Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.

ABSTRACT:

Background

Dengue virus (DENV) infects hundreds of thousands of people annually in Indonesia. However, DENV sequence data from the country are limited, as samples from outbreaks must be shipped across long-distances to suitably equipped laboratories to be sequenced. This approach is time-consuming, expensive, and frequently results in failure due to low viral load or degradation of the RNA genome.

Methods

We evaluated a method designed to address this challenge, using the 'Primal Scheme' multiplex PCR tiling approach to rapidly generate short, overlapping amplicons covering the complete DENV coding-region, and sequencing the amplicons on the portable Nanopore MinION device. The resulting sequence data was assessed in terms of genome coverage, consensus sequence accuracy and

SUBMITTER: Stubbs SCB 

PROVIDER: S-EPMC7020346 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature