29Introduction: Japanese encephalitis virus (JEV), in the genus Flavivirus, family 30 Flaviviridae, is the leading cause of viral encephalitis in the Asian-Pacific region. JEV 31 has a wide range of vector hosts, including mosquitoes, swine, and wading birds. Culex 32 species, especially Culex tritaeniorhynchus, are the main vectors for JEV transmission.
33JEV has been classified into five genotypes (G1-G5). JEV G1, G3, and G5 isolates 34 have been found in China. 35 Methods: More than 200,000 mosquitoes collected in 14 provinces in China from 2004 36 to 2016 were examined for JEV using a TaqMan real-time RT-PCR assay. The JEV 37 envelope (E) gene was sequenced from positive pools. The nucleic acid sequences were 38 analyzed and aligned using ClustalX ver. 2.0. Representative JEV envelope (E) gene 39 sequences were downloaded from GenBank and compared with the newly obtained JEV 40 sequences. MEGA 5.05 was used to generate a phylogenetic tree based on the JEV 41 sequences.42Results: More than 200,000 mosquitoes were divided into 3107 pools to test for JEV.
43Of the pools, 9.04% (281/3107) were positive. The JEV obtained from mosquitoes 44 included three genotypes (G1, G3, and G5). JEV G1 was detected from different 45 provinces during 2004-2016. G1 was the dominant genotype circulating in nature, 46 comprising 98.93% (278/281). JEV G3 was detected in Yunnan and Chongqing 47 Provinces before 2010; JEV G5 was detected only in Tibet. No pools were positive for 48 JEV G2 and G4. C. tritaeniorhynchus was the major mosquito species and the principal 49 vector for transmitting JEV in China. The results of the TaqMan real-time RT-PCR 50 assay and phylogenetic analysis consistently indicated that all 50 newly identified JEV 51 sequences belonged to JEV G1. 3 52 Conclusion: G1 is the main genotype of JEV circulating in nature in China. Some G3 53 and G5 were found, but no G2 or G4. 54 55 Author summary 56 Japanese encephalitis virus (JEV) is a member of the genus Flavivirus, family 57 Flaviviridae and is the major pathogen agent of Japanese encephalitis (JE) in the 58 Asian-Pacific region. The fatality rate of JE is 20-30%. JEV consists of five genotypes 59 (G1-G5). The predominant genotype was G3 before the 20 th century. G1 and G3 60 co-circulated in China at the end of the 20 th and early 21 st century. JEV G1 is the 61 youngest genotype and has gradually been found in many areas worldwide. Using a 62 sensitive TaqMan real-time RT-PCR assay, this study examined 3107 pools of 63 mosquito. The main genotype of Japanese encephalitis virus in China was G1, with 64 some G3 and G5, but no G2 or G4. C. tritaeniorhynchus was the major mosquito 65 species and the principal vector for transmitting JEV in China. TaqMan real-time 66 RT-PCR assay and phylogenetic analysis consistently indicated that all 50 newly 67 identified JEV sequences belonged to JEV G1. 68 69 70