{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T15:10:07Z","timestamp":1791299407403,"version":"4.1.0"},"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2018,3,23]],"date-time":"2018-03-23T00:00:00Z","timestamp":1521763200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["653316"],"award-info":[{"award-number":["653316"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0194412","type":"journal-article","created":{"date-parts":[[2018,3,23]],"date-time":"2018-03-23T17:29:01Z","timestamp":1521826141000},"page":"e0194412","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":50,"title":["Development of an improved RT-qPCR Assay for detection of Japanese encephalitis virus (JEV) RNA including a systematic review and comprehensive comparison with published methods"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6772-2855","authenticated-orcid":true,"given":"Tehmina","family":"Bharucha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Onanong","family":"Sengvilaipaseuth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manivanh","family":"Vongsouvath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malavanh","family":"Vongsouvath","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viengmon","family":"Davong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phonepasith","family":"Panyanouvong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G\u00e9raldine","family":"Piorkowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy A.","family":"Garson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul N.","family":"Newton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"de Lamballerie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Dubot-P\u00e9r\u00e8s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,3,23]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1080\/09602010600989620","article-title":"The epidemiology of acute encephalitis","volume":"17","author":"J Granerod","year":"2007","journal-title":"Neuropsychol Rehabilitation"},{"issue":"10","key":"ref2","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1212\/WNL.0b013e3181f11d65","article-title":"Challenge of the unknown: A systematic review of acute encephalitis in non-outbreak situations","volume":"75","author":"J Granerod","year":"2010","journal-title":"Neurology"},{"key":"ref3","article-title":"Epidemiology of infectious encephalitis causes in 2016","author":"A Boucher","year":"2017","journal-title":"Med Mal Infect"},{"key":"ref4","first-page":"435","article-title":"Epidemiology of Japanese encephalitis: past, present, and future prospects","volume":"11","author":"H Wang","year":"2015","journal-title":"Therapeutics and Clinical Risk Management"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"766","DOI":"10.2471\/BLT.10.085233","article-title":"Estimated global incidence of Japanese encephalitis","volume":"89","author":"G Campbell","year":"2011","journal-title":"Bulletin of the World Health Organization"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"235934","DOI":"10.1155\/2015\/235934","article-title":"Epidemiological study of Japanese encephalitis virus in Vientiane, Lao PDR, in 1990s","volume":"2015","author":"M Saito","year":"2015","journal-title":"TheScientificWorldJournal"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12985-015-0278-4","article-title":"Molecular epidemiology of Japanese encephalitis in northern Vietnam, 1964\u20132011: genotype replacement","volume":"12","author":"LP Do","year":"2015","journal-title":"Virology journal"},{"issue":"4","key":"ref8","first-page":"248","article-title":"Molecular characterization of full-length genome of Japanese encephalitis virus isolated in Liaoning Province in 2008","volume":"23","author":"Y-X Cao","year":"2009","journal-title":"Zhonghua shi yan he lin chuang bing du xue za zhi = Zhonghua shiyan he linchuang bingduxue zazhi = Chinese journal of experimental and clinical virology"},{"issue":"9","key":"ref9","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1017\/S095026881100255X","article-title":"Molecular phylogenetic and evolutionary analysis of Japanese encephalitis virus in China","volume":"140","author":"SP Chen","year":"2012","journal-title":"Epidemiology and infection"},{"issue":"12","key":"ref10","doi-asserted-by":"crossref","first-page":"3097","DOI":"10.1007\/s00705-015-2599-4","article-title":"Phylogeographic analysis of Japanese encephalitis virus in India (1956\u20132012)","volume":"160","author":"SS Cherian","year":"2015","journal-title":"Archives of virology"},{"key":"ref11","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":"X Gao","year":"2015","journal-title":"Virology journal"},{"issue":"9","key":"ref12","doi-asserted-by":"crossref","first-page":"e2459","DOI":"10.1371\/journal.pntd.0002459","article-title":"Southernmost Asia is the source of Japanese encephalitis virus (genotype 1) diversity from which the viruses disperse and evolve throughout Asia","volume":"7","author":"X Gao","year":"2013","journal-title":"PLoS neglected tropical diseases"},{"issue":"4","key":"ref13","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1007\/s12250-015-3621-4","article-title":"Investigation of the genotype III to genotype I shift in Japanese encephalitis virus and the impact on human cases","volume":"30","author":"N Han","year":"2015","journal-title":"Virologica Sinica"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1186\/1743-422X-9-271","article-title":"Molecular evidence for the occurrence of Japanese encephalitis virus genotype I and III infection associated with acute encephalitis in patients of West Bengal, India, 2010","volume":"9","author":"A Sarkar","year":"2012","journal-title":"Virology journal"},{"issue":"11","key":"ref15","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.3201\/eid1411.080542","article-title":"Change in Japanese Encephalitis Virus Distribution,Thailand","volume":"14","author":"N Narong","year":"2008","journal-title":"Emerging Infectious Disease journal"},{"issue":"1","key":"ref16","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00157-12","article-title":"Complete Genome of a Genotype I Japanese Encephalitis Virus Isolated from a Patient with Encephalitis in Vientiane, Lao PDR","volume":"1","author":"F Aubry","year":"2013","journal-title":"Genome Announc"},{"key":"ref17","first-page":"210","article-title":"Infections of the Central Nervous System","author":"PA Solomon T","year":"2014"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1093\/oxfordjournals.epirev.a036087","article-title":"The epidemiology of Japanese encephalitis:prospects for prevention","volume":"14","author":"DW Vaughn","year":"1992","journal-title":"Epidemiolog Rev"},{"key":"ref19","first-page":"1037","article-title":"Improved surveillance of Japanese encephalitis by detection of virus-specific IgM in desiccated blood specimens","volume":"63","author":"DS Burke","year":"1985","journal-title":"Bulletin of the World Health Organization"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1093\/infdis\/151.6.1093","article-title":"Kinetics of IgM and IgG Responses to Japanese Encephalitis Virus in Human Serum and Cerebrospinal Fluid","volume":"151","author":"DS Burke","year":"1985","journal-title":"J Infect Dis"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"e0004516","DOI":"10.1371\/journal.pntd.0004516","article-title":"Pre-cut Filter Paper for Detecting Anti-Japanese Encephalitis Virus IgM from Dried Cerebrospinal Fluid Spots","volume":"10","author":"T Bharucha","year":"2016","journal-title":"PLoS neglected tropical diseases"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"171","DOI":"10.4269\/ajtmh.2012.11-0729","article-title":"A Prospective Assessment of the Accuracy of Commercial IgM ELISAs in Diagnosis of Japanese Encephalitis Virus Infections in Patients with Suspected Central Nervous System Infections in Laos","volume":"87","author":"CE Moore","year":"2012","journal-title":"American Journal of Tropical Medicine and Hygiene"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.4269\/ajtmh.2010.10-0212","article-title":"Evaluation of three commercially available Japanese encephalitis virus IgM enzyme-linked immunosorbent assays","volume":"83","author":"JS Robinson","year":"2010","journal-title":"The American journal of tropical medicine and hygiene"},{"issue":"1","key":"ref24","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1007\/s13312-016-0785-4","article-title":"Public Health Laboratory Surveillance and Diagnosis of Japanese Encephalitis: Time to Revisit","volume":"53","author":"M Kakkar","year":"2016","journal-title":"Indian Pediatr"},{"key":"ref25","unstructured":"Organization WH, editor Manual for the Laboratory Diagnosis of Japanese Encephalitis Virus Infection2007."},{"key":"ref26","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1080\/00365540802227102","article-title":"Usefulness of RT-PCR for the diagnosis of Japanese encephalitis in clinical samples","volume":"40","author":"R Swami","year":"2008","journal-title":"Scandinavian journal of infectious diseases"},{"issue":"4","key":"ref27","doi-asserted-by":"crossref","first-page":"345","DOI":"10.4142\/jvs.2004.5.4.345","article-title":"TaqMan reverse transcription polymerase chain reaction for the detection of Japanese encephalitis virus","volume":"5","author":"DK Yang","year":"2004","journal-title":"Journal of veterinary science"},{"issue":"4","key":"ref28","doi-asserted-by":"crossref","first-page":"820","DOI":"10.4269\/ajtmh.15-0631","article-title":"Differential Diagnosis of Japanese Encephalitis Virus Infections with the Inbios JE Detect and DEN Detect MAC-ELISA Kits","volume":"94","author":"BW Johnson","year":"2016","journal-title":"The American journal of tropical medicine and hygiene"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0065-3527(03)61001-8","article-title":"Serodiagnosis of flaviviral infections and vaccinations in humans","volume":"61","author":"G Kuno","year":"2003","journal-title":"Adv Virus Res"},{"issue":"4","key":"ref30","doi-asserted-by":"crossref","first-page":"249","DOI":"10.4103\/0022-3859.191006","article-title":"The mysterious Zika virus: Adding to the tropical flavivirus mayhem","volume":"62","author":"B Mishra","year":"2016","journal-title":"J Postgrad Med"},{"issue":"5","key":"ref31","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/0035-9203(52)90042-4","article-title":"Zika virus. I. Isolations and serological specificity","volume":"46","author":"GW Dick","year":"1952","journal-title":"Trans R Soc Trop Med Hyg"},{"issue":"12","key":"ref32","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1016\/S1473-3099(15)00405-3","article-title":"How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis?","volume":"15","author":"A Dubot-Peres","year":"2015","journal-title":"The Lancet Infectious diseases"},{"key":"ref33","first-page":"14","article-title":"Field evaluation of commercial Immunoglobulin M antibody capture ELISA diagnostic tests for the detection of Japanese encephalitis virus infection among encephalitis patients in Nepal","author":"A Khalakdina","year":"2010","journal-title":"International Journal of Infectious Diseases"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1111\/j.1365-3156.2009.02380.x","article-title":"Epidemiology and burden of disease from Japanese encephalitis in Cambodia: results from two years of sentinel surveillance","volume":"14","author":"S Touch","year":"2009","journal-title":"Tropical medicine & international health: TM & IH"},{"issue":"10","key":"ref35","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1080\/00365540802227102","article-title":"Usefulness of RT-PCR for the diagnosis of Japanese encephalitis in clinical samples","volume":"40","author":"R Swami","year":"2008","journal-title":"Scandinavian Journal of Infectious Diseases"},{"issue":"1","key":"ref36","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.jviromet.2007.02.011","article-title":"Development and evaluation of SYBR Green I-based one-step real-time RT-PCR assay for detection and quantitation of Japanese encephalitis virus","volume":"143","author":"SR Santhosh","year":"2007","journal-title":"Journal of Virological Methods"},{"issue":"14","key":"ref37","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic Acids Research"},{"issue":"7","key":"ref38","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets","volume":"33","author":"S Kumar","year":"2016","journal-title":"Mol Biol Evol"},{"issue":"4","key":"ref39","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1373\/clinchem.2008.112797","article-title":"The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments","volume":"55","author":"SA Bustin","year":"2009","journal-title":"Clin Chem"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"W163","DOI":"10.1093\/nar\/gkn198","article-title":"IDT SciTools: a suite for analysis and design of nucleic acid oligomers","volume":"36","author":"R Owczarzy","year":"2008","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"ref41","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"issue":"13","key":"ref42","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"M Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ref43","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1136\/mp.54.2.86","article-title":"Recovery efficiencies of nucleic acid extraction kits as measured by quantitative LightCycler(TM) PCR","volume":"54","author":"SJ Read","year":"2001","journal-title":"Molecular Pathology"},{"key":"ref44","unstructured":"World Health Organization S-EAatWP, editor World Health Organisation. Japanese encephalitis surveillance standards. In: WHO-recommended standards for surveillance of selected vaccine-preventable diseases WHO\/V&amp;B\/03.012006."},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"e16142","DOI":"10.1371\/journal.pone.0016142","article-title":"RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests","volume":"6","author":"L Ninove","year":"2011","journal-title":"PloS one"},{"issue":"4","key":"ref46","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1089\/vbz.2007.0206","article-title":"A real-time RT-PCR method for the universal detection and identification of flaviviruses","volume":"7","author":"G Moureau","year":"2007","journal-title":"Vector borne zoonotic dis"},{"issue":"2","key":"ref47","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1016\/j.jviromet.2013.07.025","article-title":"Simultaneous detection of West Nile and Japanese encephalitis virus RNA by duplex TaqMan RT-PCR","volume":"193","author":"SC Barros","year":"2013","journal-title":"Journal of Virological Methods"},{"issue":"2","key":"ref48","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jviromet.2004.01.007","article-title":"Detection of Australasian Flavivirus encephalitic viruses using rapid fluorogenic TaqMan RT-PCR assays","volume":"117","author":"AT Pyke","year":"2004","journal-title":"J Virol Methods"},{"issue":"4","key":"ref49","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1002\/jmv.20218","article-title":"Sensitive and specific detection of strains of Japanese encephalitis virus using a one-step TaqMan RT-PCR technique","volume":"74","author":"JL Huang","year":"2004","journal-title":"Journal of Medical Virology"},{"issue":"1\u20132","key":"ref50","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.jviromet.2005.02.001","article-title":"Detection of West Nile virus and Japanese encephalitis virus using real-time PCR with a probe common to both viruses","volume":"126","author":"K Shirato","year":"2005","journal-title":"J Virol Methods"},{"issue":"1","key":"ref51","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1089\/vbz.2013.1373","article-title":"Applications of a sugar-based surveillance system to track arboviruses in wild mosquito populations","volume":"14","author":"AF van den Hurk","year":"2014","journal-title":"Vector borne zoonotic dis"},{"issue":"1","key":"ref52","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1111\/j.1865-1682.2012.01369.x","article-title":"Detection and differentiation of genotype I and III Japanese encephalitis virus in mosquitoes by multiplex reverse transcriptase-polymerase chain reaction","volume":"61","author":"YY Chen","year":"2014","journal-title":"Transboundary and emerging diseases"},{"issue":"4","key":"ref53","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1002\/jmv.1890330410","article-title":"Detection of flaviviruses by reverse\u2010transcriptase polymerase chain reaction","volume":"33","author":"ZA Eldadah","year":"1991","journal-title":"Journal of Medical Virology"},{"issue":"4","key":"ref54","doi-asserted-by":"crossref","first-page":"231","DOI":"10.4167\/jbv.2016.46.4.231","article-title":"Establishment of a multiplex RT-PCR for the sensitive and differential detection of Japanese encephalitis virus genotype 1 and 3","volume":"46","author":"DK Yang","year":"2016","journal-title":"Journal of Bacteriology and Virology"},{"issue":"1","key":"ref55","first-page":"157","article-title":"Japanese encephalitis virus RNA not detected in urine. Clinical infectious diseases: an official publication of the Infectious","volume":"57","author":"H Zhao","year":"2013","journal-title":"Diseases Society of America"},{"issue":"2","key":"ref56","doi-asserted-by":"crossref","first-page":"ofx046","DOI":"10.1093\/ofid\/ofx046","article-title":"Central Nervous System Infection Diagnosis by Next-Generation Sequencing: A Glimpse Into the Future?","volume":"4","author":"NTH Mai","year":"2017","journal-title":"Open Forum Infect Dis"},{"issue":"3","key":"ref57","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1111\/j.1348-0421.1997.tb01192.x","article-title":"Detection of flaviviruses by reverse transcriptase-polymerase chain reaction with the universal primer set","volume":"41","author":"F Meiyu","year":"1997","journal-title":"Microbiology and Immunology"},{"issue":"4","key":"ref58","doi-asserted-by":"crossref","first-page":"ofx203","DOI":"10.1093\/ofid\/ofx203","article-title":"Prolonged Detection of Japanese Encephalitis Virus in Urine and Whole Blood in a Returned Short-term Traveler","volume":"4","author":"GKL Huang","year":"2017","journal-title":"Open Forum Infectious Diseases"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0194412","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,30]],"date-time":"2020-10-30T02:50:26Z","timestamp":1604026226000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0194412"}},"subtitle":[],"editor":[{"given":"Luis","family":"Men\u00e9ndez-Arias","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,23]]},"references-count":58,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2018,3,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0194412","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,3,23]]}}}