Development and evaluation of a next-generation sequencing methodology for measles virus using Oxford Nanopore Technology.

ABSTRACT: We report the development of a bench protocol and evaluation of bioinformatics pipelines for the whole genome sequence (WGS) of measles virus (MeV) genotype D8. We established a bench protocol using 1 kb amplicons tiling the MeV WGS. Four different pipeline parameters were assessed based on two basecallers and two quality thresholds: Guppy simplex with Q-score thresholds of 20 and 25 (G20 and G25), and Dorado duplex with Q-score thresholds of 20 and 25 (D20 and D25). Using a reference genome, we determined that complete genomes were obtained down to 10 copies/µL with all four parameters; however, errors began to be detected in the consensus sequence at 100 copies/µL. A panel of specimens from 32 measles cases, for which measles WGS had been obtained by other methods (reference sequences),

SUBMITTER: Zubach V 

PROVIDER: S-EPMC11898632 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature