Evolutionary dynamics of Influenza A(H3N2) virus in India from 2009 to 2023

The influenza virus, with its propensity for rapid genetic evolution, remains a formidable global public health challenge. In particular, the H3N2 subtype of the Influenza A virus is known for its ability to continuously evolve, making it an ongoing concern for public health. To gain insights into the epidemiological dynamics of H3N2 in India, a comprehensive phylogenetic and phylogeographic analysis was conducted spanning the years 2009 to 2023. We analyzed 518 HA gene sequences from India (2009-2023), integrating 462 publicly available and 56 newly generated sequences from 19 different states in India (2018-2023). Bayesian phylogenetic and phylogeographic analyses revealed continuous H3N2 evolution in India since the mid-1990 s with an evolutionary rate of 4.95 × 10^-3 substitutions/site/year (R² = 0.95). The most recent common ancestor for Indian H3N2 sequences dated to 1995 (95 % HPD: 1992-2001), with 2023 strains predominantly belonging to clade 2a.3a.1 (characterized by I140K mutation) showing close match with WHO-recommended vaccine strains A/Darwin/6/2021.