Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere

Abstract

Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence of low frequency reassortment between these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages of the PB1 and PA segments in North America are of Eurasian origin. Large-scale analyses of intercontinental reassortment have shown that viruses isolated from Charadriiformes (gulls, terns, and shorebirds) are the major contributor of these outsider events. To clarify the role of gulls in AIV dynamics, specifically in movement of genes between geographic regions, we have sequenced six gull AIV isolated in Alaska and analyzed these along with 142 other available gull virus sequences. Basic investigations of host species and the locations and times of isolation reveal biases in the available sequence information. Despite these biases, our analyses reveal a high frequency of geographic reassortment in gull viruses isolated in America. This intercontinental gene mixing is not found in the viruses isolated from gulls in Eurasia. This study demonstrates that gulls are important as vectors for geographically reassorted viruses, particularly in America, and that more surveillance effort should be placed on this group of birds.

Figure 1. Locations of gull AIV identifications for which sequence data are available, 1975–2009.

Figure 2. Subtype diversity within AIV from gulls in America and Eurasia.

A. Distribution of hemagglutinin types. B. Distribution of neuraminidase subtypes.

Figure 3. Neighbour-joining trees of PB2, PB1, PA, NP, M, and NS segments.

Circles at the ends of branches identify the viruses as follows. Closed circles represent gull H13 and H16 viruses and open circles represent all subtypes except H13, H16 and H5N1. Blue represents gull viruses isolated in America and black those isolated in Eurasia. Closed grey circles represent H5N1 gull viruses. Yellow and red closed circles represent reference sequences from America and Eurasia, respectively (Table S3). The groups denoted with 1 and 2 on each panel consist of viruses that consistently group together (identified in Table S6). Scale bars indicate the number of substitutions per site. Trees with full virus identification labels and corresponding annotations are available in Figures S1, S2, S3, S4, S5, S6. All gull virus sequences used in this study are identified in Table S2.

Figure 4. Neighbour-joining tree of all complete H13 and H16 sequences.

Gull viruses isolated in Eurasia are highlighted in gray and those isolated in America in blue. Yellow and red highlight viruses from other bird species from America and Eurasia, respectively. The scale bar indicates the number of substitutions per site. Bootstrap values are provided as percentages based on 10000 replicates for selected major branch points.

Figure 5. Geographical reassortment in AIV isolated from gulls in America.

Each segment is represented by a box, and ordered by segment size from left to right (PB2, PB1, PA, NP, M, and NS). Orange boxes indicate clustering into a clade containing both avian and gull viruses (i.e. not geographically reassorted), red indicates the segment is within a clade of American viruses that all fall within a clade of Eurasian gull and avian viruses (i.e. multiple American occurrences of the Eurasian segment), and pink indicates the segment is from an American virus and falls within a clade containing only Eurasian gull and avian viruses (i.e. the Eurasian segment has been found in America only once). For the NP, M and NS segments where gull-only clades are well-supported, additional colors have been added as follows. Blue indicates clustering into a clade of American gull viruses, black indicates the segment is part of a group of American gull viruses that fall within a clade of Eurasian gull viruses, and grey indicates the segment falls within a clade containing only Eurasian gull viruses (i.e. the Eurasian segment has been found in America only once). Segments with partial sequence information available are included, but white boxes indicate no sequence information is available. The viruses are ordered by HA subtype, with a line between the H13/H16 subtypes and all other subtypes.