Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping.

We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99.7% similarity were discriminated. In addition, an accurate consensus sequence was produced for EV-A71 isolate RNA, with 99.3-99.6% similarity to the reference sequence. Thus, the long nanopore reads enabled rapid whole genome sequencing and strain level identification of EV- A71 isolate RNA. We also demonstrated potential for using MinION sequencing se for direct detection of EV in water samples, which may have application for diversity analysis, water quality monitoring, and environmental surveillance. PMID: 29763627 [PubMed - as supplied by publisher]
Source: Virus Research - Category: Virology Authors: Tags: Virus Res Source Type: research