@article{fdi:010072756,
  title = {{D}evelopment of an improved {RT}-q{PCR} {A}ssay for detection of {J}apanese encephalitis virus ({JEV}) {RNA} including a systematic review and comprehensive comparison with published methods},
  author = {{B}harucha, {T}. and {S}engvilaipaseuth, {O}. and {V}ongsouvath, {M}. and {V}ongsouvath, {M}. and {D}avong, {V}. and {P}anyanouvong, {P}. and {P}iorkowski, {G}. and {G}arson, {J}. {A}. and {N}ewton, {P}. {N}. and de {L}amballerie, {X}. and {D}ubot {P}{\'e}r{\`e}s, {A}udrey},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground {J}apanese encephalitis virus ({JEV}) is a major cause of encephalitis in {A}sia, and the commonest cause of mosquito-borne encephalitis worldwide. {D}etection of {JEV} {RNA} remains challenging due to the characteristic brief and low viraemia, with 0-25% of patients positive, and the mainstay of diagnosis remains detection of anti-{JEV} {I}g{M} antibody. {M}ethods {W}e performed a systematic review of published {RT}-{PCR} protocols, and evaluated them in silico and in vitro alongside new primers and probes designed using a multiple genome alignment of all {JEV} strains >9,000nt from {G}en{B}ank, downloaded from the {NCBI} website ({N}ovember 2016). {T}he new assays included pan-genotype and genotype specific assays targeting genotypes 1 and 3. {R}esults {T}en {RT}-q{PCR} assays were compared, a pre-existing in-house assay, three published assays and six newly designed assays, using serial {RNA} dilutions. {W}e selected three assays, one published and two novel assays, with the lowest limit of detection ({LOD}) for further optimisation and validation. {O}ne of the novel assays, detecting {NS}2{A}, showed the best results, with {LOD} approximately 4 copies/reaction, and no cross-reaction on testing closely related viruses in the {JEV} serocomplex, {W}est {N}ile {V}irus and {S}t. {L}ouis {V}irus. {T}he optimised assays were validated in consecutive patients with central nervous system infections admitted to hospitals in {L}aos, testing paired {CSF} and serum samples. {C}onclusions {W}e succeeded in developing a {JEV} specific {RT}-q{PCR} assay with at least 1 log(10) improved sensitivity as compared to existing assays. {F}urther evaluation is required, field-testing the assay in a larger group of patients.},
  keywords = {},
  booktitle = {},
  journal = {{P}los {O}ne},
  volume = {13},
  numero = {3},
  pages = {e0194412 [18 p.]},
  ISSN = {1932-6203},
  year = {2018},
  DOI = {10.1371/journal.pone.0194412},
  URL = {https://www.documentation.ird.fr/hor/fdi:010072756},
}