DOI: 10.5061/dryad.s1d37
title: Data from: Genome-wide evolutionary dynamics of influenza B viruses on a global scale

description: The global-scale epidemiology and genome-wide evolutionary dynamics of
 influenza B remain poorly understood compared with influenza A viruses. We
 compiled a spatio-temporally comprehensive dataset of influenza B viruses,
 comprising over 2,500 genomes sampled worldwide between 1987 and 2015,
 including 382 newly-sequenced genomes that fill substantial gaps in
 previous molecular surveillance studies. Our contributed data increase the
 number of available influenza B virus genomes in Europe, Africa and
 Central Asia, improving the global context to study influenza B viruses.
 We reveal Yamagata-lineage diversity results from co-circulation of two
 antigenically-distinct groups that also segregate genetically across the
 entire genome, without evidence of intra-lineage reassortment. In
 contrast, Victoria-lineage diversity stems from geographic segregation of
 different genetic clades, with variability in the degree of geographic
 spread among clades. Differences between the lineages are reflected in
 their antigenic dynamics, as Yamagata-lineage viruses show alternating
 dominance between antigenic groups, while Victoria-lineage viruses show
 antigenic drift of a single lineage. Structural mapping of amino acid
 substitutions on trunk branches of influenza B gene phylogenies further
 supports these antigenic differences and highlights two potential
 mechanisms of adaptation for polymerase activity. Our study provides new
 insights into the epidemiological and molecular processes shaping
 influenza B virus evolution globally.
description: Full genomes location
 summaryTab-delimited text file
 detailing locations and lineages of 2,651 full-length influenza B virus
 genomes in this study (Fig 1 source data).fluB_location_summary.txtFull genomes time summaryTab-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).fluB_timeseries_summary.txtMaximum likelihood treesCompressed file of bootstrapped ML phylogenies inferred using RAxML and used to characterise influenza B virus genotypes.maximum-likelihood-trees.zipBEAST XML filesCompressed file of BEAST input files (xml) used to infer the molecular clock phylogenies as well as ancestral reconstruction and phylodynamic analysis for influenza B virus genes.beast-xml-files.zipMaximum clade credibility (MCC) treesCompressed file comprising of BEAST output MCC trees.mcc-trees.zipSummary of genotypesTab-delimited text file detailing inferred genotypes for influenza B viruses, representing over 10,000 strains including 2,651 complete genomes.genotypes-summary.txtMCC trees annotated with trunk substitutionsCompressed file containing MCC trees for B/Yamagata HA, B/Victoria HA, B/Yamagata PB1, and B/Victoria NA annotated with inferred mutations along the trunk lineages.trunk-substitutions-mcc-trees.zipInput files for antigenic analysisCompressed 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.antigenic-evolution-input.zipOutput files from antigenic analysisCompressed file containing MCC trees from BMDS analysis (source data for Figure 4) and tab-delimited file summaries of mean antigenic distance from phylogenetic root inferred across 2,000 posterior trees to calculate mean antigenic drift rates (source data for Table 2). Posterior trees files were too large (&gt;50 MB in compressed form each) to be included.antigenic-evolution-output.zip