Data from: Integrating influenza antigenic dynamics with molecular evolution

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.