ArticleiScience2021
A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
35 citing papers in PubMed.
- Raman Analysis of RNA Nucleotide Strands From SARS-CoV-2 Variants and Subvariants: A Step Forward in the Definition of "Raman Genome".Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.International journal of molecular sciences · 2025Review
- Development and Validation of Amplicon-Based Protocol for Sequencing of Respiratory Syncytial Virus Genome.Journal of medical virology · 2025Article
- Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.Viruses · 2025Article
- A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method.Frontiers in genetics · 2025Article
- A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.Virology journal · 2024Article
- Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.Microbial genomics · 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
- Article
- Genomic surveillance of SARS-CoV-2 using long-range PCR primers.Frontiers in microbiology · 2024Article
- Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria.Frontiers in molecular biosciences · 2024Article
- Article
- Genomic Mutations in SARS-CoV-2 Genome following Infection in Syrian Golden Hamster and Associated Lung Pathologies.Pathogens (Basel, Switzerland) · 2023Article
- Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance.Microbial genomics · 2023Article
- Mobile Efficient Diagnostics of Infectious Diseases via On-Chip RT-qPCR: MEDIC-PCR.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Evaluation of rRNA depletion methods for capturing the RNA virome from environmental surfaces.BMC research notes · 2023Article
- Article
- Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021.Frontiers in public health · 2023Article
- Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era.Viruses · 2022Review
- Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France.Nature communications · 2022Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging new type of coronavirus that is responsible for the COVID-19 pandemic and the unprecedented global health emergency. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions with low and high viral inputs. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility, and precision of single-nucleotide variant calling across different protocols. For certain amplicon-based protocols, an appropriate primer trimming step is critical for accurate single-nucleotide variant calling. We ranked the performance of protocols based on six different metrics. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution.
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Registered trials
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