Japanese encephalitis virus genotype V (JEV GV) was originally identified from human encephalitis cases in Malaysia and Singapore in 1952. After a long interval without detection, JEV GV reemerged when it was isolated from field-collected Culex tritaeniorhynchus mosquitoes in Medog County, Tibet, China, in 2009. Since 2015, JEV GV has been associated with multiple human encephalitis cases in South Korea and has been increasingly recognized as an emerging pathogen with important public health implications. Prior to the case described here, mainland China surveillance after 2009 had predominantly detected genotype I (GI) in mosquito and human samples, leading to the impression that JEV GV circulation in mainland China may have been limited or discontinuous.
The reported patient was a male neonate born by vaginal delivery on October 6, 2025, in Wuhan, China. Both mother and neonate were reportedly in good health at hospital discharge, and neither had recent travel to or residence in a JEV-endemic area outside Wuhan. The mother had no laboratory evidence of recent or past JEV infection (IgM- and IgG-negative) and had not received Japanese encephalitis vaccination; her JEV qRT-PCR result tested negative when assessed 3 days after the infant’s illness onset.
On postnatal day 21 the neonate developed a high fever (measured up to 39.3°C) and was admitted to Wuhan Children’s Hospital on October 27, 2025. During the hospitalization period (October 27–November 6, 2025), the clinical course was notable for persistent high fever (37.8–40.0°C), progressive neurologic involvement with coma, and convulsions. A clinical diagnosis of suspected viral encephalitis was made. Despite care, the neonate died on November 7, 2025.
Five clinical specimens were collected for laboratory investigation: two cerebrospinal fluid (CSF) samples and three serum samples at various time points during the illness. The admission CSF sample, obtained on hospital presentation, tested positive for JEV nucleic acid by qRT-PCR, confirming the presence of viral RNA in the central nervous system. A serum specimen collected on illness day 10 was positive for JEV-specific IgM by capture ELISA, supporting recent infection. All other specimens in the series were reported as negative for both JEV RNA and IgM. The combined detection of JEV RNA in CSF at admission and the later serum IgM response established laboratory confirmation of JEV infection in this neonate.
Next-generation sequencing was performed on the admission CSF specimen. The investigators assembled a complete JEV genome from that sample and designated it the neonate strain (GenBank accession no. PZ393248). Phylogenetic analysis using open reading frame sequences from genotypes I–V indicated that JEV GV segregates into two broad clades: one containing the 1952 prototype strains (Muar and Tengah) and a second composed of contemporary isolates, which included the neonate strain and the XZ0934 strain isolated from Tibet in 2009.
Further phylogenetic analysis focused on the envelope gene sequences of JEV GV and resolved three distinct evolutionary clades: clade A (the 1952 prototype strains), clade B (including the neonate strain and the XZ0934 Tibet strain), and clade C (containing all South Korea isolates). This topology indicates a phylogeographic structure among GV viruses and suggests independent evolution of distinct GV populations in mainland China versus South Korea since the 2009 reemergence.
JEV GV has become established in South Korea where it has been detected in multiple mosquito species and has replaced GI as the dominant genotype in that region, with human cases reported since 2015. In mainland China, JEV GV had been isolated from mosquitoes in Tibet in 2009, but until this report, human cases had not been confirmed in the mainland population. Retrospective serologic analysis of laboratory-confirmed JE cases from 2018–2020 previously identified two patients with possible JEV GV infection in eastern China (Shandong and Zhejiang provinces), suggesting prior, perhaps cryptic, circulation.
The detection of a confirmed JEV GV human case in central China (Wuhan) in 2025, together with previous detections such as the XZ0934 strain from Tibet and retrospective indications in eastern provinces, supports the presence of JEV GV across multiple regions of China (southwestern, central, and eastern). The authors highlight that, alongside reported increases and geographic expansion of other emergent genotypes (GIV and GV) into regions such as Australia and South Korea, these observations underscore the need to strengthen genotype-based detection and surveillance of JEV. Genotype-specific monitoring can better inform prevention, vaccination policy considerations, and vector control strategies.
This report confirms a laboratory-documented human infection with Japanese encephalitis virus genotype V in mainland China in 2025, demonstrated by CSF qRT-PCR positivity, JEV IgM serology, and complete-genome sequencing with phylogenetic placement. The neonate’s fatal clinical course emphasizes the potential severity of JEV GV infection. Phylogenetic findings show distinct clades among GV strains with a clear phylogeographic pattern, reflecting independent viral evolution in China and South Korea after reemergence. These findings point to an ongoing and evolving public health threat from JEV GV and argue for enhanced, genotype-informed surveillance and detection to guide JE prevention and control efforts.
The work reported was supported by Major Projects of the National Nature Science Foundation of China (project no. 81290342).