Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data

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.

Fig. 1.. ML trees for PB2 and PB1 displaying the genetic diversity of avian IAVs in Eurasian wild birds. The taxa colour indicates the bird species group from which the sample was isolated.

Fig. 2.. Maximum clade credibility (MCC) trees summarizing the results of the Bayesian phylogenetic inference of PB1 and PB2, and displaying the genetic diversity in different locations in Eurasia. The taxa colour indicates the regional location from where the sample was isolated. Year is indicated.

Fig. 3.. Patterns of viral migration among regions, visualized for each segment on a Eurasian map. A Bayes factor (BF) test was applied to assess the statistical support for viral migration between the discrete geographical states. Lines connecting discrete regions (cyan, Oceania; red, East Eurasia; green, Central Eurasia; blue, West Eurasia) indicate statistically supported ancestral state changes. Dotted lines, 8 ≤ BF ≤ 100 (supported); solid lines, BF>100 (strongly supported).

Fig. 4.. Tanglegrams constructed by rooting the MCC nucleotide substitution trees by older Australian strains. Corresponding taxa in the two trees are connected by a line. In the absence of reassortment one would expect to see a horizontal, or near horizontal, line connecting taxa between trees. The connecting lines are coloured by the region of sampling of the taxa. We show only the tree comparison for each segment with PB2 as the reference topology, but reassortment patterns were similar when other gene segments were used as the reference.