ArticleVirus evolution2020
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation.
Article in Virus evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed, 161 citations in OpenAlex.
- Detecting and supporting COVID-19 outbreak response in a small-scale nursing home through passive wastewater surveillance of SARS-CoV-2.Applied and environmental microbiology · 2026Article
- Protein language models enable accurate viral host range prediction.Scientific reports · 2026Article
- How benchmarking of bioinformatics tools is essential for informed workflow selection: a case study on SARS-CoV-2 subgenomic RNA detection.Frontiers in bioinformatics · 2026Article
- Molecular Epidemiology of SARS-CoV-2 in Northern Greece from the Index Case up to Early 2025 Using Nanopore Sequencing.Epidemiologia (Basel, Switzerland) · 2025Article
- A Benchmark of methods for SARS-CoV-2 whole genome sequencing and development of a more sensitive method.Frontiers in genetics · 2025Article
- Amplification of Filovirus Genomes from Clinical Samples for Next Generation Sequencing.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Reflective Evaluation of Next-Generation Sequencing Data during Early Phase Detection of the Delta Variant.OBM genetics · 2025Article
- Associations between social determinants of health and COVID-19 outcomes by variants of concern: a Bayesian spatiotemporal analysis.BMJ public health · 2025Article
- Pulmonary microbial spectrum in late-stage SARS-CoV-2 infection: a case series.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2024Article
- Enhancing the epidemiological surveillance of SARS-CoV-2 using Sanger sequencing to identify circulating variants and recombinants.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- SARS-CoV-2 infections before, during, and after the Omicron wave: a 2-year Indian community cohort study.The Lancet regional health. Southeast Asia · 2024Article
- Target enrichment metaviromics enables comprehensive surveillance of coronaviruses in environmental and animal samples.Heliyon · 2024Article
- A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.Virology journal · 2024Article
- A novel fast hybrid capture sequencing method for high-efficiency common human coronavirus whole-genome acquisition.mSystems · 2024Article
- Unveiling Inter- and Intra-Patient Sequence Variability with a Multi-Sample Coronavirus Target Enrichment Approach.Viruses · 2024Article
- Comparison of analytical performance and economic value of two biosurveillance methods for tracking SARS-COV-2 variants of concern.Microbiology spectrum · 2024Article
- Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing.Virologica Sinica · 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
- 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
40 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next-Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty-four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialised kits including a hybridisation capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP), and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples (
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