Identification of epistatic mutations and insights into the evolution of the influenza virus using a mass-based protein phylogenetic approach

Abstract

A mass-based protein phylogenetic approach developed in this laboratory has been applied to study mutation trends and identify consecutive or near-consecutive mutations typically associated with positive epistasis. While epistasis is thought to occur commonly during the evolution of viruses, the extent of epistasis in influenza, and its role in the evolution of immune escape and drug resistant mutants, remains to be systematically investigated. Here putative epistatic mutations within H3 hemagglutinin in type A influenza are identified where leading parent mutations were found to predominate within reported antigenic sites of the protein. Frequent subsequent mutations resided exclusively in different antigenic regions, providing the virus with a possible immune escape mechanism, or at other remote sites that drive beneficial protein structural and functional change. The results also enable a “small steps” evolutionary model to be proposed where the more frequent consecutive, or near-consecutive, non-conservative mutations exhibited less structural, and thus functional, change. This favours the evolutionary survival of the virus over mutations associated with more substantive change that may cause or risk its own extinction.