Molecular characterization and whole-genome sequencing-based genetic evolution of coxsackievirus A16 in Taiyuan City, 2023-2025.

Coxsackievirus A16 (CVA16) is a major causative agent of hand, foot, and mouth disease (HFMD) in China. Based on 35 CVA16-positive strains isolated in Taiyuan (2023-2025), we characterized the post-pandemic evolutionary dynamics. Genomic analysis revealed the highest conservation in VP4 and the lowest in the 3' UTR. Temporally, a shift from B1a/B1b co-circulation to a three-lineage pattern (including a novel B1c subgenotype) was observed. Intertypic recombination was the primary driver, specifically targeting the 5'UTR and VP1/2A junction (B1a with EV71; B1b with CVA4; B1c with both). Crucially, the core P1 capsid region remained intact and recombination-free, preserving major antigenic determinants. Complementing this, positive selection acted on four internal structural residues (VP1‑T97I, VP2‑D139T, VP3‑I2V, VP3‑M126T), stability predictions indicated these substitutions moderately reduced capsid stability, suggesting adaptive tuning of assembly kinetics rather than antigenic drift. Three B1b-specific markers including L23M, I235V and T240A in VP1 further supported temporal adaptation, with no significant geographic divergence between northern and southern strains during overlapping time periods. This study clarifies that CVA16 evolution is driven by non-coding recombination and subtle structural refinement, providing molecular evidence for the sustained antigenic relevance of current vaccine candidates.