Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection
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...
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| Format: | Article |
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MDPI AG
2020-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/15/5585 |
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| author | Mathieu Gand Kevin Vanneste Isabelle Thomas Steven Van Gucht Arnaud Capron Philippe Herman Nancy H. C. Roosens Sigrid C. J. De Keersmaecker |
| author_facet | Mathieu Gand Kevin Vanneste Isabelle Thomas Steven Van Gucht Arnaud Capron Philippe Herman Nancy H. C. Roosens Sigrid C. J. De Keersmaecker |
| author_sort | Mathieu Gand |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:58:19Z |
| format | Article |
| id | doaj.art-afdfee14234d46b999a8bc97dec5164b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T17:58:19Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-afdfee14234d46b999a8bc97dec5164b2023-11-20T09:04:14ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-08-012115558510.3390/ijms21155585Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 DetectionMathieu Gand0Kevin Vanneste1Isabelle Thomas2Steven Van Gucht3Arnaud Capron4Philippe Herman5Nancy H. C. Roosens6Sigrid C. J. De Keersmaecker7Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumViral Diseases, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumViral Diseases, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumQuality of Laboratories, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumExpertise and Service Provision, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumTransversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, B-1050 Brussels, BelgiumThe 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.https://www.mdpi.com/1422-0067/21/15/5585SARS-CoV-2COVID-19detectiondiagnosisRT-qPCRin silico specificity evaluation |
| spellingShingle | Mathieu Gand Kevin Vanneste Isabelle Thomas Steven Van Gucht Arnaud Capron Philippe Herman Nancy H. C. Roosens Sigrid C. J. De Keersmaecker 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 SARS-CoV-2 COVID-19 detection diagnosis RT-qPCR in silico specificity evaluation |
| title | Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection |
| title_full | Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection |
| title_fullStr | Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection |
| title_full_unstemmed | Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection |
| title_short | Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection |
| title_sort | use of whole genome sequencing data for a first in silico specificity evaluation of the rt qpcr assays used for sars cov 2 detection |
| topic | SARS-CoV-2 COVID-19 detection diagnosis RT-qPCR in silico specificity evaluation |
| url | https://www.mdpi.com/1422-0067/21/15/5585 |
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