ArticleFrontiers in microbiology2022
Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.
Article in Frontiers in microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 35 citations in OpenAlex.
- Enhancing low-level genome-edited crop detection and identification in food mixtures using nanopore adaptive sampling: Rice-Soybean mixture as proof-of-concept.NPJ science of food · 2026Article
- Proof-of-principle: nanopore adaptive sampling enables full blood group genome analysis and resolution of hybrid alleles.Blood advances · 2026Article
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.BMC medical genomics · 2025Article
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
- A comprehensive benchmarking of adaptive sampling tools for nanopore sequencing.Genome biology · 2025Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Nanopore adaptive sampling for bacterial identification from periprosthetic joint replacement tissue.Microbial genomics · 2025Article
- Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization fromMicrobiology spectrum · 2025Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.Nature communications · 2024Article
- NASCarD (Nanopore Adaptive Sampling with Carrier DNA): A Rapid, PCR-Free Method for SARS-CoV-2 Whole-Genome Sequencing in Clinical Samples.Pathogens (Basel, Switzerland) · 2024Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Article
- Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects.Parasites & vectors · 2023Article
- DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing.BMC bioinformatics · 2023Article
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- Application of nanopore adaptive sequencing in pathogen detection of a patient withFrontiers in cellular and infection microbiology · 2023Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nanopore sequencing has been widely used for the real-time detection and surveillance of pathogens with portable MinION. Nanopore adaptive sequencing can enrich on-target sequences without additional pretreatment. In this study, the performance of adaptive sequencing was evaluated for viral genome enrichment of clinical respiratory samples. Ligation-based nanopore adaptive sequencing (LNAS) and rapid PCR-based nanopore adaptive sequencing (RPNAS) workflows were performed to assess the effects of enrichment on nasopharyngeal swab samples from human adenovirus (HAdV) outbreaks. RPNAS was further applied for the enrichment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples to evaluate sensitivity and timeliness. The RPNAS increased both the relative abundance (7.87-12.86-fold) and data yield (1.27-2.15-fold) of HAdV samples, whereas the LNAS increased only the relative abundance but had no obvious enrichment on the data yield. Compared with standard nanopore sequencing, RPNAS detected the SARS-CoV-2 reads from two low-abundance samples, increased the coverage of SARS-CoV-2 by 36.68-98.92%, and reduced the time to achieve the same coverage. Our study highlights the utility of RPNAS for virus enrichment directly from clinical samples, with more on-target data and a shorter sequencing time to recover viral genomes. These findings promise to improve the sensitivity and timeliness of rapid identification and genomic surveillance of infectious diseases.
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