian influenza A viruses (IAVs) circulating in waterfowl (Anatidae) and shorebirds (Neoaves) [1,2] presents an ongoing threat of spillover into poultry, and potential economic losses
The genetic diversity and evolution of IAVs in North American wild birds have been tracked for several decades, in locations where wild birds are known to congregate during migration [7]
We sought to understand the role of Duck hunting preserves (DHP) in the epidemiology and ecology of IAVs, and we hypothesized that DHPs could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations
Summary
The high genetic diversity of avian influenza A viruses (IAVs) circulating in waterfowl (Anatidae) and shorebirds (Neoaves) [1,2] presents an ongoing threat of spillover into poultry, and potential economic losses. IAVs that evolve in one region can quickly spread to other locations through wild bird movements and mix with local viruses to create novel reassortants [6]. Asia into North American wild birds and poultry led to severe economic losses, further intensifying interest in the role of wild bird populations in maintaining and disseminating. By feeding high densities of farm-raised mallards outdoors, DHPs potentially create conditions that are conducive to long-term transmission of IAVs. DHP birds share habitat and freely intermingle with wild birds, and potentially play a role in local IAV ecology and evolution. We sought to understand the role of DHPs in the epidemiology and ecology of IAVs, and we hypothesized that DHPs could serve as regional sentinel sites that mimic the viral diversity found in local wild duck populations. By applying phylodynamic methods based on a Bayesian framework, we determined that the IAV populations identified in the DHPs are shaped primarily by asymmetrical inbound viral gene flow from wild birds, with little evidence that the resident mallards sustained viral transmission beyond a single season
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