Human influenza A is one of the fastest-mutating viruses — and a laboratory for evolutionary innovation. But how many of these mutations are adaptive and drive influenza's antigenic evolution? We analyze viral genome sequences by a new method and find this number is surprisingly large. In a typical year, several driver mutations coexist in different strains and compete for fixation. This is the first evidence of clonal interference in a wild system.
Given that multiple clades compete for evolutionary success, which clade will win? We have developed a fitness model for influenza that predicts the evolution of the viral population from one year to the next. Our analysis provides a principled method to select influenza vaccine strains.
Adaptation map of influenza: Strains between 2003 and 2008 are colored by year and linked by their lineages. The vertical coordinate shows the production of fitness in the adaptive process.