Genetic characterization and molecular epidemiological analysis of enterovirus C99 in China

Enterovirus C99 (EV‐C99) is a newly identified EV serotype within the species Enterovirus C. Few studies on EV‐C99 have been conducted globally. More information and research on EV‐C99 are needed to assess its genetic characteristics, phylogenetic relationships, and associations with enteroviral diseases. Here, the phylogenetic characteristics of 11 Chinese EV‐C99 strains have been reported. The full‐length genomic sequences of these 11 strains show 79.4–80.5% nucleotide identity and 91.7–94.3% amino acid (aa) identity with the prototype EV‐C99. A maximum likelihood phylogenetic tree constructed based on the entire VP1 coding region identified 13 genotypes (A–M), revealing a high degree of variation among the EV‐C99 strains. Phylogeographic analysis showed that the Xinjiang Uygur Autonomous Region is an important source of EV‐C99 epidemics in various regions of China. Recombination analysis revealed inter‐serotype recombination events of 16 Chinese EV‐C99 strains in 5′ untranslated regions and 3D regions, resulting in the formation of a single recombination form. Additionally, the Chinese strain of genotype J showed rich aa diversity in the P1 region, indicating that the genotype J of EV‐C99 is still going through variable dynamic changes. This study contributes to the global understanding of the EV‐C99 genome sequence and holds substantial implications for the surveillance of EV‐C99.