{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T11:52:08Z","timestamp":1789386728815,"version":"build-2803163510"},"reference-count":104,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T00:00:00Z","timestamp":1748304000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["32002312"],"award-info":[{"award-number":["32002312"]}]},{"name":"National Natural Science Foundation of China","award":["Y2023024"],"award-info":[{"award-number":["Y2023024"]}]},{"name":"Science and Technology Project of Wenzhou, Zhejiang, China","award":["32002312"],"award-info":[{"award-number":["32002312"]}]},{"name":"Science and Technology Project of Wenzhou, Zhejiang, China","award":["Y2023024"],"award-info":[{"award-number":["Y2023024"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The Japanese encephalitis virus is an arbovirus that causes severe damage to the central nervous system. At present, there are still 67,900 cases of Japanese encephalitis worldwide every year, which poses a global public health concern and causes great economic losses to animal husbandry. In this study, we analyzed the epidemiology, transmission, and evolution of JEV based on the NCBI database. E and NS1 were emphatically analyzed for amino acid variation and predicted protein structure. Gene recombination and the evolutionary rate of JEV were analyzed using RDP 4 and BEAST. The maximum clade credibility tree of E was reconstructed to estimate the time of the most recent common ancestor. Chinese genotype \u2160 (GI) strain recombination events occurred in the C, M\/PrM, E, NS2A, NS4B, and NS5 proteins, and genotype III (GIII) strains occurred in the E, NS1, NS3, NS4A, and NS5 proteins. The average evolutionary rates of JEV were comparable (3.3830 \u00d7 10\u22124, 2.0481 \u00d7 10\u22124, 3.5650 \u00d7 10\u22124, 2.2423 \u00d7 10\u22124, 3.0844 \u00d7 10\u22124, and 1.9757 \u00d7 10\u22124 substitutions\/site\/year for the JEV-I whole genome, JEV-III whole genome, JEV-I E gene, JEV-III E gene, JEV-I NS1 gene, and JEV-III NS1 gene, respectively). The MCC tree revealed the evolutionary order was G\u2162, G\u2160, G\u2164, G\u2161, and G\u2163. This study was expected to provide theoretical support for vaccine development and comprehensive prevention and treatment of JEV.<\/jats:p>","DOI":"10.3390\/microorganisms13061226","type":"journal-article","created":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T09:29:36Z","timestamp":1748338176000},"page":"1226","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Epidemiology, Transmission, and Evolution of Japanese Encephalitis Virus"],"prefix":"10.3390","volume":"13","author":[{"given":"Chengcheng","family":"Peng","sequence":"first","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiling","family":"Qin","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Yu","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujia","family":"Hao","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuge","family":"Yuan","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenzhou","family":"Ma","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengpeng","family":"Xiao","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Li","sequence":"additional","affiliation":[{"name":"Wenzhou Key Laboratory for Virology and Immunology, Institute of Virology, Wenzhou University, Wenzhou 325035, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"704","DOI":"10.4269\/ajtmh.2003.68.704","article-title":"Acute undifferentiated fever caused by infection with Japanese encephalitis virus","volume":"68","author":"Watt","year":"2003","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1007\/s00705-019-04218-9","article-title":"Development and application of a monoclonal-antibody-based blocking ELISA for detection of Japanese encephalitis virus NS1 antibodies in swine","volume":"164","author":"Zhou","year":"2019","journal-title":"Arch. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1007\/s11262-018-1559-y","article-title":"Genomic changes in an attenuated genotype I Japanese encephalitis virus and comparison with virulent parental strain","volume":"54","author":"Zhou","year":"2018","journal-title":"Virus Genes"},{"key":"ref_4","unstructured":"Cook, H., Hayes, D., Myer, S., Weaver, M., and Wagstrom, L. (2023). Potential Impacts of Introduction and Establishment of Japanese Encephalitis Virus in the United States Swine Herd, Swine Health Information Center."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/0042-6822(87)90144-9","article-title":"Complete nucleotide sequence of the Japanese encephalitis virus genome RNA","volume":"161","author":"Sumiyoshi","year":"1987","journal-title":"Virology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/375291a0","article-title":"The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution","volume":"375","author":"Rey","year":"1995","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1016\/j.celrep.2019.01.036","article-title":"Flavivirus NS1 Triggers Tissue-Specific Vascular Endothelial Dysfunction Reflecting Disease Tropism","volume":"26","author":"Glasner","year":"2019","journal-title":"Cell Rep."},{"key":"ref_8","unstructured":"Dan, M. (2021). The Clinical Characteristics of Japanese Encephalitis in Adults and the Value of Serum Biomarkers in its Diagnosis and Prognostic Evaluation. [Master\u2019s Thesis, Ningxia Medical University]."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"242","DOI":"10.4269\/ajtmh.2001.65.242","article-title":"Phylogenetic analysis of Japanese encephalitis virus: Envelope gene based analysis reveals a fifth genotype, geographic clustering, and multiple introductions of the virus into the Indian subcontinent","volume":"65","author":"Uchil","year":"2001","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Li, C., Chen, X., Hu, J., Jiang, D., Cai, D., and Li, Y. (2022). A Recombinant Genotype I Japanese Encephalitis Virus Expressing a Gaussia Luciferase Gene for Antiviral Drug Screening Assay and Neutralizing Antibodies Detection. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232415548"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Van den Eynde, C., Sohier, C., Matthijs, S., and De Regge, N. (2022). Japanese Encephalitis Virus Interaction with Mosquitoes: A Review of Vector Competence, Vector Capacity and Mosquito Immunity. Pathogens, 11.","DOI":"10.3390\/pathogens11030317"},{"key":"ref_12","unstructured":"Gao, Y. (2022). Signaling Pathways of Inflammatory Response in SwineTestis Cells Infected by Japanese Encephalitis Virus. [Master\u2019s Thesis, Yanbian University]."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2438661","DOI":"10.1080\/22221751.2024.2438661","article-title":"Mosquito populations originating from nonendemic areas have the potential to transmit recently emerging Japanese encephalitis virus genotype IV","volume":"14","author":"Faizah","year":"2024","journal-title":"Emerg. Microbes Infect."},{"key":"ref_14","first-page":"269","article-title":"Natural infection of bat with Japanese Encephalitis Virus","volume":"6","author":"Zhang","year":"1990","journal-title":"Chin. J. Virol."},{"key":"ref_15","first-page":"22","article-title":"Isolation of encephalitis B virus from Taiwan midge, Lasiohelea fuscatus, of the family Mytilidae","volume":"3","author":"Wu","year":"1957","journal-title":"Acta Microbiol. Sin."},{"key":"ref_16","first-page":"293","article-title":"Small mammals; Natural-focus disease","volume":"21","author":"Ju","year":"2010","journal-title":"Chin. J. Vector Biol. Control"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Arai, S., Kuwata, R., Higa, Y., Maekawa, Y., Tsuda, Y., Roychoudhury, S., Bertuso, A.G., Phong, T.V., Yen, N.T., and Etoh, T. (2022). Two hidden taxa in the Japanese encephalitis vector mosquito, Culex tritaeniorhynchus, and the potential for long-distance migration from overseas to Japan. PLoS Neglected Trop. Dis., 16.","DOI":"10.1371\/journal.pntd.0010543"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Sewgobind, S., Johnson, N., and Mansfield, K.L. (2022). JMM Profile: Japanese encephalitis virus: An emerging threat. J. Med. Microbiol., 71.","DOI":"10.1099\/jmm.0.001620"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Wang, Q., Yang, S., Yang, K., Li, X., Dai, Y., Zheng, Y., Cao, S., Yan, Q., Huang, X., and Wen, Y. (2023). CD4 is an important host factor for Japanese encephalitis virus entry and replication in PK-15 cells. Vet. Microbiol., 287.","DOI":"10.1016\/j.vetmic.2023.109913"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Majumdar, A., Siva Venkatesh, I.P., Swarup, V., and Basu, A. (2024). Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR-200a-3p\/ZBTB20\/IK\u03b2\u03b1 axis. mBio, 15.","DOI":"10.1128\/mbio.01321-24"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Marti, A., Nater, A., Pego Magalhaes, J., Almeida, L., Lewandowska, M., Liniger, M., Ruggli, N., Grau-Roma, L., Brito, F., and Alnaji, F.G. (2024). Fitness adaptations of Japanese encephalitis virus in pigs following vector-free serial passaging. PLoS Pathog., 20.","DOI":"10.1101\/2024.02.20.581151"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Chapagain, S., Pal Singh, P., Le, K., Safronetz, D., Wood, H., and Karniychuk, U. (2022). Japanese encephalitis virus persists in the human reproductive epithelium and porcine reproductive tissues. PLoS Neglected Trop. Dis., 16.","DOI":"10.1371\/journal.pntd.0010656"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Calder\u00f3n-Pel\u00e1ez, M.A., Velandia-Romero, M.L., Bastidas-Legarda, L.Y., Beltr\u00e1n, E.O., Camacho-Ortega, S.J., and Castellanos, J.E. (2019). Dengue Virus Infection of Blood-Brain Barrier Cells: Consequences of Severe Disease. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01435"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"263","DOI":"10.4161\/hv.26902","article-title":"Japanese encephalitis: The virus and vaccines","volume":"10","author":"Yun","year":"2014","journal-title":"Hum. Vaccin Immunother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1093\/cid\/cis883","article-title":"Cross-protective capacity of Japanese encephalitis (JE) vaccines against circulating heterologous JE virus genotypes","volume":"56","author":"Erra","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Lee, A.R., Kim, W.J., Choi, H., Kim, S.H., Hong, S.Y., Shim, S.M., Lee, H.I., Song, J.M., Kim, S.J., and Ishikawa, T. (2024). Genotype III-Based Japanese Encephalitis Vaccines Exhibit Diminished Neutralizing Response to Re-emerging Genotype V. J. Infect. Dis.","DOI":"10.1093\/infdis\/jiae589"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1093\/jtm\/tay009","article-title":"Japanese encephalitis: The vectors, ecology and potential for expansion","volume":"25","author":"Pearce","year":"2018","journal-title":"J. Travel Med."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Mulvey, P., Duong, V., Boyer, S., Burgess, G., Williams, D.T., Dussart, P., and Horwood, P.F. (2021). The Ecology and Evolution of Japanese Encephalitis Virus. Pathogens, 10.","DOI":"10.3390\/pathogens10121534"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: Homology modelling of protein structures and complexes","volume":"46","author":"Waterhouse","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"D313","DOI":"10.1093\/nar\/gkw1132","article-title":"The SWISS-MODEL Repository-new features and functionality","volume":"45","author":"Bienert","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"S162","DOI":"10.1002\/elps.200900140","article-title":"Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective","volume":"30","author":"Guex","year":"2009","journal-title":"Electrophoresis"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1093\/bioinformatics\/btz828","article-title":"QMEANDisCo-distance constraints applied on model quality estimation","volume":"36","author":"Studer","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., and Schwede, T. (2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci. Rep., 7.","DOI":"10.1038\/s41598-017-09654-8"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s12985-023-01961-z","article-title":"A new PEDV strain CH\/HLJJS\/2022 can challenge current detection methods and vaccines","volume":"20","author":"Yao","year":"2023","journal-title":"Virol. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: Protein structure and function prediction","volume":"12","author":"Yang","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: A unified platform for automated protein structure and function prediction","volume":"5","author":"Roy","year":"2010","journal-title":"Nat. Protoc."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-40"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/s12985-022-01892-1","article-title":"Molecular characteristics of a coxsackievirus A12 strain in Zhejiang of China, 2019","volume":"19","author":"Hu","year":"2022","journal-title":"Virol. J."},{"key":"ref_40","unstructured":"Schrodinger, LLC (2015). The PyMOL Molecular Graphics System, Version 1.8, Schrodinger, LLC."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Nageeb, W.M., AlHarbi, N., Alrehaili, A.A., Zakai, S.A., Elfadadny, A., and Hetta, H.F. (2023). Global genomic epidemiology of chromosomally mediated non-enzymatic carbapenem resistance in Acinetobacter baumannii: On the way to predict and modify resistance. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1271733"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_43","first-page":"310","article-title":"Prediction of glycosylation across the human proteome and the correlation to protein function","volume":"7","author":"Gupta","year":"2002","journal-title":"Pac. Symp. Biocomput."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"W325","DOI":"10.1093\/nar\/gku383","article-title":"GPS-SUMO: A tool for the prediction of sumoylation sites and SUMO-interaction motifs","volume":"42","author":"Zhao","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"5640","DOI":"10.1128\/JVI.02427-08","article-title":"Role of N-linked glycosylation for sindbis virus infection and replication in vertebrate and invertebrate systems","volume":"83","author":"Knight","year":"2009","journal-title":"J. Virol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3409","DOI":"10.1002\/pmic.200800646","article-title":"Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0","volume":"9","author":"Ren","year":"2009","journal-title":"Proteomics"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e1037","DOI":"10.1111\/tbed.14395","article-title":"Origin, genetic diversity, adaptive evolution and transmission dynamics of Getah virus","volume":"69","author":"Shi","year":"2022","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1093\/protein\/gzn039","article-title":"CSS-Palm 2.0: An updated software for palmitoylation sites prediction","volume":"21","author":"Ren","year":"2008","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Peng, C., Zhang, D., Li, C., Li, Y., Zhang, H., Li, N., and Xiao, P. (2022). Rhinolophus sinicus virome revealed multiple novel mosquito-borne zoonotic viruses. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.960507"},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Fang, Y., Zhang, W., Xue, J.B., and Zhang, Y. (2021). Monitoring Mosquito-Borne Arbovirus in Various Insect Regions in China in 2018. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.640993"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"198229","DOI":"10.1016\/j.virusres.2020.198229","article-title":"A highly pathogenic recombinant infectious bronchitis virus with adaptability in cultured cells","volume":"292","author":"Huang","year":"2021","journal-title":"Virus Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1111\/1755-0998.13096","article-title":"PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies","volume":"20","author":"Zhang","year":"2020","journal-title":"Mol. Ecol. Resour."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Jagtap, S., Pattabiraman, C., Sankaradoss, A., Krishna, S., and Roy, R. (2023). Evolutionary dynamics of dengue virus in India. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1010862"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Murrell, B., Wertheim, J.O., Moola, S., Weighill, T., Scheffler, K., and Kosakovsky Pond, S.L. (2012). Detecting individual sites subject to episodic diversifying selection. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002764"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: A sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: A comparison of methods for detecting amino acid sites under selection","volume":"22","author":"Frost","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: A fast, unconstrained bayesian approximation for inferring selection","volume":"30","author":"Murrell","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/bti079","article-title":"HyPhy: Hypothesis testing using phylogenies","volume":"21","author":"Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1093\/molbev\/msz197","article-title":"HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies","volume":"37","author":"Poon","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: A suite of phylogenetic analysis tools for evolutionary biology","volume":"26","author":"Delport","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1093\/molbev\/msx335","article-title":"Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes","volume":"35","author":"Weaver","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1093\/molbev\/msv035","article-title":"Gene-wide identification of episodic selection","volume":"32","author":"Murrell","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"e14419","DOI":"10.7717\/peerj.14419","article-title":"Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand","volume":"10","author":"Noisumdaeng","year":"2022","journal-title":"PeerJ"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Yang, X.C., Hong, Z.P., Wang, Y., Meng, N., Hu, Y., Xiong, Q.Y., Qin, D.W., Shen, D., and Yang, X.L. (2023). Growth history of hepatitis C virus among HIV\/HCV co-infected patients in Guizhou Province. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1171892"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"e0157524","DOI":"10.1128\/jvi.01575-24","article-title":"Tracing more than two decades of Japanese encephalitis virus circulation in mainland China","volume":"99","author":"Li","year":"2025","journal-title":"J. Virol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"10832","DOI":"10.1038\/ncomms10832","article-title":"Vector-free transmission and persistence of Japanese encephalitis virus in pigs","volume":"7","author":"Ricklin","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/JVI.00108-18","article-title":"Acidity\/Alkalinity of Japanese Encephalitis Virus E Protein Residue 138 Alters Neurovirulence in Mice","volume":"92","author":"Zheng","year":"2018","journal-title":"J. Virol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1007\/s00705-018-3765-2","article-title":"Mutation of I176R in the E coding region weakens Japanese encephalitis virus neurovirulence, but not its growth rate in BHK-21 cells","volume":"163","author":"Zhou","year":"2018","journal-title":"Arch. Virol."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Yang, J., Yang, H., Li, Z., Wang, W., Lin, H., Liu, L., Ni, Q., Liu, X., Zeng, X., and Wu, Y. (2017). Envelope Protein Mutations L107F and E138K Are Important for Neurovirulence Attenuation for Japanese Encephalitis Virus SA14-14-2 Strain. Viruses, 9.","DOI":"10.3390\/v9010020"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Yun, S.I., Song, B.H., Kim, J.K., Yun, G.N., Lee, E.Y., Li, L., Kuhn, R.J., Rossmann, M.G., Morrey, J.D., and Lee, Y.M. (2014). A molecularly cloned, live-attenuated japanese encephalitis vaccine SA14-14-2 virus: A conserved single amino acid in the ij Hairpin of the Viral E glycoprotein determines neurovirulence in mice. PLoS Pathog., 10.","DOI":"10.1371\/journal.ppat.1004290"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"6328","DOI":"10.1128\/JVI.00219-15","article-title":"Genetic Determinants of Japanese Encephalitis Virus Vaccine Strain SA14-14-2 That Govern Attenuation of Virulence in Mice","volume":"89","author":"Gromowski","year":"2015","journal-title":"J. Virol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.micpath.2017.08.046","article-title":"Enhanced cytopathic effect of Japanese encephalitis virus strain SA14-14-2: Probable association of mutation in amino acid of its envelope protein","volume":"111","author":"Nath","year":"2017","journal-title":"Microb. Pathog."},{"key":"ref_81","first-page":"67","article-title":"Post-translational modifications in viral infection","volume":"7","author":"Shan","year":"2017","journal-title":"Chin. J. Viral. Di"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"182","DOI":"10.4161\/rna.8.2.15663","article-title":"RNA virus replication, transcription and recombination","volume":"8","author":"White","year":"2011","journal-title":"RNA Biol."},{"key":"ref_83","unstructured":"Zhou, Y. (2018). Neurovirulence Study of I176R Mutation in the E-Coding Region of Japanese Encephalitis Virus. [Master\u2019s Thesis, Sichuan Agricultural University]."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.3201\/eid1508.090149","article-title":"Past, present, and future of Japanese encephalitis","volume":"15","author":"Hills","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Ghosh, D., and Basu, A. (2009). Japanese encephalitis-a pathological and clinical perspective. PLoS Neglected Trop. Dis., 3.","DOI":"10.1371\/journal.pntd.0000437"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1099\/vir.0.79797-0","article-title":"Shift in Japanese encephalitis virus (JEV) genotype circulating in northern Vietnam: Implications for frequent introductions of JEV from Southeast Asia to East Asia","volume":"85","author":"Nga","year":"2004","journal-title":"J. Gen. Virol."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Wang, A., Pang, Z., Liu, L., Ma, Q., Han, Y., Guan, Z., Qin, H., and Niu, G. (2021). Detection and Phylogenetic Analysis of a Novel Tick-Borne Virus in Yunnan and Guizhou Provinces, Southwestern China. Pathogens, 10.","DOI":"10.3390\/pathogens10091143"},{"key":"ref_88","unstructured":"Qu, L. (2023). Screening and Identification of Arboviruses Carried by Ticks and Mosquitoes in Some Parts of Yunnan. [Master\u2019s Thesis, Kunming University of Science and Technology]."},{"key":"ref_89","unstructured":"Ma, X. (2021). Population Genetic Structure of Culex Tritaeniorhynchus in Mainland China. [Master\u2019s Thesis, Northeast Agricultural University]."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1186\/s13071-020-04285-x","article-title":"Laboratory transmission potential of British mosquitoes for equine arboviruses","volume":"13","author":"Chapman","year":"2020","journal-title":"Parasit Vectors"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/JVI.01164-20","article-title":"Mosquito Defensins Enhance Japanese Encephalitis Virus Infection by Facilitating Virus Adsorption and Entry within the Mosquito","volume":"94","author":"Liu","year":"2020","journal-title":"J. Virol."},{"key":"ref_92","doi-asserted-by":"crossref","unstructured":"Sun, Y., Ding, H., Zhao, F., Yan, Q., Li, Y., Niu, X., Zeng, W., Wu, K., Ling, B., and Fan, S. (2022). Genomic Characteristics and E Protein Bioinformatics Analysis of JEV Isolates from South China from 2011 to 2018. Vaccines, 10.","DOI":"10.3390\/vaccines10081303"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Kotaki, T., Nagai, Y., Yamanaka, A., Konishi, E., and Kameoka, M. (2022). Japanese Encephalitis DNA Vaccines with Epitope Modification Reduce the Induction of Cross-Reactive Antibodies against Dengue Virus and Antibody-Dependent Enhancement of Dengue Virus Infection. Vaccines, 10.","DOI":"10.3390\/vaccines10091411"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1099\/vir.0.040238-0","article-title":"Mutation analysis of the cross-reactive epitopes of Japanese encephalitis virus envelope glycoprotein","volume":"93","author":"Chiou","year":"2012","journal-title":"J. Gen. Virol."},{"key":"ref_95","doi-asserted-by":"crossref","unstructured":"Banerjee, S., Sen Gupta, P.S., and Bandyopadhyay, A.K. (2017). Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India. BMC Immunol., 18.","DOI":"10.1186\/s12865-017-0197-9"},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1172\/JCI131116","article-title":"Defective glycosylation and multisystem abnormalities characterize the primary immunodeficiency XMEN disease","volume":"130","author":"Ravell","year":"2020","journal-title":"J. Clin. Investig."},{"key":"ref_97","first-page":"359","article-title":"Effect of tunicamycin on expression of epitopes on Japanese encephalitis virus glycoprotein E in porcine kidney cells","volume":"44","author":"Lad","year":"2000","journal-title":"Acta Virol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"4162","DOI":"10.1128\/JVI.76.9.4162-4171.2002","article-title":"Japanese encephalitis virus infection initiates endoplasmic reticulum stress and an unfolded protein response","volume":"76","author":"Su","year":"2002","journal-title":"J. Virol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"7846","DOI":"10.1128\/JVI.00789-08","article-title":"A single N-linked glycosylation site in the Japanese encephalitis virus prM protein is critical for cell type-specific prM protein biogenesis, virus particle release, and pathogenicity in mice","volume":"82","author":"Kim","year":"2008","journal-title":"J. Virol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1186\/1743-422X-8-138","article-title":"Mutation of putative N-linked glycosylation sites in Japanese encephalitis virus premembrane and envelope proteins enhances humoral immunity in BALB\/C mice after DNA vaccination","volume":"8","author":"Zhang","year":"2011","journal-title":"Virol. J."},{"key":"ref_101","doi-asserted-by":"crossref","unstructured":"Ishida, K., Yagi, H., Kato, Y., and Morita, E. (2023). N-linked glycosylation of flavivirus E protein contributes to viral particle formation. PLoS Pathog., 19.","DOI":"10.1371\/journal.ppat.1011681"},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"e0038223","DOI":"10.1128\/jvi.00382-23","article-title":"Palmitoylation at Residue C221 of Japanese Encephalitis Virus NS2A Protein Contributes to Viral Replication Efficiency and Virulence","volume":"97","author":"Ma","year":"2023","journal-title":"J. Virol."},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Sistrom, M., Andrews, H., and Edwards, D.L. (2024). Comparative genomics of Japanese encephalitis virus shows low rates of recombination and a small subset of codon positions under episodic diversifying selection. PLoS Neglected Trop. Dis., 18.","DOI":"10.1371\/journal.pntd.0011459"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"2023","DOI":"10.3201\/eid2012.140684","article-title":"Molecular evolution of peste des petits ruminants virus","volume":"20","author":"Muniraju","year":"2014","journal-title":"Emerg. Infect. Dis."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/6\/1226\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:41:34Z","timestamp":1760031694000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/13\/6\/1226"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,27]]},"references-count":104,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6]]}},"alternative-id":["microorganisms13061226"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms13061226","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,27]]}}}