ArticleInternational journal of molecular sciences2020
Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Improved protocol forExperimental biology and medicine (Maywood, N.J.) · 2023Article
- Progress of the "Molecular Informatics" Section in 2022.International journal of molecular sciences · 2023Article
- In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT-qPCR assays for SARS-CoV-2 detection using whole genome sequencing.Journal of medical virology · 2023Article
- Is diagnostic performance of SARS-CoV-2 detection dogs reduced -due to virus variation- over the time?Applied animal behaviour science · 2023Article
- Identification of mutations in SARS-CoV-2 PCR primer regions.Scientific reports · 2022Article
- Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach.Journal of medical virology · 2022Article
- High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination.International journal of molecular sciences · 2022Article
- Challenges and complexities in evaluating severe acute respiratory syndrome coronavirus 2 molecular diagnostics during the COVID-19 pandemic.African journal of laboratory medicine · 2022Article
- The Emergence of SARS-CoV-2 Variants With a Lower Antibody Response: A Genomic and Clinical Perspective.Frontiers in medicine · 2022Review
- Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2.PloS one · 2022Article
- Systematic Tracing of Susceptible Animals to SARS-CoV-2 by a Bioinformatics Framework.Frontiers in microbiology · 2022Article
- Strategy to Develop and Evaluate a Multiplex RT-ddPCR in Response to SARS-CoV-2 Genomic Evolution.Current issues in molecular biology · 2021Article
- Single base mutations in the nucleocapsid gene of SARS-CoV-2 affects amplification efficiency of sequence variants and may lead to assay failure.Journal of clinical virology plus · 2021Article
- Emerging SARS-CoV-2 variants of concern and potential intervention approaches.Critical care (London, England) · 2021Review
- Misdiagnosis of SARS-CoV-2: A Critical Review of the Influence of Sampling and Clinical Detection Methods.Medical sciences (Basel, Switzerland) · 2021Review
- Deepening of In Silico Evaluation of SARS-CoV-2 Detection RT-qPCR Assays in the Context of New Variants.Genes · 2021Article
- Summary of the Available Molecular Methods for Detection of SARS-CoV-2 during the Ongoing Pandemic.International journal of molecular sciences · 2021Review
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time points, to evaluate the specificity of 12 RT-qPCR tests (consisting of a total of 30 primers and probe sets) used for SARS-CoV-2 detection and the impact of the virus' genetic evolution on four of them. The exclusivity of these methods was also assessed using the human reference genome and 2624 closely related other respiratory viral genomes. The specificity of the assays was generally good and stable over time. An exception is the first method developed by the China Center for Disease Control and prevention (CDC), which exhibits three primer mismatches present in 358 SARS-CoV-2 genomes sequenced mainly in Europe from February 2020 onwards. The best results were obtained for the assay of Chan et al. (2020) targeting the gene coding for the spiking protein (S). This demonstrates that our user-friendly strategy can be used for a first in silico specificity evaluation of future RT-qPCR tests, as well as verifying that the former methods are still capable of detecting circulating SARS-CoV-2 variants.
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