ArticleClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2021
Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.
Article in Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 42 citations in OpenAlex.
- Enabling global-scale nucleic acid repositories through versatile, scalable biochemical selection from room-temperature archives.Nature communications · 2026Article
- Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.Virus evolution · 2026Article
- MhGeneS: An Analytical Pipeline to Allow for Robust Microhaplotype Genotyping.Molecular ecology resources · 2025Article
- Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2.Microbiology spectrum · 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
- Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City.Frontiers in cellular and infection microbiology · 2023Article
- Sensitivity of Detection and Variant Typing of SARS-CoV-2 in European Laboratories.Journal of clinical microbiology · 2022Article
- Challenges and Opportunities for Global Genomic Surveillance Strategies in the COVID-19 Era.Viruses · 2022Review
- A Serotype-Specific and Multiplex PCR Method for Whole-Genome Sequencing of Dengue Virus Directly from Clinical Samples.Microbiology spectrum · 2022Article
- Article
- OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.NAR genomics and bioinformatics · 2022Article
- A simplified alternative diagnostic algorithm for SARS-CoV-2 suspected symptomatic patients and confirmed close contacts (asymptomatic): A consensus of Latin American experts.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.BMC genomics · 2022Article
- Genomic surveillance of SARS-CoV-2 in Puerto Rico reveals emergence of an autochthonous lineage and early detection of variants.Research square · 2022Article
- Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters.Virus evolution · 2022Article
- Mutation profile of SARS-CoV-2 genome in a sample from the first year of the pandemic in Colombia.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2022Article
- Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants.Communications medicine · 2022Article
- Sequencing SARS-CoV-2 genomes from saliva.Virus evolution · 2022Article
- Detection of SARS-CoV-2 infection clusters: The useful combination of spatiotemporal clustering and genomic analyses.Frontiers in public health · 2022Article
- Decreased Fetal Movements: A Sign of Placental SARS-CoV-2 Infection with Perinatal Brain Injury.Viruses · 2021Article
Corrections and comments
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Authors and funding
29 authors at 12 institutions in 8 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesGenotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping.
methodsWe established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result in miscalls when using alternative pipelines to process clinical samples and synthetic viral genomes with an amplicon-based genotyping approach. We evaluated the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination.
resultsWe found that at least 1000 viral genomes are necessary to confidently detect variants in the SARS-CoV-2 genome at frequencies of ≥10%. The broad applicability of our recommendations was validated in over 200 clinical samples from six independent laboratories. The genotypes we determined for clinical isolates with sufficient quality cluster by sampling location and period. Our analysis also supports the rise in frequencies of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was facilitated by travel during the summer of 2020.
conclusionsWe present much-needed recommendations for the reliable determination of SARS-CoV-2 genome sequences and demonstrate their broad applicability in a large cohort of clinical samples.
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