The effect of vaccination on the dynamics of influenza virus variants remains largely unknown in humans, unlike in poultry. In this study, we compared influenza hemagglutinin (HA) gene sequences isolated from vaccinated and unvaccinated populations with the yearly vaccine strains. In total, 181 influenza A/H3N2 virus samples isolated from 82 vaccinated and 99 unvaccinated patients (2011–15, four Japanese influenza seasons) were genetically analyzed using a next-generation sequencer. Amino acid (AA) differences from corresponding vaccine strains were found in 74 of 329 HA1 sites. There was a maximum of four AA differences within the epitopes in the former three seasons (2011–14) and fifteen in the latter season (2014–15). Deviation to a greater number of AA differences was found more significantly in the isolates from vaccinated patients as compared to unvaccinated patients (P = 0.0005 in 2011–14; P = 0.0096 in 2014–15). AA difference rates within epitopes were also significantly higher in the isolates from vaccinated patients than from unvaccinated patients (2.64% vs. 2.14% for 2011–14, P = 0.033; 7.78% vs. 6.59% for 2014–15, P = 0.058). The AA differences at seven sites (48I-278K, 128A-142G, 145S, 158K, and 193S) became dominant in the following seasons. In all of these sites, the dominance was retained during the mismatch of isolates with the vaccine strains and was lost after vaccine match. Our data suggest that in humans, immune pressure induced by vaccination works to select influenza variants genetically distant from vaccine strains.
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