Whole-genome analysis of CVA4 in children with herpangina in two cities of Shandong, China

Sporadic epidemics of herpangina caused by Coxsackievirus A4 (CVA4) have been reported globally, however, research on CVA4 remains relatively scarce. In this study, 60 Coxsackievirus A4 (CVA4) strains were successfully isolated from 256 throat swab specimens and 50 high-quality complete genome sequences were generated using high-throughput sequencing technology. Phylogenetic analysis based on the VP1 region demonstrated that all CVA4 were classified into the C2 genotype. Whole-genome analysis revealed that the strains in this study clustered within the same major evolutionary clade as CVA4 strains isolated from other regions of China. The strains exhibited high sequence homology (85.1–85.7%) with the CVA4 prototype strain (AY421764) in the P1 region, while displaying notable similarity to non-CVA4 prototype strains in the P2 and P3 regions. This observation was supported by the discordant topological positions of the sequences analyzed in the individual phylogenetic trees of P1, P2, and P3 regions. Both RDP4 and Simplot analyses confirmed active intertypic recombination events involving CVA2 and CVA8. This study provides evidence of genetic recombination among circulating CVA4 strains in Shandong Province, China, highlighting their complex evolutionary dynamics within the Enterovirus A (EV-A) species.