Integrating influenza antigenic dynamics with molecular evolution

TL;DR

This paper presents a model that combines molecular and antigenic evolution to analyze influenza virus dynamics, revealing lineage-specific antigenic drift patterns and their impact on incidence.

Contribution

It extends antigenic cartography by integrating genetic data, enabling detailed analysis of antigenic and genetic evolution in influenza viruses.

Findings

A/H3N2 evolves faster and more punctuated than other lineages.

Year-to-year antigenic drift influences influenza incidence patterns.

The model facilitates future studies of antigenically-variable pathogens.

Abstract

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.