ArticlePloS one2021
Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals.
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 25 papers.
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Who cites it
25 citing papers in PubMed, 37 citations in OpenAlex.
- Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.Nature communications · 2026Article
- Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment.Scientific reports · 2025Article
- INTRA- AND INTER-HOST EVOLUTION OF HUMAN NOROVIRUS IN HEALTHY ADULTS.bioRxiv : the preprint server for biology · 2024Article
- Examining intra-host genetic variation of RSV by short read high-throughput sequencing.bioRxiv : the preprint server for biology · 2024Article
- 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
- A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition.mSystems · 2024Article
- Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance.Virus evolution · 2024Article
- Comparative analysis of bioinformatics tools to characterize SARS-CoV-2 subgenomic RNAs.Life science alliance · 2023Article
- sgRNAs: A SARS-CoV-2 emerging issue.Aspects of molecular medicine · 2023Review
- Capturing SARS-CoV-2 from patient samples with low viral abundance: a comparative analysis.Scientific reports · 2022Article
- Direct comparison of RT-ddPCR and targeted amplicon sequencing for SARS-CoV-2 mutation monitoring in wastewater.The Science of the total environment · 2022Article
- Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory.Scientific reports · 2022Article
- Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol.Frontiers in medicine · 2022Article
- Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform.Frontiers in public health · 2022Article
- SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples.Journal of clinical microbiology · 2021Article
- First report of severe acute respiratory syndrome coronavirus 2 detection in two asymptomatic cats in the state of Pernambuco, Northeastern Brazil.Veterinary world · 2021Article
- Review
- Towards population-scale long-read sequencing.Nature reviews. Genetics · 2021Review
- Article
- COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.Nature communications · 2021Article
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Authors and funding
21 authors at 1 institution in 1 country.
Funding
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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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.