{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T23:27:13Z","timestamp":1776986833716,"version":"3.51.4"},"reference-count":48,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2023,6,2]],"date-time":"2023-06-02T00:00:00Z","timestamp":1685664000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003787","name":"Natural Science Foundation of Hebei Province","doi-asserted-by":"publisher","award":["C2020402050"],"award-info":[{"award-number":["C2020402050"]}],"id":[{"id":"10.13039\/501100003787","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Japanese encephalitis virus (JEV) causes acute viral encephalitis in humans and reproductive disorders in pigs. JEV emerged during the 1870s in Japan, and since that time, JEV has been transmitted exclusively throughout Asia, according to known reporting and sequencing records. A recent JEV outbreak occurred in Australia, affecting commercial piggeries across different temperate southern Australian states, and causing confirmed infections in humans. A total of 47 human cases and 7 deaths were reported. The recent evolving situation of JEV needs to be reported due to its continuous circulation in endemic regions and spread to non-endemics areas. Here, we reconstructed the phylogeny and population dynamics of JEV using recent JEV isolates for the future perception of disease spread. Phylogenetic analysis shows the most recent common ancestor occurred about 2993 years ago (YA) (95% Highest posterior density (HPD), 2433 to 3569). Our results of the Bayesian skyline plot (BSP) demonstrates that JEV demography lacks fluctuations for the last two decades, but it shows that JEV genetic diversity has increased during the last ten years. This indicates the potential JEV replication in the reservoir host, which is helping it to maintain its genetic diversity and to continue its dispersal into non-endemic areas. The continuous spread in Asia and recent detection from Australia further support these findings. Therefore, an enhanced surveillance system is needed along with precautionary measures such as regular vaccination and mosquito control to avoid future JEV outbreaks.<\/jats:p>","DOI":"10.3390\/v15061312","type":"journal-article","created":{"date-parts":[[2023,6,2]],"date-time":"2023-06-02T01:33:54Z","timestamp":1685669634000},"page":"1312","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Recent Population Dynamics of Japanese Encephalitis Virus"],"prefix":"10.3390","volume":"15","author":[{"given":"Jinpeng","family":"Xu","sequence":"first","affiliation":[{"name":"School of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China"},{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1919-3653","authenticated-orcid":false,"given":"Abdul","family":"Wahaab","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sawar","family":"Khan","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"},{"name":"Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohsin","family":"Nawaz","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"},{"name":"Faculty of Veterinary and Animal sciences, University of Poonch, Rawalakot 12350, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4762-1635","authenticated-orcid":false,"given":"Muhammad Naveed","family":"Anwar","sequence":"additional","affiliation":[{"name":"Institute of Microbiology, University of Agriculture, Faisalabad 38000, Pakistan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3246-6273","authenticated-orcid":false,"given":"Jianchao","family":"Wei","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muddassar","family":"Hameed","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"},{"name":"Center for Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiyong","family":"Ma","sequence":"additional","affiliation":[{"name":"Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"766","DOI":"10.2471\/BLT.10.085233","article-title":"Estimated global incidence of Japanese encephalitis: A systematic review","volume":"89","author":"Campbell","year":"2011","journal-title":"Bull. World Health Organ."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Schuh, A.J., Ward, M.J., Brown, A.L., and Barrett, A.D.T. (2013). Phylogeography of Japanese encephalitis virus: Genotype is associated with climate. PLoS Negl. Trop. Dis., 7.","DOI":"10.1371\/journal.pntd.0002411"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Hameed, M., Liu, K., Anwar, M.N., Wahaab, A., Safdar, A., Di, D., Boruah, P., Xu, J., Wang, X., and Li, B. (2019). The emerged genotype I of Japanese encephalitis virus shows an infectivity similar to genotype III in Culex pipiens mosquitoes from China. PLoS Negl. Trop. Dis., 13.","DOI":"10.1371\/journal.pntd.0007716"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Hameed, M., Wahaab, A., Nawaz, M., Khan, S., Nazir, J., Liu, K., Wei, J., and Ma, Z. (2021). Potential Role of Birds in Japanese Encephalitis Virus Zoonotic Transmission and Genotype Shift. Viruses, 13.","DOI":"10.20944\/preprints202101.0549.v1"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1016\/S0140-6736(08)60238-X","article-title":"Pathogenic flaviviruses","volume":"371","author":"Gould","year":"2008","journal-title":"Lancet"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.pneurobio.2010.01.008","article-title":"Overview: Japanese encephalitis","volume":"91","author":"Misra","year":"2010","journal-title":"Prog. Neurobiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"579","DOI":"10.15585\/mmwr.mm6622a3","article-title":"Japanese Encephalitis Surveillance and Immunization\u2014Asia and Western Pacific Regions, 2016","volume":"66","author":"Heffelfinger","year":"2017","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s12985-015-0270-z","article-title":"Insights into the evolutionary history of Japanese encephalitis virus (JEV) based on whole-genome sequences comprising the five genotypes","volume":"12","author":"Gao","year":"2015","journal-title":"Virol. J."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Xu, G., Gao, T., Wang, Z., Zhang, J., Cui, B., Shen, X., Zhou, A., Zhang, Y., Zhao, J., and Liu, H. (2023). Re-Emerged Genotype IV of Japanese Encephalitis Virus Is the Youngest Virus in Evolution. Viruses, 15.","DOI":"10.3390\/v15030626"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.3201\/eid2306.152115","article-title":"Epidemiologic Survey of Japanese Encephalitis Virus Infection, Tibet, China, 2015","volume":"23","author":"Zhang","year":"2017","journal-title":"Emerg. Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"69","DOI":"10.4103\/0972-9062.203186","article-title":"Evidence of JEV in Culex tritaeniorhynchus and pigs from high altitude regions of Tibet, China","volume":"54","author":"Zhang","year":"2017","journal-title":"J. Vector Borne Dis."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.ijregi.2022.05.005","article-title":"Japanese encephalitis virus genotype III from mosquitoes in Tarlac, Philippines","volume":"4","author":"Aure","year":"2022","journal-title":"IJID Reg."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Howard-Jones, A.R., Pham, D., Jeoffreys, N., Eden, J.-S., Hueston, L., Kesson, A.M., Nagendra, V., Samarasekara, H., Newton, P., and Chen, S.C.-A. (2022). Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia. Viruses, 14.","DOI":"10.3390\/v14091853"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1056\/NEJMc2207004","article-title":"Japanese Encephalitis in Australia\u2014A Sentinel Case","volume":"387","author":"Waller","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Liu, W., Fu, S., Ma, X., Chen, X., Wu, D., Zhou, L., Yin, Q., Li, F., He, Y., and Lei, W. (2020). An outbreak of Japanese encephalitis caused by genotype Ib Japanese encephalitis virus in China, 2018: A laboratory and field investigation. PLoS Negl. Trop. Dis., 14.","DOI":"10.1371\/journal.pntd.0008312"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/s40249-021-00838-z","article-title":"Molecular epidemiology of mosquito-borne viruses at the China\u2013Myanmar border: Discovery of a potential epidemic focus of Japanese encephalitis","volume":"10","author":"Fang","year":"2021","journal-title":"Infect. Dis. Poverty"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"591478","DOI":"10.3389\/fmicb.2020.591478","article-title":"A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan\u2013Myanmar Border of China","volume":"11","author":"Hameed","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1111\/tbed.13697","article-title":"Detection of Japanese encephalitis virus in mosquitoes from Xinjiang during next-generation sequencing arboviral surveillance","volume":"68","author":"Hameed","year":"2021","journal-title":"Transbound. Emerg. Dis."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Sanborn, M.A., Wuertz, K.M., Heung-Chul, K., Yang, Y., Li, T., Pollett, S.D., Jarman, R.G., Berry, I.M., Klein, T.A., and Hang, J. (2021). Identification of Japanese Encephalitis Virus Genotype V and Other Mosquito-borne Viruses in Camp Humphreys, Republic of Korea, using Metagenomic Analysis. bioRxiv.","DOI":"10.1101\/2021.03.15.435489"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Mackenzie, J.S., Williams, D.T., Hurk, A.F.v.D., Smith, D.W., and Currie, B.J. (2022). Japanese Encephalitis Virus: The Emergence of Genotype IV in Australia and Its Potential Endemicity. Viruses, 14.","DOI":"10.3390\/v14112480"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Hurk, A.F.V.D., Skinner, E., Ritchie, S.A., and Mackenzie, J.S. (2022). The Emergence of Japanese Encephalitis Virus in Australia in 2022: Existing Knowledge of Mosquito Vectors. Viruses, 14.","DOI":"10.3390\/v14061208"},{"key":"ref_22","unstructured":"Hall, T.A. (1999). BioEdit: A User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95\/98\/NT, Information Retrieval Ltd."},{"key":"ref_23","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_24","doi-asserted-by":"crossref","unstructured":"Bouckaert, R., Heled, J., K\u00fchnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M.A., Rambaut, A., and Drummond, A.J. (2014). BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Comput. Biol., 10.","DOI":"10.1371\/journal.pcbi.1003537"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/genetics\/161.3.1307","article-title":"Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data","volume":"161","author":"Drummond","year":"2002","journal-title":"Genetics"},{"key":"ref_26","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_27","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1001\/archneurpsyc.1947.02300270048004","article-title":"Japanese B encephalitis; clinical observations in an outbreak on Okinawa Shima","volume":"57","author":"Lewis","year":"1947","journal-title":"Arch. Neurol. Psychiatry"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Gao, X., Nasci, R., and Liang, G. (2010). The neglected arboviral infections in mainland China. PLoS Negl. Trop. Dis., 4.","DOI":"10.1371\/journal.pntd.0000624"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3635","DOI":"10.1016\/j.vaccine.2010.02.105","article-title":"Phenotypic and genotypic characteristics of Japanese encephalitis attenuated live vaccine virus SA14-14-2 and their stabilities","volume":"28","author":"Yu","year":"2010","journal-title":"Vaccine"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"9847","DOI":"10.1128\/JVI.00825-11","article-title":"Emergence of genotype I of Japanese encephalitis virus as the dominant genotype in Asia","volume":"85","author":"Pan","year":"2011","journal-title":"J. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.coviro.2019.01.001","article-title":"Emergence and re-emergence of mosquito-borne arboviruses","volume":"34","author":"Huang","year":"2019","journal-title":"Curr. Opin. Virol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Peinado, R.D.S., Eberle, R.J., Arni, R.K., and Coronado, M.A. (2022). A Review of Omics Studies on Arboviruses: Alphavirus, Orthobunyavirus and Phlebovirus. Viruses, 14.","DOI":"10.3390\/v14102194"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/molbev\/msv207","article-title":"Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales","volume":"33","author":"Holmes","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"A\u00f1ez, G., Grinev, A., Chancey, C., Ball, C., Akolkar, N., Land, K.J., Winkelman, V., Stramer, S.L., Kramer, L.D., and Rios, M. (2013). Evolutionary dynamics of West Nile virus in the United States, 1999\u20132011: Phylogeny, selection pressure and evolutionary time-scale analysis. PLoS Negl. Trop. Dis., 7.","DOI":"10.1371\/journal.pntd.0002245"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1016\/j.ttbdis.2018.03.032","article-title":"Hungarian tickborne encephalitis viruses isolated from a 0.5-ha focus are closely related to Finnish strains","volume":"9","author":"Egyed","year":"2018","journal-title":"Ticks Tick-Borne Dis."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Bryant, J.E., Holmes, E.C., and Barrett, A.D.T. (2007). Out of Africa: A molecular perspective on the introduction of yellow fever virus into the Americas. PLoS Pathog., 3.","DOI":"10.1371\/journal.ppat.0030075"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1016\/j.actatropica.2018.08.017","article-title":"Japanese encephalitis in Indonesia: An update on epidemiology and transmission ecology","volume":"187","author":"Garjito","year":"2018","journal-title":"Acta Trop."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3091","DOI":"10.1128\/JVI.77.5.3091-3098.2003","article-title":"Origin and evolution of Japanese encephalitis virus in southeast Asia","volume":"77","author":"Solomon","year":"2003","journal-title":"J. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Xiao, C., Li, C., Di, D., Cappelle, J., Liu, L., Wang, X., Pang, L., Xu, J., Liu, K., and Li, B. (2018). Differential replication efficiencies between Japanese encephalitis virus genotype I and III in avian cultured cells and young domestic ducklings. PLoS Negl. Trop. Dis., 12.","DOI":"10.1371\/journal.pntd.0007046"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s40462-015-0029-6","article-title":"Mapping migratory flyways in Asia using dynamic Brownian bridge movement models","volume":"3","author":"Palm","year":"2015","journal-title":"Mov. Ecol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e70","DOI":"10.3346\/jkms.2018.33.e70","article-title":"Changes of epidemiological characteristics of Japanese encephalitis viral infection and birds as a potential viral transmitter in Korea","volume":"33","author":"Bae","year":"2018","journal-title":"J. Korean Med. Sci."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Marini, G., Manica, M., Arnoldi, D., Inama, E., Ros\u00e0, R., and Rizzoli, A. (2020). Influence of Temperature on the Life-Cycle Dynamics of Aedes albopictus Population Established at Temperate Latitudes: A Laboratory Experiment. Insects, 11.","DOI":"10.3390\/insects11110808"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Roche, B., L\u00e9ger, L., L\u2019ambert, G., Lacour, G., Foussadier, R., Besnard, G., Barr\u00e9-Cardi, H., Simard, F., and Fontenille, D. (2015). The Spread of Aedes albopictus in Metropolitan France: Contribution of Environmental Drivers and Human Activities and Predictions for a Near Future. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0125600"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1093\/jme\/tjw165","article-title":"How Zoophilic Japanese Encephalitis Vector Mosquitoes Feed on Humans","volume":"54","author":"Tuno","year":"2017","journal-title":"J. Med. \u00c8ntomol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.envint.2014.07.004","article-title":"The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China","volume":"73","author":"Wang","year":"2014","journal-title":"Environ. Int."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Tu, T., Xu, K., Xu, L., Gao, Y., Zhou, Y., He, Y., Liu, Y., Liu, Q., Ji, H., and Tang, W. (2021). Association between meteorological factors and the prevalence dynamics of Japanese encephalitis. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0247980"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Srivastava, K.S., Jeswani, V., Pal, N., Bohra, B., Vishwakarma, V., Bapat, A.A., Patnaik, Y.P., Khanna, N., and Shukla, R. (2023). Japanese Encephalitis Virus: An Update on the Potential Antivirals and Vaccines. Vaccines, 11.","DOI":"10.3390\/vaccines11040742"},{"key":"ref_48","first-page":"49","article-title":"Japanese Encephalitis Vaccine","volume":"103","author":"Mileno","year":"2020","journal-title":"Rhode Isl. Med. J."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/6\/1312\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:47:29Z","timestamp":1760125649000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/6\/1312"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,2]]},"references-count":48,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,6]]}},"alternative-id":["v15061312"],"URL":"https:\/\/doi.org\/10.3390\/v15061312","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,2]]}}}