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Article

Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection

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Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium
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Viral Diseases, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium
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Quality of Laboratories, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium
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Expertise and Service Provision, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, Belgium
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Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(15), 5585; https://doi.org/10.3390/ijms21155585
Received: 3 July 2020 / Revised: 30 July 2020 / Accepted: 31 July 2020 / Published: 4 August 2020
(This article belongs to the Special Issue Research of COVID-19 on the Bioinformatics Field)
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. View Full-Text
Keywords: SARS-CoV-2; COVID-19; detection; diagnosis; RT-qPCR; in silico specificity evaluation; bioinformatics tool; WGS data; mismatches; primers and probes SARS-CoV-2; COVID-19; detection; diagnosis; RT-qPCR; in silico specificity evaluation; bioinformatics tool; WGS data; mismatches; primers and probes
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MDPI and ACS Style

Gand, M.; Vanneste, K.; Thomas, I.; Van Gucht, S.; Capron, A.; Herman, P.; Roosens, N.H.C.; De Keersmaecker, S.C.J. Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection. Int. J. Mol. Sci. 2020, 21, 5585. https://doi.org/10.3390/ijms21155585

AMA Style

Gand M, Vanneste K, Thomas I, Van Gucht S, Capron A, Herman P, Roosens NHC, De Keersmaecker SCJ. Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection. International Journal of Molecular Sciences. 2020; 21(15):5585. https://doi.org/10.3390/ijms21155585

Chicago/Turabian Style

Gand, Mathieu, Kevin Vanneste, Isabelle Thomas, Steven Van Gucht, Arnaud Capron, Philippe Herman, Nancy H.C. Roosens, and Sigrid C.J. De Keersmaecker. 2020. "Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection" International Journal of Molecular Sciences 21, no. 15: 5585. https://doi.org/10.3390/ijms21155585

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