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Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping.

08:00 EDT 12th May 2018 | BioPortfolio

Summary of "Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping."

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.

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This article was published in the following journal.

Name: Virus research
ISSN: 1872-7492
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A species of ENTEROVIRUS infecting humans and consisting of 2 serotypes: Human enterovirus 68 and Human enterovirus 70.

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A species in the family ENTEROVIRUS infecting cattle.

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