Components of Selection in the Evolution of the Influenza Virus: Linkage Effects Beat Inherent Selection

Abstract

The influenza virus is an important human pathogen, with a rapid rate of evolution in the human population. The rate of homologous recombination within genes of influenza is essentially zero. As such, where two alleles within the same gene are in linkage disequilibrium, interference between alleles will occur, whereby selection acting upon one allele has an influence upon the frequency of the other. We here measured the relative importance of selection and interference effects upon the evolution of influenza. We considered time-resolved allele frequency data from the global evolutionary history of the haemagglutinin gene of human influenza A/H3N2, conducting an in-depth analysis of sequences collected since 1996. Using a model that accounts for selection-caused interference between alleles in linkage disequilibrium, we estimated the inherent selective benefit of individual polymorphisms in the viral population. These inherent selection coefficients were in turn used to calculate the total selective effect of interference acting upon each polymorphism, considering the effect of the initial background upon which a mutation arose, and the subsequent effect of interference from other alleles that were under selection. Viewing events in retrospect, we estimated the influence of each of these components in determining whether a mutant allele eventually fixed or died in the global viral population. Our inherent selection coefficients, when combined across different regions of the protein, were consistent with previous measurements of dN/dS for the same system. Alleles going on to fix in the global population tended to be under more positive selection, to arise on more beneficial backgrounds, and to avoid strong negative interference from other alleles under selection. However, on average, the fate of a polymorphism was determined more by the combined influence of interference effects than by its inherent selection coefficient.

Author Summary

Success in life is the product of many factors. Inherent ability often underlies great achievement. But other factors may play their part. The circumstances a child is born into may help or hinder his or her progress. Later events also have their effect; a life may be influenced by a lucky break, or an unforeseen disaster. In this work, we examine the factors underlying success for mutations in the HA gene of human influenza virus A/H3N2, defining success as the attainment of a high frequency in the global population. We examined the history of the gene from 1968 until 2010. For each observed mutation, a mathematical model was used to estimate the inherent benefit or disadvantage it conferred to the virus. We calculated the advantageousness or otherwise of the background upon which it arose, and the subsequent effect of interference from other mutations under selection. We found that successful mutations tended to have an advantageous background, and were subsequently fortunate in avoiding negative events throughout their lifetime. Beneficial mutations were more likely to be successful. But a mutation's chances of success were influenced more by circumstances of birth and subsequent events, than by its inherent effect on the virus.