ArticleMicrobiology spectrum2021
Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights.
Article in Microbiology spectrum, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Methodological Approaches to Dengue Virus Detection in Wastewater: A Systematic Review and Meta-Analysis of Positivity Rate.Viruses · 2026Pooled it
- Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.The Journal of allergy and clinical immunology · 2026Article
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.Nature communications · 2025Article
- Article
- Age- and disease severity-associated changes in the nasopharyngeal microbiota of COVID-19 patients.iScience · 2025Article
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Communications 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
- A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples.Journal of clinical microbiology · 2024Article
- The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest.Molecular genetics and genomics : MGG · 2024Article
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Research square · 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
- Efficacy of targeted next generation sequencing for pathogen detection in lower respiratory tract infections.American journal of translational research · 2024Article
- The nasopharyngeal microbiome in COVID-19.Emerging microbes & infections · 2023Article
- SARS-CoV-2 genomics and impact on clinical care for COVID-19.The Journal of antimicrobial chemotherapy · 2023Article
- Assessment and validation of enrichment and target capture approaches to improveJournal of clinical microbiology · 2023Article
- Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection.Microbiology spectrum · 2023Article
- Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 + .Scientific reports · 2023Article
- A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2023Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates.
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