Computational protocol: Development of simple and rapid assay to detect viral RNA of tick-borne encephalitis virus by reverse transcription-loop-mediated isothermal amplification

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Protocol publication

[…] A set of six primers comprising two outer primers (forward outer primer F3 and backward outer primer B3), two inner primers (forward inner primer FIP and backward inner primer LB), and two loop primers (forward loop primer FP and backward loop primer BP), were designed for the LAMP assay by using a software PrimerExplorer (version 4; Eiken Chemical Co., Ltd. Tokyo, Japan). The TBEV-specific primers were designed to be specific for NS1 gene based on the consensus sequence identified in 47 strains of TBEV. On the other hand, the TBEV subtype-specific primers were designed to be specific to E gene based on each consensus sequence identified in 63, 96 and 182 strains for FE, Sib and Eu subtypes, respectively. All primers were synthesized by Genenet Co., Japan. The details for each primer and the location in the genomic sequences are shown in the Table . […]

Pipeline specifications

Software tools PrimerExplorer, GeneNet
Application qPCR
Organisms Homo sapiens, Tick-borne encephalitis virus, Mus musculus, Japanese encephalitis virus
Diseases Encephalitis, Encephalitis, Tick-Borne, Hereditary Central Nervous System Demyelinating Diseases