Abstract
Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian IAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.
Highlights
To explore the evolutionary and ecological dynamics of avian influenza virus (AIV) in Eurasian wild birds, we used whole-genome sequences of AIVs isolated from several Anseriformes species sampled in West Eurasia along the East Atlantic flyway as part of an intensive wild bird surveillance study
To study the spatio-temporal dynamics of AIVs in wild birds in Eurasia, more than 100 virus isolates collected from 1999 to 2007 were selected for full genomic sequencing of the coding regions. These virus isolates represented a diverse range of wild bird hosts, and included different subtypes and sampling locations predominantly within West Eurasia (Table 1)
To focus on evolution of Low pathogenic avian influenza (LPAI) viruses in wild birds, we excluded all sequences from domestic birds and all sequences related to poultry outbreaks, highly pathogenic avian influenza (HPAI) H5N1, H7 and H9
Summary
Extensive surveillance studies of AIV in ducks and shorebirds in North America have permitted analyses of reassortment rates, selection pressures and patterns of genetic diversity, but until recently there has only been limited whole-genome sequence data available for AIVs in Eurasia, Africa, South America and Oceania. To explore the evolutionary and ecological dynamics of AIV in Eurasian wild birds, we used whole-genome sequences of AIVs isolated from several Anseriformes species sampled in West Eurasia along the East Atlantic flyway as part of an intensive wild bird surveillance study.
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