Frequent inter-species transmission and geographic subdivision in avian influenza viruses from wild birds

Abstract

Revealing the factors that shape the genetic structure of avian influenza viruses (AIVs) in wild bird populations is essential to understanding their evolution. However, the relationship between epidemiological dynamics and patterns of genetic diversity in AIV is not well understood, especially at the continental scale. To address this question, we undertook a phylogeographic analysis of complete genome sequences of AIV sampled from wild birds in North America. In particular, we asked whether host species, geographic location or sampling time played the major role in shaping patterns of viral genetic diversity. Strikingly, our analysis revealed no strong species effect, yet a significant viral clustering by time and place of sampling, as well as the circulation of multiple viral lineages in single locations. These results suggest that AIVs can readily infect many of the bird species that share breeding/feeding areas.

Fig. 1

Distribution (color-coded) of sampling (a) times, (b) locations, and (c) species in the maximum likelihood tree of the representative PB2 segment of avian influenza A viruses. Similar patterns are seen in the other gene segments (see Supplementary Information). All trees are unrooted, drawn in circular orientation, and all horizontal branch lengths have been drawn to a scale of nucleotide substitutions per site.

Fig. 2

Maximum likelihood trees of North American AIVs based on the representative (a) PB2 segment (n = 290) and (b) HA (n = 281) segments. Taxa and terminal branches are colored by sample location. Colored blocks represent the clusters in which samples come from the same location within a certain range of time. The tree is mid-point rooted (for purposes of clarity only) and all horizontal branch lengths have been drawn to a scale of nucleotide substitutions per site.