Molecular Characteristics of VP1 Region of Enterovirus 71 Strains in China

Background Enterovirus 71 (EV71) is the most common causative agent of severe and fetal hand, foot, and mouth disease (HFMD) outbreaks worldwide, and the VP1 protein, a capsid protein of EV71, is responsible for the genotype of EV71, which is important for vaccine selection and effectiveness. We performed an observational study of the genetic characteristics and genotype of EV71 isolates in China. Methods The VP1 gene sequences of 3712 EV71 virus strains from China, excluding repetitive sequences, and 30 known EV71 genotypes, as reference strains, between 1986 and 2019 were obtained from GenBank. A phylogenetic tree, amino acid homology, genetic variation and genotype analysis of the EV71-VP1 protein were performed with MEGA 6.0 software. Results The amino acid identity of all Chinese EV71 strains was 88.33%-100%, 93.47%-100% with the vaccine strain H07, and 93.04%-100% with the vaccine strains FY7VP5 and FY-23K-B. Since 2000, the prevalent strains of EV71 were mainly the C4 genotype; the C4a subgenotype was predominant, the C4b subgenotype was the second, and other subgenotypes appeared sporadically between 2005 and 2018 in mainland China. The B4 genotype was the main genotype in Taiwan, and the epidemic strains were constantly changing. Some amino acid variations in VP1 of EV71 occurred with high frequencies: A289T (20.99%), H22Q (16.49%), A293S (15.95%), S283T (15.11%), V249I (7.76%), N31D (7.25%), and E98K (6.65%). Conclusion The C4 genotype of EV71 in China can match the vaccine, which can effectively control EV71 epidemiology. However, the efficacy of the vaccine strain is partially affected by the continuous change in epidemic strains in Taiwan, China. These studies suggested that the genetic characteristics of the EV71-VP1 region should be continuously monitored, which is critical for epidemic control and vaccine design against EV71 infection in children.