Molecular evolution of coxsackievirus A6 associated with atypical hand, foot, and mouth disease in Northern Brazil in 2019.

Globally, coxsackievirus A6 (CVA6) is a major cause of hand, foot, and mouth disease (HFMD) outbreaks, although studies on its evolutionary and transmission dynamics are limited. Here, we analyzed samples from atypical HFMD cases in Brazil. Enteroviruses were detected in 49.2% (156/317) of the specimens, with CVA6 being the primary pathogen. Phylogenetic analysis based on VP1 gene sequences revealed that Brazilian CVA6 isolates belonged to the lineage D3 and were divided into two distinct clades from different regions. Temporal analysis indicated that the most recent common ancestor dates back 72 years and that there has been stable coevolution of genotypes. These findings shed light on the epidemiological dynamics of CVA6 and highlight the importance of surveillance of atypical HFMD cases.