ArticleViruses2020
Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples.
Article in Viruses, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 24 citations in OpenAlex.
- Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC.Microbiology spectrum · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.Viruses · 2024Review
- Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples.Journal of clinical microbiology · 2024Article
- Application of Host-Depleted Nanopore Metagenomic Sequencing in the Clinical Detection of Pathogens in Pigs and Cats.Animals : an open access journal from MDPI · 2023Article
- Review
- Application of nanopore adaptive sequencing in pathogen detection of a patient withFrontiers in cellular and infection microbiology · 2023Article
- Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.Viruses · 2022Article
- Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region.Transboundary and emerging diseases · 2022Article
- Untangling an AGS Outbreak Caused by the Recombinant GII.12[P16] Norovirus With Nanopore Sequencing.Frontiers in cellular and infection microbiology · 2022Article
- Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.Frontiers in microbiology · 2022Article
- Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing.Virus evolution · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 2 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challenge and may lead to poor detection and data acquisition for detailed analysis. To improve sensitivity, we assessed a broad scope targeted sequence capture (TSC) panel (ViroCap) in both human and animal samples. Moreover, we adjusted TSC for the Oxford Nanopore MinION and compared the performance to an SMg approach. TSC on the Illumina NextSeq served as the gold standard. Overall, TSC increased the viral read count significantly in challenging human samples, with the highest genome coverage achieved using the TSC on the MinION. TSC also improved the genome coverage and sequencing depth in clinically relevant viruses in the animal samples, such as influenza A virus. However, SMg was shown to be adequate for characterizing a highly diverse animal virome. TSC on the MinION was comparable to the NextSeq and can provide a valuable alternative, offering longer reads, portability and lower initial cost. Developing new viral enrichment approaches to detect and characterize significant human and animal viruses is essential for the One Health Initiative.
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Registered trials
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.