{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T15:08:16Z","timestamp":1791299296287,"version":"4.1.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T00:00:00Z","timestamp":1549411200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Total Foundation","award":["653316"],"award-info":[{"award-number":["653316"]}]},{"name":"Institute of Research for Development"},{"DOI":"10.13039\/100007586","name":"Aix-Marseille University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007586","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Japanese encephalitis virus (JEV) is a leading cause of central nervous system (CNS) infections in Asia and results in significant morbidity and mortality. JEV RNA is rarely detected in serum or cerebrospinal fluid (CSF), and diagnosis of JEV infection is usually based on serological tests that are frequently difficult to interpret. Unlike serum or CSF, urine is relatively easy to obtain, but, to date, there has been minimal work on the feasibility of testing urine for JEV RNA.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We investigated the use of lysis buffer and a Microsep device to optimize urine storage for detection of JEV RNA by reverse transcription real-time polymerase chain reaction (RT-qPCR). The best of the studied methods was then evaluated in consecutive patients admitted to the hospital with suspected CNS infections in Laos.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We demonstrated degradation of JEV RNA in urine after even short storage periods at 4\u00b0C or \u201380\u00b0C. Although there was no advantage in using a Microsep concentration device alone, immediate addition of lysis buffer to fresh urine improved the detection of JEV RNA at the limit of detection.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>In 2 studies of 41 patients with acute encephalitis syndrome, 11 (27%) were positive for JEV IgM in CSF and\/or serum, and 2 (4.9%) were JEV RT-qPCR positive from throat swabs. JEV RNA was not detected in any of these patients\u2019 urine samples. However, lysis buffer was only used during a prospective study, that is, for only 17\/41 (41%) patient urine samples. Our findings suggest a need for larger studies testing urine for JEV RNA, with urine collected at different times from symptom onset, and using lysis buffer, which stabilizes RNA, for storage.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ofid\/ofz048","type":"journal-article","created":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T17:50:04Z","timestamp":1549475404000},"source":"Crossref","is-referenced-by-count":11,"title":["Viral RNA Degradation Makes Urine a Challenging Specimen for Detection of Japanese Encephalitis Virus in Patients With Suspected CNS Infection"],"prefix":"10.1093","volume":"6","author":[{"given":"Tehmina","family":"Bharucha","sequence":"first","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"},{"name":"Division of Infection and Immunity, University College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Onanong","family":"Sengvilaipaseuth","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malee","family":"Seephonelee","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malavanh","family":"Vongsouvath","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manivanh","family":"Vongsouvath","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sayaphet","family":"Rattanavong","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G\u00e9raldine","family":"Piorkowski","sequence":"additional","affiliation":[{"name":"Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ \u2013 IRD 190 \u2013 Inserm 1207 \u2013 IHU M\u00e9diterran\u00e9e Infection), Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Lecuit","sequence":"additional","affiliation":[{"name":"Biology of Infection Unit, Inserm U1117, Institut Pasteur, Paris, France"},{"name":"Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris Descartes University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Gorman","sequence":"additional","affiliation":[{"name":"Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-David","family":"Pommier","sequence":"additional","affiliation":[{"name":"Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy A","family":"Garson","sequence":"additional","affiliation":[{"name":"Division of Infection and Immunity, University College London, London, UK"},{"name":"Transfusion Microbiology, NHS Blood and Transplant, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul N","family":"Newton","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"},{"name":"Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"de Lamballerie","sequence":"additional","affiliation":[{"name":"Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ \u2013 IRD 190 \u2013 Inserm 1207 \u2013 IHU M\u00e9diterran\u00e9e Infection), Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Dubot-P\u00e9r\u00e8s","sequence":"additional","affiliation":[{"name":"Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao P.D.R"},{"name":"Nuffield Department of Clinical Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Churchill Hospital, Oxford, UK"},{"name":"Unit\u00e9 des Virus \u00c9mergents (UVE: Aix-Marseille Univ \u2013 IRD 190 \u2013 Inserm 1207 \u2013 IHU M\u00e9diterran\u00e9e Infection), Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,2,6]]},"reference":[{"key":"2020081003482903900_CIT0001","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":"2020081003482903900_CIT0002","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s11908-018-0635-8","article-title":"Evolving epidemiology of Japanese encephalitis: implications for vaccination","volume":"20","author":"Caldwell","year":"2018","journal-title":"Curr Infect Dis Rep"},{"key":"2020081003482903900_CIT0003","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1056\/NEJMc1701600","article-title":"Autochthonous Japanese encephalitis with yellow fever coinfection in Africa","volume":"376","author":"Simon-Loriere","year":"2017","journal-title":"N Engl J Med"},{"key":"2020081003482903900_CIT0004","doi-asserted-by":"crossref","first-page":"579","DOI":"10.15585\/mmwr.mm6622a3","article-title":"Japanese encephalitis surveillance and immunization - Asia and Western Pacific Regions, 2016","volume":"66","author":"Heffelfinger","year":"2017","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"2020081003482903900_CIT0005","doi-asserted-by":"crossref","first-page":"e0194412","DOI":"10.1371\/journal.pone.0194412","article-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","volume":"13","author":"Bharucha","year":"2018","journal-title":"PLoS One"},{"key":"2020081003482903900_CIT0006","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":"Robinson","year":"2010","journal-title":"Am J Trop Med Hyg"},{"key":"2020081003482903900_CIT0007","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1016\/j.ijid.2009.11.020","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","volume":"14","author":"Khalakdina","year":"2010","journal-title":"Int J Infect Dis"},{"key":"2020081003482903900_CIT0008","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":"Dubot-P\u00e9r\u00e8s","year":"2015","journal-title":"Lancet Infect Dis"},{"key":"2020081003482903900_CIT0009","doi-asserted-by":"crossref","first-page":"8018","DOI":"10.1038\/s41598-018-26333-4","article-title":"Detection of Japanese encephalitis","volume":"8","author":"Bharucha","year":"2018","journal-title":"Sci Rep"},{"key":"2020081003482903900_CIT0010","doi-asserted-by":"crossref","first-page":"e0004100","DOI":"10.1371\/journal.pntd.0004100","article-title":"Value of routine dengue diagnostic tests in urine and saliva specimens","volume":"9","author":"Andries","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"key":"2020081003482903900_CIT0011","doi-asserted-by":"crossref","first-page":"84","DOI":"10.3201\/eid2101.140894","article-title":"Detection of Zika virus in urine","volume":"21","author":"Gourinat","year":"2015","journal-title":"Emerg Infect Dis"},{"key":"2020081003482903900_CIT0012","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1007\/s00705-016-2844-5","article-title":"Detection and sequencing of West Nile virus RNA from human urine and serum samples during the 2014 seasonal period","volume":"161","author":"Nagy","year":"2016","journal-title":"Arch Virol"},{"key":"2020081003482903900_CIT0013","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/infdis\/jit290","article-title":"Excretion of West Nile virus in urine during acute infection","volume":"208","author":"Barzon","year":"2013","journal-title":"J Infect Dis"},{"key":"2020081003482903900_CIT0014","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1002\/rmv.1840","article-title":"Urine-based viral diagnostics: an innovation in waiting","volume":"25","author":"Mortimer","year":"2015","journal-title":"Rev Med Virol"},{"key":"2020081003482903900_CIT0015","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1002\/rmv.1980010204","article-title":"Non-invasive virological diagnosis: are saliva and urine specimens adequate substitutes for blood?","volume":"1","author":"Mortimer","year":"1991","journal-title":"Rev Med Virol"},{"key":"2020081003482903900_CIT0016","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/nrneurol.2018.30","article-title":"Japanese encephalitis - the prospects for new treatments","volume":"14","author":"Turtle","year":"2018","journal-title":"Nat Rev Neurol"},{"key":"2020081003482903900_CIT0017","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1093\/cid\/cit169","article-title":"Japanese encephalitis virus RNA not detected in urine","volume":"57","author":"Zhao","year":"2013","journal-title":"Clin Infect Dis"},{"issue":"X","key":"2020081003482903900_CIT0018","first-page":"XXX","article-title":"Central nervous system infection diagnosis by next-generation sequencing: a glimpse into the future?","volume":"4","author":"Mai","year":"2017","journal-title":"Open Forum Infect Dis"},{"issue":"X","key":"2020081003482903900_CIT0019","first-page":"XXX","article-title":"Prolonged detection of Japanese encephalitis virus in urine and whole blood in a returned short-term traveler","volume":"4","author":"Huang","year":"2017","journal-title":"Open Forum Infect Dis"},{"key":"2020081003482903900_CIT0020","doi-asserted-by":"crossref","first-page":"e00157","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":"Aubry","year":"2013","journal-title":"Genome Announc"},{"key":"2020081003482903900_CIT0021","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":"Ninove","year":"2011","journal-title":"PLoS One"},{"key":"2020081003482903900_CIT0022","volume-title":"South East Asia Encephalitis Project (SEAe) 2013","year":"2017"},{"key":"2020081003482903900_CIT0023","volume-title":"Training Report Fourth Hands-on Training Workshop on the Laboratory Diagnosis of Japanese Encephalitis","author":"World Health Organization. Regional Office for the Western Pacific. Western WHOROft","year":"2014"},{"key":"2020081003482903900_CIT0024","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\u2122 and DEN Detect\u2122 MAC-ELISA kits","volume":"94","author":"Johnson","year":"2016","journal-title":"Am J Trop Med Hyg"},{"key":"2020081003482903900_CIT0025","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.jviromet.2004.09.018","article-title":"Concentration and detection of hepatitis A virus and rotavirus in spring water samples by reverse transcription-PCR","volume":"123","author":"Brassard","year":"2005","journal-title":"J Virol Methods"},{"key":"2020081003482903900_CIT0026","doi-asserted-by":"crossref","first-page":"e0004100","DOI":"10.1371\/journal.pntd.0004100","article-title":"Value of routine dengue diagnostic tests in urine and saliva specimens","volume":"9","author":"Andries","year":"2015","journal-title":"PLoS Negl Trop Dis"},{"key":"2020081003482903900_CIT0027","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1002\/jmv.25280","article-title":"Quantitative detection of hepatitis C virus RNA in urine of patients with chronic hepatitis C using a novel real-time PCR assay","volume":"91","author":"Lu","year":"2019","journal-title":"J Med Virol"},{"key":"2020081003482903900_CIT0028","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.jviromet.2017.04.018","article-title":"Stability of Zika virus in urine: specimen processing considerations and implications for the detection of RNA targets in urine","volume":"248","author":"Tan","year":"2017","journal-title":"J Virol Methods"},{"key":"2020081003482903900_CIT0029","doi-asserted-by":"crossref","first-page":"427","DOI":"10.4269\/ajtmh.18-0755","article-title":"Optimizing PCR detection of Zika virus from various body fluids","volume":"100(2)","author":"Gorchakov","year":"2019","journal-title":"Am J Trop Med Hyg"},{"key":"2020081003482903900_CIT0030","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"}],"container-title":["Open Forum Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/ofid\/article-pdf\/6\/3\/ofz048\/33590318\/ofz048.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/ofid\/article-pdf\/6\/3\/ofz048\/33590318\/ofz048.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T08:05:16Z","timestamp":1597046716000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ofid\/article\/doi\/10.1093\/ofid\/ofz048\/5308109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,2,6]]},"references-count":30,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/ofid\/ofz048","relation":{},"ISSN":["2328-8957"],"issn-type":[{"value":"2328-8957","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,3]]},"published":{"date-parts":[[2019,2,6]]},"article-number":"ofz048"}}