An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity.

•In the 2016–2017 influenza season, multiple clades of the influenza A(H3N2) virus co-circulated in Taiwan as well as in other countries.•These viruses were continuing to diversify worldwide with complicated and rapid dynamics.•Most of the circulating viruses were antigenically related to the current vaccine strain and infection by different clade viruses did not correlate with immunization with the 2016–2017 vaccine.