ArticleEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2023
A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.
Article in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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
21 citing papers in PubMed, 30 citations in OpenAlex.
- No Remdesivir Resistance Observed in the Phase 3 Severe and Moderate COVID-19 SIMPLE Trials.Viruses · 2024Trial
- Review
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens.Genes · 2026Article
- Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.Molecular biology reports · 2026Article
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Large-Scale Saliva-Based Clinical Surveillance Enables Real Time SARS-CoV-2 Outbreak Detection and Genomic Tracking (Arizona, 2020-2023).Diagnostics (Basel, Switzerland) · 2025Article
- Comparative Meta-Analysis of Long-Read and Short-Read Sequencing for Metagenomic Profiling of the Lower Respiratory Tract Infections.Microorganisms · 2025Review
- Direct comparison of clear DX Nanopore and Illumina sequencing of SARS-CoV-2.Microbiology spectrum · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples.Journal of medical virology · 2025Article
- Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.Scientific reports · 2025Article
- An Advanced Molecular Detection Roadmap for Nonlaboratorians.Emerging infectious diseases · 2025Article
- Short-Read and Long-Read Whole Genome Sequencing for SARS-CoV-2 Variants Identification.Viruses · 2025Article
- Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand.NPJ genomic medicine · 2024Article
- Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater.Viruses · 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
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- The application of long-read sequencing in clinical settings.Human genomics · 2023Review
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log
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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.