Transition of the D3c branch and novel recombination events contribute to the diversity of Coxsackievirus A6 in Beijing, China, from 2019 to 2023

Coxsackievirus A6 (CVA6) is a major pathogen responsible for numerous outbreaks of hand, foot, and mouth disease (HFMD) worldwide since 2008. This study investigates the molecular evolution and recombination of CVA6 in Beijing, China. Full-length sequences of 54 CVA6 from Beijing (2019–2023) were obtained through metagenomic next-generation sequencing (mNGS) and Sanger sequencing. These sequences were compared with representative sequences from GenBank to analyze their phylogenetic characteristics, recombination diversity, and evolutionary dynamics. The 54 CVA6 samples co-circulated with samples from multiple provinces in China, as well as from South Korea and Japan. Phylogenetic analysis revealed a novel D3c branch, with the VP1 T283A amino acid mutation identified as a key change in its formation. One sequence belonged to the D3a branch, while 53 sequences belonged to the D3c branch. Recombination analysis identified RF-A (46, 85.1%) and three novel recombinant forms (RFs): RF-Z (1, 1.9%), RF-AA (1, 1.9%), and RF-AB (6, 11.1%). Bayesian phylogenetic analysis estimated that the most recent common ancestor (tMRCA) of D3c emerged in 2013 (95% HPD: 2012–2014), with recombination events occurring in RF-Z (2017–2019), RF-AA (2019–2023), and RF-AB (2021–2023). In conclusion, we revealed a globally circulating CVA6 D3c branch and identified three novel recombinant lineages, providing valuable insights for the intervention and control of HFMD.