ArticleJournal of clinical microbiology2021
SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples.
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 30 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Review
- Genomic Surveillance of Endemic Human Coronaviruses in Côte d'Ivoire Using Targeted Hybrid-Capture Sequencing.Viruses · 2026Article
- Microfluidic toolbox using padlock probes and rolling circle amplification for direct detection and genotyping of viral RNA.RSC advances · 2026Article
- Acute SARS-CoV-2 infection.Nature reviews. Disease primers · 2025Review
- Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.International journal of molecular sciences · 2025Review
- Article
- 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
- A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.Virology journal · 2024Article
- Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.Microbial genomics · 2024Article
- Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics.Frontiers in microbiology · 2024Article
- Article
- A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs.Microbiology spectrum · 2023Article
- The Modification of the IlluminaInternational journal of molecular sciences · 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
- 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
- Detection of SARS-CoV-2 Variants via Different Diagnostics Assays Based on Single-Nucleotide Polymorphism Analysis.Diagnostics (Basel, Switzerland) · 2023Article
- Article
- Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens.International journal of molecular sciences · 2023Article
- Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era.Viruses · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic surveillance has been vital in understanding the spread of coronavirus disease 2019 (COVID-19), the emergence of viral escape mutants, and variants of concern. However, low viral loads in clinical specimens affect variant calling for phylogenetic analyses and detection of low-frequency variants, important in uncovering infection transmission chains. We systematically evaluated three widely adopted SARS-CoV-2 whole-genome sequencing methods for their sensitivity, specificity, and ability to reliably detect low-frequency variants. Our analyses reveal that the ARTIC v3 protocol consistently displays high sensitivity for generating complete genomes at low viral loads compared with the probe-based Illumina Respiratory Viral Oligo panel and a pooled long-amplicon method. We show substantial variability in the number and location of low-frequency variants detected using the three methods, highlighting the importance of selecting appropriate methods to obtain high-quality sequence data from low-viral-load samples for public health and genomic surveillance purposes.
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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.