ArticleGigaScience2015
Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
- Evaluation of amplicon-based nanopore sequencing for foot-and-mouth disease viruses in clinical and environmental samples.Microbiology spectrum · 2026Article
- Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.Nucleic acids research · 2026Review
- The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses · 2024Review
- Molecular detection and sequencing of beet necrotic yellow vein virus and beet cryptic virus 2 in sugar beet from Kazakhstan.Frontiers in microbiology · 2024Article
- Article
- Rapid diagnosis of fatalFrontiers in medicine · 2023Article
- Detection and sequence analysis of Canine morbillivirus in multiple species of the Mustelidae family.BMC veterinary research · 2022Article
- Article
- Mixed Infection of Cytomegalovirus and Pulmonary Nocardiosis Caused by Nocardia elegans Diagnosed Using Nanopore Sequencing Technology.Internal medicine (Tokyo, Japan) · 2022Article
- Complete genomic sequencing of canine distemper virus with nanopore technology during an epizootic event.Scientific reports · 2022Article
- Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing.Pathogens (Basel, Switzerland) · 2022Article
- Metagenomic nanopore sequencing of ocular microbiome in patients with meibomian gland dysfunction.Frontiers in medicine · 2022Article
- Comparable outcomes from long and short read random sequencing of total RNA for detection of pathogens in chicken respiratory samples.Frontiers in veterinary science · 2022Article
- Application of third-generation sequencing in cancer research.Medical review (2021) · 2021Article
- Article
- The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii.Molecular ecology · 2021Article
- Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing.International journal of molecular sciences · 2021Article
- Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents.Pathogens (Basel, Switzerland) · 2021Article
- Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?FEMS microbiology ecology · 2021Article
- Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance.International journal of molecular sciences · 2021Review
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION™ nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade.
resultsUsing a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains. The ability to differentiate strains by amplicon sequencing on the MinION™ was accomplished despite an observed per-base error rate of approximately 30%.
conclusionsWhile nanopore sequencing, using the MinION™ platform from Oxford Nanopore in particular, continues to mature into a commercially available technology, practical uses are sought for the current versions of the technology. This study offers evidence of the utility of amplicon sequencing by demonstrating that the current versions of MinION™ technology can accurately identify and differentiate both viral and bacterial species present within biological samples via amplicon sequencing.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.