Window-averaged scores for sequence identity among polyproteins of the 33 SVA strains.

<p>Identity scores are averaged over running windows of 21 amino acids and centered at consecutive amino acid positions. The variable regions are indicated by their represented mature proteins.</p

Locations of the amino acid alterations at the major antigenic sites of HA1 molecule in the H3 crystal structure.

<p>(I) Side view of a HA monomer in cartoon format with major antigenic sites A, B, C and D shown in spheres (II, III, IV, and V??amino acid changes identified at the major antigenic sites. The locations of changed amino acids are indicated and colored in red. (VI, VII, VIII, IX, and X) Back view of panels I, II, III, IV, and V, respectively. The view in panels I to V is rotated 180° along Y-axis.TK/ON/FAV-003/2011 vs. DK/MN/1979 (II and VII); TK/ON/FAV-009/2011 vs. DK/MN/1979 (III and VIII); TK/ON/FAV-003/2011 vs. SW/ON/33853/2005 (IV and IX); TK/ON/FAV-009/2011 vs. SW/ON/33853/2005 (V and X).</p

Antigenic characterization of triple reassortant H3N2 viruses isolated from turkeys by hemagglutination-inhibition assay using turkey red blood cells and various reference H3 antisera.

<p>Antigenic characterization of triple reassortant H3N2 viruses isolated from turkeys by hemagglutination-inhibition assay using turkey red blood cells and various reference H3 antisera.</p

Percent similarities in the amino acid residues of the HA0 and HA1 of the three H3N2 isolates from turkeys compared to a prototype cluster IV TR H3N2 strain.

<p>ND = Not done [full HA sequence of A/Mallard duck/MN/79/1979 (H3N4) was not available].</p

Non-synonymous mutations detected in all 33 SVA strains compared to prototype strain SVV-001.

<p>Non-synonymous mutations detected in all 33 SVA strains compared to prototype strain SVV-001.</p

SVA strains used in phylogenetic analysis.

<p>SVA strains used in phylogenetic analysis.</p

Top BLAST matches of the 8 gene segments from FAV-003 and FAV-009 obtained from NCBI influenza A virus nucleotide database.

<p>Top BLAST matches of the 8 gene segments from FAV-003 and FAV-009 obtained from NCBI influenza A virus nucleotide database.</p

Phylogenetic analysis of the HA and NA genes.

<p>The HA (a) and NA (b) gene segments of the unique TR H3N2 viruses isolated from turkeys were compared with other TR H3N2 viruses from turkey (open circle), quail (open diamond) and pig (open triangles) that were previously sequenced by our laboratory <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032858#pone.0032858-Nfon1" target="_blank">[24]</a>.</p

Time-scaled phylogenetic tree inferred using Bayesian MCMC analysis for the polyprotein coding sequences of 33 SVA strains.

<p>Branches are coloured according to geographic origin of the country. Strains from Manitoba are highlighted in magenta and from Ontario in cyan. Nodes supported by ≥ 0.7 posterior probability are indicated by the solid circles and sized by posterior probability. A, B, and C are sequences from assembly yards A, B, and C, respectively.</p

Influenza A matrix gene real time RT-PCR and virus isolation results for the swab specimens received from the three turkey farms.

<p>ND = not determined.</p