Epidemiological and Genomic Characterization of Japanese Encephalitis Virus in Mosquitoes in China

Japanese encephalitis (JE), caused by mosquito-borne Japanese encephalitis virus (JEV), presents significant public health challenges. To facilitate effective prevention and control, this study conducted an epidemiological and genomic characterization of JEV in mosquitoes across China during the period from 2021 to 2022, utilizing the national surveillance system for mosquito-borne pathogens. In total, 832 734 female mosquitoes were collected at 130 surveillance sites spanning 29 provinces. with a minimum infection rate (MIR) of 0.20‰. JEV was detected in 12 provinces and five different mosquito species. The highest MIR was observed in Culex tritaeniorhynchus, reaching 0.73‰. The highest detection rate of JEV was found in the pigsty habitat (MIR: 0.95‰). Notably, peak JEV infections in mosquitoes occurred in July, preceding the peak incidence of human cases observed in August. Eight JEV sequences were obtained from six provinces, seven of which were near full-length. Phylogenetic analysis of the whole genome showed that eight JEV strains obtained from provinces in northern and southern China belonged to the emerging variant of GIb-clade 2. In comparison to vaccine strains, current strains displayed between 12 and 14 amino acid variations within the E protein, and there was an additional glycosylation site at N108 resulting from a G110S mutation. These findings underscore active transmission of JEV across multiple mosquito species within China, highlight critical vector and habitat risks, and advocate for enhanced mosquito surveillance as an early warning system. The nationwide dissemination of GIb-clade 2 strains provides a scientific foundation for targeted control measures against JE.