Analysis of influenza A viruses from gulls: An evaluation of inter-regional movements and interactions with other avian and mammalian influenza A viruses

<p>Birds, including members of the families Anatidae (waterfowl) and Laridae (gulls and terns), serve as the major reservoir of influenza A viruses (IAVs). The ecogeographic contributions of gulls to global IAV dynamics, in terms of geographic scale and virus movements, are important and are distinct from those of waterfowl. Gulls primarily carry the H13 and H16 subtypes, yet can be infected by additional subtypes. Also, gulls are frequently infected by IAVs that contain mixtures of genes from different geographic phylogenetic lineages (e.g. North American and Eurasian). The present analysis examines a variety of viruses isolated from gulls and terns across the world that exhibit particularly high phylogenetic affinities to viruses found in other hosts. This illustrates the potential for gulls to act as highly pathogenic virus carriers, disseminators of viruses over long distances, and contributors in the genesis of pandemic strains. The historical evolution of an entirely Eurasian gull virus isolated in North America was also traced and indicates the Caspian Sea, in southwestern Asia, was an important area for the generation of this virus, and analysis of IAVs from terns also points to this region as relevant for the generation of novel strains.</p

Spatial distribution of detections of the Atlantic flyway duck AIV sub-lineages in North American flyways.

<p>The box plots show the proportions of detections in each of the flyways for the gene sub-lineages that were identified in the 2006–2011 Atlantic flyway duck AIVs. The solid line in the box is the median. The top and bottom of the box are the first and third quartiles, respectively. The upper and lower horizontal lines represent 1.5X the difference between the first and third quartiles and any values falling outside of those are plotted as points. The detailed results for the each segment are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086999#pone.0086999.s005" target="_blank">Figure S5</a>.</p

Summary of gene lineage and gene type diversity by segment for the 109 Atlantic flyway duck AIVs from 2006–2011.

a<p>Gene lineages, sub-lineages and types are defined as sharing ≥90%, ≥95% and ≥99% nucleotide identity, respectively.</p

Genetic structure of the gene lineages and sub-lineages of the Atlantic flyway duck AIVs.

<p>The numbers of genes in each detected sub-lineage for each of the segments of the 109 Atlantic flyway duck AIVs are shown in the pie charts. AIV genes with ≥95% nucleotide identity by pairwise distance analysis were assigned in a sub-lineage. For the HA genes, sub-lineages 7F-1, 7F-2, 11C-2, 12A-1, 13A-1 and 16D-1 were each detected once and are not labelled. Similarly for the NA genes, sub-lineages 2G-1, 3A-1, 3D-1, 8A-3, 9A-2 and 9A-3 were each detected once and are not labelled.</p

Perpetuation of Atlantic flyway duck AIV gene types across time.

<p>The proportions of gene types identified in the Atlantic flyway viruses that were detected for >5 and >10 years in North America are shown for each segment. There were significant differences among the proportions for the HA, M and NS segments relative to the other segments for >5 years (χ² = 53.1, df = 7, P<0.0001) and >10 years (χ² = 66.5, df = 7, P<0.0001). Statistically different proportions for the segments are indicated with different letters (a, b and c).</p

Inter-continental reassortants identified in the 109 Atlantic flyway duck AIVs.

a<p>Eurasian avian origin.</p>b<p>Eurasian gull origin.</p>c<p>North American gull origin.</p