ArticleJournal of clinical microbiology2021
Assessment of SARS-CoV-2 Genome Sequencing: Quality Criteria and Low-Frequency Variants.
Article in Journal of clinical microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
- Targeted sequence capture of coxsackievirus A6 using nanopore sequencing directly from clinical specimens.Microbiology spectrum · 2026Article
- Baseline cohort profile: clinical and molecular characterisation of SARS-CoV-2 infected patients recruited into a longitudinal COVID-19 cohort study (COVGEN) in Malaysia.BMC infectious diseases · 2026Article
- Intra-host diversity of SARS-CoV-2 in children with long-term and short-term excretion in nasopharyngeal samples.BMC infectious diseases · 2025Article
- Molecular Evidence of SARS-CoV-2 Virus in Dogs and Cats from Grenada.Veterinary sciences · 2025Article
- Tradeoffs between proliferation and transmission in virus evolution- insights from evolutionary and functional analyses of SARS-CoV-2.Virology journal · 2025Article
- External quality assessment of molecular detection and variant typing of SARS-CoV-2 in European expert laboratories in 2023.Journal of clinical microbiology · 2025Article
- PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.Bioinformatics (Oxford, England) · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Considerations for Severe Acute Respiratory Syndrome Coronavirus 2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories.The Journal of molecular diagnostics : JMD · 2025Review
- Tracking SARS-CoV-2 variants in wastewater in San Pedro de la Paz, Chile.Journal of water and health · 2024Article
- How Trustworthy Are the Genomic Sequences of SARS-CoV-2 in GenBank?Microorganisms · 2024Article
- SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene.Environmental science & technology letters · 2024Article
- Genomic Mutations in SARS-CoV-2 Genome following Infection in Syrian Golden Hamster and Associated Lung Pathologies.Pathogens (Basel, Switzerland) · 2023Article
- A Simulation Framework for Modeling the Within-Patient Evolutionary Dynamics of SARS-CoV-2.Genome biology and evolution · 2023Article
- A simulation framework for modeling the within-patient evolutionary dynamics of SARS-CoV-2.bioRxiv : the preprint server for biology · 2023Article
- Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting.Scientific reports · 2023Article
- Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories.Journal of clinical microbiology · 2022Article
- Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution.Microbiology spectrum · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only a few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low-quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over 10 tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for 11 selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low-frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations, or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low-frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose 11 metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which are cycle thresholds, mean depth, proportion of genome covered at least 10×, and the number of low-frequency variants combined with mutation prevalence data.
Indexed as
Identifiers
What OpenQuestion holds
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.