H7 Australian Avian Influenza Supplemental Material

H7 Australian Avian Influenza Supplemental Materia

H7 Australian Avian Influenza Sequences

H7 Australian Avian Influenza Sequence

North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses

<div><p>Avian influenza virus (AIV) in wild birds has been of increasing interest over the last decade due to the emergence of AIVs that cause significant disease and mortality in both poultry and humans. While research clearly demonstrates that AIVs can move across the Pacific or Atlantic Ocean, there has been no data to support the mechanism of how this occurs. In spring and autumn of 2010 and autumn of 2011 we obtained cloacal swab samples from 1078 waterfowl, gulls, and shorebirds of various species in southwest and west Iceland and tested them for AIV. From these, we isolated and fully sequenced the genomes of 29 AIVs from wild caught gulls (Charadriiformes) and waterfowl (Anseriformes) in Iceland. We detected viruses that were entirely (8 of 8 genomic segments) of American lineage, viruses that were entirely of Eurasian lineage, and viruses with mixed American-Eurasian lineage. Prior to this work only 2 AIVs had been reported from wild birds in Iceland and only the sequence from one segment was available in GenBank. This is the first report of finding AIVs of entirely American lineage and Eurasian lineage, as well as reassortant viruses, together in the same geographic location. Our study demonstrates the importance of the North Atlantic as a corridor for the movement of AIVs between Europe and North America.</p></div

Bahl et al H6 Dataset

Bahl et al H6 Datase

Optimal inferred frequencies at high and low reassortment rates.

<p>Viral allele frequencies are shown for the example subjects as black dots. The optimised fit to the data, based on the assumption of a consistent fitness landscape across all subjects, is shown as a red dotted line, for the case of rapid reassortment between segments, and as a blue dotted line for the case of no reassortment between segments. Limiting reassortment between segments allows for the possibility of linkage disequilibrium between alleles on different segments, fitting observed correlations in allele frequencies. Data are shown for all polymorphic alleles at loci included in the model for the subjects <b>A.</b> Flu5001 and <b>B.</b> Flu013.</p

Bahl et al H9 Dataset

Bahl et al H9 Datase

Bahl et al H3 Dataset

Bahl et al H3 Datase

Information on the RSV Strains Sequenced.

<p>^a These sequences were sequenced by Next-Gen sequencing.</p><p>^b Partial G CDS sequences have previously been published for these samples with different strain names. Accession numbers for these sequences are HQ711732, HQ711709, HQ711688, and HQ711801 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0120098#pone.0120098.ref011" target="_blank">11</a>].</p><p>^c These sequences were produced from viruses isolated in tissue culture.</p><p>Information on the RSV Strains Sequenced.</p

G Protein Entropy Plot and Positive Selected Sites.

<p>This is an entropy plot of the G protein sequences with positively selected sites also shown. Entropy values were calculated using BioEdit 7.0 from the alignments used for the positive selection analysis and the plot was generated using Microsoft Excel. Black bars are for RSVA sequences and red bars are for RSVB sequences. Sites predicted to be under positive selection in this study are shown with black diamonds for RSVA and red diamonds for RSVB. Near the top are shown sites predicted to be under positive selection or diversifying selection from previously published studies with black pluses for RSVA and red pluses for RSVB.</p

Figure 2

<p>A. Map showing position of Iceland relative to the East Atlantic Flyway (red arrows) and the North American Atlantic Flyway (yellow arrows). Flyways represent generalized migration movements of birds with most using only portions of the flyways. Actual regions of flyways used by migratory birds are dependent on species and breeding population. B. Map of Iceland depicting bird sampling locations (red dots) used in this study and Reykjavik (red star) is provided for reference. Breiðafjörður and Selfoss sampling locations are generalized as samples provided by hunters and fisherman were obtained over a larger area within these marked regions.</p