Spread of predominant neuraminidase and hemagglutinin co-mutations in the influenza A/H3N2 virus genome

Genetic variation of influenza neuraminidase (NA), unlike for hemagglutinin (HA), has not been fully characterized. Therefore, we determined the relation between mutations in the NA and HA genome segments of 205 influenza A/H3N2 viruses isolated from patients in Japan during the five seasons from 2010 to 2015. The amino acid (AA) sequences of the NA and HA proteins in these isolates were then determined. In the 2011-2012 season, there was the emergence of isolates with NA and HA sequences containing AA93G (NA93G) and AA278K (HA278K), respectively (24/48 isolates, 50.0%). This was in contrast to NA93D-HA278N being detected exclusively in the previous 2010-2011 season (24/24 isolates, 100.0%). The isolates with the NA93G-HA278K substitutions became predominant in the following 2012-2013 season (95.8%, 46/48 isolates). The NA and HA phylogenetic trees of the 2011-2012 and 2012-2013 seasons were segregated by clades with NA93D-HA278N or NA93G-HA278K. In the subsequent 2013-2014 and 2014-2015 seasons, the strong relationship between NA93D-HA278N and NA93G-HA278K observed in the previous seasons, was no longer present and NA93G-HA278N (33/52 isolates, 63.5% in the 2014-2015 season) became predominant. In addition, the clades within the NA and HA trees could no longer be segregated based on NA AA93 and HA AA278. These findings suggest that the co-mutation of NA and HA AA sequences is present and may contribute to the formation of an epidemic lineage.