Recently, influenza A(H3N2) virus variants carrying substitutions N121K, S144K and T135K have been reported in Canada, Denmark, Israel and the United Kingdom (UK), causing outbreaks during the northern hemisphere 2016/17 influenza season and suboptimal vaccine effectiveness (VE). Information on clinical characteristics of patients infected with these variants is lacking, and the impact on public health practice remains unknown.

In Taiwan, the influenza season usually starts from December, and peaks in January to February of the following year. The 2016/17 influenza season in Taiwan has been characterised by an unusual summer peak, which started in mid-May, peaked in late June and returned to baseline in August, with predominant circulation of influenza A(H3N2) viruses. We performed a phylogenetic analysis of the variants and analysed the characteristics of patients with severe illness to fill the gap between knowledge about virological characteristics and their possible implications for public health practice.