A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses.

ABSTRACT: Nucleic acid test (NAT), most typically quantitative PCR, is one of the standard methods for species specific flavivirus diagnosis. Semi-comprehensive NATs such as pan-flavivirus PCR which covers genus Flavivirus are also available; however, further specification by sequencing is required for species level differentiation. In this study, a semi-comprehensive detection system that allows species differentiation of flaviviruses was developed by integration of the pan-flavivirus PCR and Nanopore sequencing. In addition, a multiplexing method was established by adding index sequences through the PCR with a streamlined bioinformatics pipeline. This enables defining cut-off values for observed read counts. In the laboratory setting, this approach allowed the detection of up to nine different fla

SUBMITTER: Reteng P 

PROVIDER: S-EPMC8463598 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature