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.
A/H1N1 HI data
Tab-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.txt
A/H3N2 HI data
Tab-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.txt
B/Victoria HI data
Tab-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.txt
B/Yamagata HI data
Tab-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.txt
A/H1N1 sequence data
Tab-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.txt
A/H3N2 sequence data
Tab-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.txt
B/Victoria sequence data
Tab-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.txt
B/Yamagata sequence data
Tab-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.txt
Incidence data
Incidence 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