J. Granerod and N. J. Crowcroft, The epidemiology of acute encephalitis, Neuropsychological Rehabilitation, vol.11, issue.4-5, pp.406-428, 2007.
DOI : 10.1056/NEJMoa042207

E. Simon-loriere, Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa, New England Journal of Medicine, vol.376, issue.15, pp.1483-1485, 2017.
DOI : 10.1056/NEJMc1701600

A. Tarantola, Estimating the Burden of Japanese Encephalitis Virus and Other Encephalitides in Countries of the Mekong Region, PLoS Neglected Tropical Diseases, vol.47, issue.1, 2014.
DOI : 10.1371/journal.pntd.0002533.t001
URL : https://hal.archives-ouvertes.fr/pasteur-01739391

, World Health Organization, South-East Asia and the Western Pacific. Asia Pacific Strategy for Strengthening Health Laboratory Services, Report, pp.2010-2025, 2010.

A. Dubot-peres, O. Sengvilaipaseuth, A. Chanthongthip, P. N. Newton, and X. De-lamballerie, How many patients with anti-JEV IgM in cerebrospinal fluid really have Japanese encephalitis? The Lancet, Infectious diseases, vol.15, issue.15, pp.1376-1377, 2015.

A. Khalakdina, Field evaluation of commercial Immunoglobulin M antibody capture ELISA diagnostic tests for the detection of Japanese encephalitis virus infection among encephalitis patients in Nepal, International Journal of Infectious Diseases, vol.14, 2010.
DOI : 10.1016/j.ijid.2009.11.020

J. S. Robinson, Evaluation of three commercially available Japanese encephalitis virus IgM enzyme-linked immunosorbent assays. The American journal of tropical medicine and hygiene 83, pp.1146-115510, 2010.

R. Swami, R. K. Ratho, B. Mishra, and M. Singh, Usefulness of RT-PCR for the diagnosis of Japanese encephalitis in clinical samples, Scandinavian Journal of Infectious Diseases, vol.40, issue.10, pp.815-82000365540802227102, 2008.
DOI : 10.1080/00365540802227102

S. Touch, Epidemiology and burden of disease from Japanese encephalitis in Cambodia: results from two years of sentinel surveillance, Tropical Medicine & International Health, vol.26, issue.11, pp.1365-1373, 2009.
DOI : 10.1016/j.vaccine.2006.12.016

N. T. Mai, Central Nervous System Infection Diagnosis by Next-Generation Sequencing: A Glimpse Into the Future?, Open Forum Infectious Diseases, vol.7, issue.2, p.46, 2017.
DOI : 10.1186/s13073-015-0254-z

A. C. Andries, Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens, PLOS Neglected Tropical Diseases, vol.8, issue.Suppl 1, 2015.
DOI : 10.1371/journal.pntd.0004100.s013
URL : https://hal.archives-ouvertes.fr/pasteur-01738738

A. Gourinat, O. O-'connor, E. Calvez, C. Goarant, and M. Dupont-rouzeyrol, Detection of Zika Virus in Urine, Emerging Infectious Diseases, vol.21, issue.1, pp.84-86, 2015.
DOI : 10.3201/eid2101.140894
URL : https://hal.archives-ouvertes.fr/pasteur-01114781

G. K. Huang, Prolonged Detection of Japanese Encephalitis Virus in Urine and Whole Blood in a Returned Short-term Traveler, Open Forum Infectious Diseases, vol.16, issue.4, p.203, 2017.
DOI : 10.1111/j.1708-8305.2009.00333.x

M. E. Ricklin, Vector-free transmission and persistence of Japanese encephalitis virus in pigs, Nature Communications, vol.27, p.10832, 2016.
DOI : 10.1093/oxfordjournals.aje.a118408

H. Zhao, Japanese encephalitis virus RNA not detected in urine Clinical infectious diseases: an official publication of the Infectious Diseases Society of, America, vol.57, pp.157-158, 2013.

, https://research.pasteur.fr/en/program_project/the-southeast-asia-encephalitis-project, 2013.

, World Health Organisation Regional Office for the Western, Training Report Fourth Hands-on Training Workshop on the Laboratory Diagnosis of Japanese Encephalitis. WHO Report, 2014.

L. Ninove, RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests, PLoS ONE, vol.45, issue.2, 2011.
DOI : 10.1371/journal.pone.0016142.s004

J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997.
DOI : 10.1093/nar/25.24.4876

, SCIENTIFIC RePoRTS |, vol.8, 2018.

, Man.V. supervised the laboratory testing and reviewed the submitted manuscript. S.R. recruited and managed patients, and reviewed the submitted manuscript. G.P. performed the sequencing, and reviewed the submitted manuscript. M.L. has jointly had overall responsibility and direction of the SEAe study, and reviewed the submitted manuscript. C.G. has jointly had overall responsibility and direction of the SEAe study, and reviewed the submitted manuscript provided the clinical datasets, has jointly had overall responsibility and direction of the SEAe study, and reviewed the submitted manuscript. P.N.N. conceived the concept and design of the study, has jointly had overall responsibility and direction of the SEAe study, supervised drafting and submission of the manuscript, laboratory testing, and reviewed the submitted manuscript. Mal.V. performed the laboratory testing, and reviewed the submitted manuscript X.D.L. conceived the concept and design of the study, has jointly had overall responsibility and direction of the SEAe study, and reviewed the submitted manuscript. A.D.P. conceived the concept and design of the study, supervised the laboratory testing, has jointly had overall responsibility and direction of the SEAe study, supervised drafting and submission of the manuscript