Genetic characterization of influenza A viruses circulating in Hong Kong, China, 2023: the first influenza epidemic after the lifting of 2.5 years of COVID-19 non-pharmaceutical interventions

During the COVID-19 pandemic, stringent public health measures led to historically low influenza activity in Hong Kong. However, after these interventions were relaxed in 2023, Influenza A viruses (IAV), including A(H1N1)pdm09 and A(H3N2), rapidly resurfaced. In this study, 1,046 clinical cases collected throughout 2023 underwent comprehensive genomic analysis using Oxford Nanopore Technologies (ONT). Phylogenetic analyses of the assembled genome segments were conducted alongside several global public sequences for comparison. The dataset is comprised of 593 A(H1N1)pdm09 sequences, predominantly of hemagglutinin (HA) subclade 5a.2a and neuraminidase (NA) subclade C.5.3, and 453 A(H3N2) sequences classified mainly as HA subclade 2a.3a.1 and NA subclade B.4.3. Phylogenetic comparisons revealed close genetic relationships between the studied viruses and 30 A(H1N1)pdm09 and 27 A(H3N2) sequences published in other regions during the same time. Additionally, identified amino acid substitutions may affect antigenicity and viral fitness. These findings underscore Hong Kong’s high post–COVID–19 influenza diversity and the need for ongoing molecular surveillance to monitor emerging viral variants.