ArticlePloS one2021
Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 25 citations in OpenAlex.
- Article
- Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.BMC infectious diseases · 2025Article
- vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.Nature communications · 2025Article
- Development and performance evaluation of a clinical metagenomics approach for identifying pathogens in the whole blood from patients with undifferentiated fever.Frontiers in cellular and infection microbiology · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Validation of an Automated, End-to-End Metagenomic Sequencing Assay for Agnostic Detection of Respiratory Viruses.The Journal of infectious diseases · 2024Article
- Article
- Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences.Molecular biology reports · 2023Review
- First report and genetic characterization of the highly pathogenic avian influenza A(H5N1) virus in Cabot's tern (Veterinary and animal science · 2023Article
- Diversity of Human Enterovirus Co-Circulations in Five Kindergartens in Bangkok between July 2019 and January 2020.Viruses · 2023Article
- Agnostic Sequencing for Detection of Viral Pathogens.Clinical microbiology reviews · 2023Review
- A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level.Frontiers in molecular biosciences · 2023Review
- BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.Communications biology · 2022Article
- PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2.PeerJ · 2022Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesThe COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2.
methodsWe performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies.
resultsOur assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia.
conclusionsThis study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.
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