DOI: 10.5061/dryad.pc641
title: Data from: Global circulation patterns of seasonal influenza viruses vary with antigenic drift

description: Understanding the spatiotemporal patterns of emergence and circulation of
 new human seasonal influenza virus variants is a key scientific and public
 health challenge. The global circulation patterns of influenza A/H3N2
 viruses are well characterized1, 2, 3, 4, 5, 6, 7, but the patterns of
 A/H1N1 and B viruses have remained largely unexplored. Here we show that
 the global circulation patterns of A/H1N1 (up to 2009), B/Victoria, and
 B/Yamagata viruses differ substantially from those of A/H3N2 viruses, on
 the basis of analyses of 9,604 haemagglutinin sequences of human seasonal
 influenza viruses from 2000 to 2012. Whereas genetic variants of A/H3N2
 viruses did not persist locally between epidemics and were reseeded from
 East and Southeast Asia, genetic variants of A/H1N1 and B viruses
 persisted across several seasons and exhibited complex global dynamics
 with East and Southeast Asia playing a limited role in disseminating new
 variants. The less frequent global movement of influenza A/H1N1 and B
 viruses coincided with slower rates of antigenic evolution, lower ages of
 infection, and smaller, less frequent epidemics compared to A/H3N2
 viruses. Detailed epidemic models support differences in age of infection,
 combined with the less frequent travel of children, as probable drivers of
 the differences in the patterns of global circulation, suggesting a
 complex interaction between virus evolution, epidemiology, and human
 behaviour.
description: Phylogeographic tree
 sample for H1N1BEAST .trees file for
 geo-tagged locations for H1N1h1_large_geo.treesPhylogeographic tree sample for H3N2BEAST .trees file for geo-tagged locations for H3N2h3_large_geo.treesPhylogeographic tree sample for VicBEAST .trees file for geo-tagged locations for Vicvic_large_geo.treesPhylogeographic tree sample for YamBEAST .trees file for geo-tagged locations for Yamyam_large_geo.treesPhylogeographic H1N1 control fileBEAST .xml file to run phylogeographic analysis for H1N1. Requires "h1_large_sample.trees" as input.h1_large_geo.xmlPhylogeographic H3N2 control fileBEAST .xml file to run phylogeographic analysis for H3N2. Requires "h3_large_sample.trees" as input.h3_large_geo.xmlPhylogeographic Vic control fileBEAST .xml file to run phylogeographic analysis for Vic. Requires "vic_large_sample.trees" as input.vic_large_geo.xmlPhylogeographic Yam control fileBEAST .xml file to run phylogeographic analysis for Yam. Requires "yam_large_sample.trees" as input.yam_large_geo.xmlTree sample for H1N1BEAST .trees file for H1N1h1_large_sample.treesTree sample for H3N2BEAST .trees file for H3N2h3_large_sample.treesTree sample for VicBEAST .trees file for Vicvic_large_sample.treesTree sample for YamBEAST .trees file for Yamyam_large_sample.treesPhylogenetic H1N1 control fileBEAST .xml file to run phylogenetic analysis for H1N1.h1_large_tree.xmlPhylogenetic H3N2 control fileBEAST .xml file to run phylogenetic analysis for H3N2.h3_large_tree.xmlPhylogenetic Vic control fileBEAST .xml file to run phylogenetic analysis for Vic.vic_large_tree.xmlPhylogenetic Yam control fileBEAST .xml file to run phylogenetic analysis for Yam.yam_large_tree.xmlSequence data and metadata for H1N1Geographic, temporal and sequence data for H1N1.h1_large.tsvSequence data and metadata for H3N2Geographic, temporal and sequence data for H3N2.h3_large.tsvSequence data and metadata for VicGeographic, temporal and sequence data for Vic.vic_large.tsvSequence data and metadata for YamGeographic, temporal and sequence data for Yam.yam_large.tsvStrain tableAll strains used in the study, along with IRD accession numbers and geographic and temporal metadata.strain_table.tsvVirus isolations by ageVirus isolations by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza tagged with virus type (H3, H1, B) and subject age. Used to generate Extended Data Figure 5b.melb_isolations.tsvVic antigenic dataHI table for B/Vic used to generate Extended Data Figure 5a.vic_antigenic_data.txt