Journal article
Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping
Virus Research, Vol.252, pp.8-12
2018
Abstract
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. 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.
Details
- Title
- Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping
- Authors
- Emily Rames (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and EngineeringJoanne Macdonald (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
- Publication details
- Virus Research, Vol.252, pp.8-12
- Publisher
- Elsevier BV
- Date published
- 2018
- DOI
- 10.1016/j.virusres.2018.05.010
- ISSN
- 0168-1702
- Copyright note
- Copyright © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
- Organisation Unit
- School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
- Language
- English
- Record Identifier
- 99450733302621
- Output Type
- Journal article
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