Evolutionary consequences of a decade of vaccination against subtype H6N2 influenza

The evolutionary dynamics of chicken-origin H6N2 viruses isolated in South Africa between 2002 and 2013 were investigated. Sub-lineages I and II continued to co-circulate under vaccination pressure, but sub-lineage I, from which the inactivated vaccine was derived, displayed a markedly higher mutation rate and a three-fold increase in the emergence of potential antigenic sites on the globular head of HA compared to sub-lineage II. Immunological pressure culminated in a critical phenotypic change as four of the five isolates from 2012 to 2013 had lost the ability to haemagglutinate chicken erythrocytes, correlating with a pattern of predicted O-glycosylation sites at residues 134, 137 and 141 within the critical 130 loop of the receptor binding domain site. Coassortment of the HA, NA and M genes in the respective sub-lineages contrasted reassortment of the other internal protein genes, and the vaccine seed strain itself was the probable donor of segments to sub-lineage II field strains.