Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford*, Marc A. Suchard, Philippe Lemey, Gytis Dudas, Victoria Gregory, Alan J. Hay, John W. McCauley, Colin A. Russell, Derek J. Smith, Andrew Rambaut

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number01914
Number of pages26
Publication statusPublished - 4 Feb 2014


  • A H1N1 viruses
  • B viruses
  • epidemic influenza
  • amino acid
  • hemagglutinin gene
  • sequence analysis
  • genomic analyses
  • United Kingdom
  • drift
  • variants


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