19 research outputs found
Maximum likelihood trees
Compressed file of bootstrapped ML phylogenies inferred using RAxML and used to characterise influenza B virus genotypes
Full genomes time summary
Tab-delimited text file detailing year of isolation and lineage of 2,651 full-length influenza B virus genomes from this study (Fig 1 source data)
Summary of genotypes
Tab-delimited text file detailing inferred genotypes for influenza B viruses, representing over 10,000 strains including 2,651 complete genomes
Input files for antigenic analysis
Compressed file comprising of: tab-delimited HI data file, BEAST XML file for generation of set of empirical trees and XML file for running BMDS models for B/Yamagata and B/Victoria
Maximum clade credibility (MCC) trees
Compressed file comprising of BEAST output MCC trees
Estimated time of most recent common ancestor (TMRCA) for Yamagata-lineage clade 2 and clade 3 viruses.
<p>Estimated time of most recent common ancestor (TMRCA) for Yamagata-lineage clade 2 and clade 3 viruses.</p
Structural mapping of major Yamagata-lineage ‘clade-defining’ trunk substitutions on influenza B virus polymerase complex.
<p>(A) Crystal structure of influenza B virus polymerase (PDB: 5MSG) bound to template vRNA shown in cartoon view colored by subunit, highlighting locations of residues of interest as spheres colored by presence of change in Yamagata-lineage clade 2 (orange) or clade 3 (red) viruses. Zoomed-in view of substitutions (B, C) at PB1-PA interface fixed in clade 2 viruses and (D, E) at PB1-vRNA interface fixed in clade 3 viruses.</p
Maximum clade credibility tree inferred from 1,169 Yamagata-lineage HA gene sequences and corresponding genotype constellations.
<p>Branches of the phylogeny are labeled with amino acid substitutions occurring along the phylogenetic ‘trunk’ and colored by well-supported clade distinction (see legend). Clade classifications of each gene are similarly indicated by colored bars. White bars indicate that no sequence was available for that gene. Nodes with greater than 0.70 posterior probability support are shown with circle node shapes.</p
Time-resolved NA gene phylogenies of influenza B viruses isolated in four global regions from 2001–2014.
<p>Maximum-clade credibility (MCC) trees are shown for Victoria- (blue) and Yamagata-lineages (red) circulating in (A, E) USA, (B, F) Europe, (C, G) Southern China and Southeast Asia, and (D, H) Oceania. Clades are highlighted in colored blocks, Victoria-lineage: B/Brisbane/60/2008 clade (clade 1A; BR08) in blue, B/Malaysia/2506/2004 (MA04) in light green, B/Cambodia/30/2011 (CA11) in purple and B/Dakar/10/2012 (DA12) in dark green. For clarity, B/Odessa/3886/2010 clade (clade 1B) is shown as part of clade 1A (BR08). Yamagata-lineage: B/Massachusetts/2/2012 (clade 2; MA12) in orange and B/Wisconsin/1/2010 (clade 3; WI10) in light red.</p
Source and distribution of available influenza B virus full genomes.
<p>(A) Geographic source and (B) temporal distribution of 2,651 unique complete genomes analyzed in this study. Circle areas are proportional to the number of unique viruses originating from a location; smallest circle size represents 1 genome, largest circle size represents 332 genomes. Pie chart fractions reflect proportion of unique full genomes that were either newly generated in this study or downloaded from IVR and GISAID (on 25 August 2015). Viruses are classified as Victoria- or Yamagata-lineage by HA gene.</p