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.


Journal Details

This article was published in the following journal.

Name: Virus research
ISSN: 1872-7492


DeepDyve research library

PubMed Articles [12922 Associated PubMed Articles listed on BioPortfolio]

Identification and genetic characterization of bovine enterovirus by combination of two next generation sequencing platforms.

Prompt and accurate diagnosis is warranted for infectious diseases of domestic animals which may have a significant impact on animal production or clinical practice. In this study, the identification ...

Forensic tri-allelic SNP genotyping using nanopore sequencing.

The potential and current state-of-the-art of forensic SNP genotyping using nanopore sequencing was investigated with a panel of 16 tri-allelic single nucleotide polymorphisms (SNPs), multiplexing fiv...

MinIONQC: fast and simple quality control for MinION sequencing data.

MinIONQC provides rapid diagnostic plots and quality control data from one or more flowcells of sequencing data from Oxford Nanopore Technologies' MinION instrument. It can be used to assist with the ...

Virus genotyping by massive parallel amplicon sequencing: adenovirus and enterovirus in the Norwegian MIDIA study.

Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types...

Evaluation and application of RNA-Seq by MinION.

The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure fo...

Clinical Trials [2985 Associated Clinical Trials listed on BioPortfolio]

Live Enterovirus Vaccine and Type 1 Diabetes

Enterovirus infections may either increase or decrease the risk of type 1 diabetes depending on the age of infection and the type of enterovirus in question. This study evaluated whether e...

Safety Study of Enterovirus 71 Vaccine in Children Aged 6-35 Months Old

This phase IV clinical study evaluates the safety of enterovirus 71 vaccine in children aged 6-35 months old by the method of both passive and active surveillance.

Detection of Factor V Leiden G1691A and Factor II (Prothrombin) G20210A Point Mutations in DNA

As an external validation test of the performance of the VeraCode Genotyping Test for Factor V and Factor II on the BeadXpress System, clinical trials will be conducted at three sites. Thi...

Perinatal Precision Medicine

This study will seek to determine if rapid genomic sequencing improves outcomes for acutely ill infants. The investigator will enroll up to 1,000 acutely ill infants in a prospective, rand...

Rapid Whole Genome Sequencing Study

Rapid Whole Genome Sequencing (rWGS) has proven to provide much faster diagnoses than traditional clinical testing, including clinical Whole Exome Sequencing (WES) and standard Whole Genom...

Medical and Biotech [MESH] Definitions

A species of ENTEROVIRUS infecting humans and consisting of 2 serotypes: Human enterovirus 68 and Human enterovirus 70.

Species of ENTEROVIRUS causing mild to severe neurological diseases among pigs especially in Eastern Europe. Mild strains are also present in Canada, U.S., and Australia. Specific species include Porcine enterovirus A and Porcine enterovirus B.

A species in the family ENTEROVIRUS infecting cattle.

A species of ENTEROVIRUS infecting humans and containing 10 serotypes, mostly coxsackieviruses.

A species of ENTEROVIRUS infecting humans and containing 11 serotypes, all coxsackieviruses.

Quick Search


DeepDyve research library

Relevant Topics

DNA sequencing
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...

Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Searches Linking to this Article