DOI: 10.5061/dryad.rc515
title: Data from: Integrating influenza antigenic dynamics with molecular evolution

description: Influenza viruses undergo continual antigenic evolution allowing mutant
 viruses to evade host immunity acquired to previous virus strains.
 Antigenic phenotype is often assessed through pairwise measurement of
 cross-reactivity between influenza strains using the hemagglutination
 inhibition (HI) assay. Here, we extend previous approaches to antigenic
 cartography, and simultaneously characterize antigenic and genetic
 evolution by modeling the diffusion of antigenic phenotype over a shared
 virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1,
 B/Victoria and B/Yamagata, we determine patterns of antigenic drift across
 viral lineages, showing that A/H3N2 evolves faster and in a more
 punctuated fashion than other influenza lineages. We also show that
 year-to-year antigenic drift appears to drive incidence patterns within
 each influenza lineage. This work makes possible substantial future
 advances in investigating the dynamics of influenza and other
 antigenically-variable pathogens by providing a model that intimately
 combines molecular and antigenic evolution.
description: A/H1N1 HI
 dataTab-delimited text file
 giving hemagglutination inhibition (HI) titers for seasonal A/H1N1
 influenza viruses and ferret antisera isolated between 1977 and 2009. The
 virus strain used in the HI assay as well as the specific virus isolate
 are listed. The strain used as antiserum and the specific antiserum
 isolate are also listed. Data was compiled from multiple sources, listed
 in the sources column and fully referenced in the
 publication.H1N1_HI_data.txtA/H3N2 HI dataTab-delimited text file giving hemagglutination inhibition (HI) titers for seasonal A/H3N2 influenza viruses and ferret antisera isolated between 1968 and 2011. The virus strain used in the HI assay as well as the specific virus isolate are listed. The strain used as antiserum and the specific antiserum isolate are also listed. Data was compiled from multiple sources, listed in the sources column and fully referenced in the publication.H3N2_HI_data.txtB/Victoria HI dataTab-delimited text file giving hemagglutination inhibition (HI) titers for seasonal B/Victoria influenza viruses and ferret antisera isolated between 1986 and 2011. The virus strain used in the HI assay as well as the specific virus isolate are listed. The strain used as antiserum and the specific antiserum isolate are also listed. Data was compiled from multiple sources, listed in the sources column and fully referenced in the publication.Vic_HI_data.txtB/Yamagata HI dataTab-delimited text file giving hemagglutination inhibition (HI) titers for seasonal B/Yamagata influenza viruses and ferret antisera isolated between 1987 and 2011. The virus strain used in the HI assay as well as the specific virus isolate are listed. The strain used as antiserum and the specific antiserum isolate are also listed. Data was compiled from multiple sources, listed in the sources column and fully referenced in the publication.Yam_HI_data.txtA/H1N1 sequence dataTab-delimited text file giving sequence accession numbers for seasonal A/H1N1 influenza viruses isolated between 1977 and 2009. Sequences come from both the Influenza Research Database (http://www.fludb.org/) and the EpiFlu Database that is part of GISAID (http://www.gisaid.org/).H1N1_seq_data.txtA/H3N2 sequence dataTab-delimited text file giving sequence accession numbers for seasonal A/H3N2 influenza viruses isolated between 1968 and 2011. Sequences come from both the Influenza Research Database (http://www.fludb.org/) and the EpiFlu Database that is part of GISAID (http://www.gisaid.org/).H3N2_seq_data.txtB/Victoria sequence dataTab-delimited text file giving sequence accession numbers for seasonal B/Victoria influenza viruses isolated between 1986 and 2011. Sequences come from both the Influenza Research Database (http://www.fludb.org/) and the EpiFlu Database that is part of GISAID (http://www.gisaid.org/).Vic_seq_data.txtB/Yamagata sequence dataTab-delimited text file giving sequence accession numbers for seasonal B/Yamagata influenza viruses isolated between 1987 and 2011. Sequences come from both the Influenza Research Database (http://www.fludb.org/) and the EpiFlu Database that is part of GISAID (http://www.gisaid.org/).Yam_seq_data.txtIncidence dataIncidence data for seasonal influenza viruses A/H3N2, A/H1N1, B/Vic and B/Yam. Each row represents a USA winter influenza season. The column "flu" gives the frequency of influenza positive isolates from all isolates tested. The columns "typeA" and "typeB" give the relative frequencies of influenza A and influenza B in samples that tested positive. The columns "subtypeH3", "subtypeH1", "subtypeH1pdm" give the relative frequencies of A/H3N2, A/H1N1 and pandemic A/H1N1 among type A samples. The columns "subtypeVic" and "subtypeYam" give the relative frequencies of B/Vic and B/Yam among type B samples. The column "ili" gives the influenza-like illness (ILI) frequency over the same season.incidence_data.txt