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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.

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.
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Bharucha T, Sengvilaipaseuth O, Vongsouvath M, Vongsouvath M, Davong V, Panyanouvong P, Piorkowski G, Garson JA, Newton PN, de Lamballerie X, Dubot-Pérès A,


Bharucha T, Sengvilaipaseuth O, Vongsouvath M, Vongsouvath M, Davong V, Panyanouvong P, Piorkowski G, Garson JA, Newton PN, de Lamballerie X, Dubot-Pérès A, (click to view)

Bharucha T, Sengvilaipaseuth O, Vongsouvath M, Vongsouvath M, Davong V, Panyanouvong P, Piorkowski G, Garson JA, Newton PN, de Lamballerie X, Dubot-Pérès A,

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PloS one 2018 03 2313(3) e0194412 doi 10.1371/journal.pone.0194412
Abstract
BACKGROUND
Japanese encephalitis virus (JEV) is a major cause of encephalitis in Asia, and the commonest cause of mosquito-borne encephalitis worldwide. Detection 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 IgM antibody.

METHODS
We 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 GenBank, downloaded from the NCBI website (November 2016). The new assays included pan-genotype and genotype specific assays targeting genotypes 1 and 3.

RESULTS
Ten RT-qPCR assays were compared, a pre-existing in-house assay, three published assays and six newly designed assays, using serial RNA dilutions. We selected three assays, one published and two novel assays, with the lowest limit of detection (LOD) for further optimisation and validation. One of the novel assays, detecting NS2A, showed the best results, with LOD approximately 4 copies/ reaction, and no cross-reaction on testing closely related viruses in the JEV serocomplex, West Nile Virus and St. Louis Virus. The optimised assays were validated in consecutive patients with central nervous system infections admitted to hospitals in Laos, testing paired CSF and serum samples.

CONCLUSIONS
We succeeded in developing a JEV specific RT-qPCR assay with at least 1 log10 improved sensitivity as compared to existing assays. Further evaluation is required, field-testing the assay in a larger group of patients.

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