ArticleNature communications2021
COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Economic Evaluation of COVID-19 Screening Tests and Surveillance Strategies in Low-Income, Middle-Income, and High-Income Countries: A Systematic Review.Medical science monitor : international medical journal of experimental and clinical research · 2024Pooled it
- 'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.PloS one · 2026Article
- Enhancing public health surveillance: a comparative study of platform-specific and hybrid assembly approaches in SARS-CoV-2 genome sequencing.Microbial genomics · 2025Article
- Genomic surveillance of SARS-CoV-2 variants using pooled WGS.Scientific reports · 2025Article
- Analytical Performance of a Novel Nanopore Sequencing for SARS-CoV-2 Genomic Surveillance.Journal of medical virology · 2024Article
- Article
- COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2.Briefings in bioinformatics · 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
- Sierra SARS-CoV-2 sequence and antiviral resistance analysis program.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2022Article
- Receptor-Binding-Motif-Targeted Sanger Sequencing: a Quick and Cost-Effective Strategy for Molecular Surveillance of SARS-CoV-2 Variants.Microbiology spectrum · 2022Article
- Article
- VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.Microbiology spectrum · 2022Article
- Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program.BMC infectious diseases · 2022Article
- Article
- Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory.Scientific reports · 2022Article
- Genomic surveillance unfolds the SARS-CoV-2 transmission and divergence dynamics in Bangladesh.Frontiers in genetics · 2022Article
- Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting.Diagnostics (Basel, Switzerland) · 2021Article
- COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.Nature communications · 2021Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While mass-scale vaccination campaigns are ongoing worldwide, genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical to monitor the emergence and global spread of viral variants of concern (VOC). Here, we present a streamlined workflow-COVseq-which can be used to generate highly multiplexed sequencing libraries compatible with Illumina platforms from hundreds of SARS-CoV-2 samples in parallel, in a rapid and cost-effective manner. We benchmark COVseq against a standard library preparation method (NEBNext) on 29 SARS-CoV-2 positive samples, reaching 95.4% of concordance between single-nucleotide variants detected by both methods. Application of COVseq to 245 additional SARS-CoV-2 positive samples demonstrates the ability of the method to reliably detect emergent VOC as well as its compatibility with downstream phylogenetic analyses. A cost analysis shows that COVseq could be used to sequence thousands of samples at less than 15 USD per sample, including library preparation and sequencing costs. We conclude that COVseq is a versatile and scalable method that is immediately applicable for SARS-CoV-2 genomic surveillance and easily adaptable to other pathogens such as influenza viruses.
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