S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5
During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath<sup>TM</sup> COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting t...
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MDPI AG
2024-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/2/321 |
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| author | Dominique Hilti Faina Wehrli Sabine Berchtold Susanna Bigler Thomas Bodmer Helena M. B. Seth-Smith Tim Roloff Philipp Kohler Christian R. Kahlert Laurent Kaiser Adrian Egli Lorenz Risch Martin Risch Nadia Wohlwend |
| author_facet | Dominique Hilti Faina Wehrli Sabine Berchtold Susanna Bigler Thomas Bodmer Helena M. B. Seth-Smith Tim Roloff Philipp Kohler Christian R. Kahlert Laurent Kaiser Adrian Egli Lorenz Risch Martin Risch Nadia Wohlwend |
| author_sort | Dominique Hilti |
| collection | DOAJ |
| description | During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath<sup>TM</sup> COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between “true” SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid’s midpoint (t<sub>0</sub>) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein. |
| first_indexed | 2024-03-07T22:20:49Z |
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| id | doaj.art-5f26ec04ca1b422385ff3cbcdf45d433 |
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| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-07T22:20:49Z |
| publishDate | 2024-02-01 |
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| series | Microorganisms |
| spelling | doaj.art-5f26ec04ca1b422385ff3cbcdf45d4332024-02-23T15:28:11ZengMDPI AGMicroorganisms2076-26072024-02-0112232110.3390/microorganisms12020321S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5Dominique Hilti0Faina Wehrli1Sabine Berchtold2Susanna Bigler3Thomas Bodmer4Helena M. B. Seth-Smith5Tim Roloff6Philipp Kohler7Christian R. Kahlert8Laurent Kaiser9Adrian Egli10Lorenz Risch11Martin Risch12Nadia Wohlwend13Laboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandInstitute of Medical Microbiology, University of Zurich, 8006 Zurich, SwitzerlandInstitute of Medical Microbiology, University of Zurich, 8006 Zurich, SwitzerlandZentrallabor, Kantonsspital Graubünden, 7000 Chur, SwitzerlandDivision of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, SwitzerlandDivision of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, SwitzerlandInstitute of Medical Microbiology, University of Zurich, 8006 Zurich, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandLaboratory Dr. Risch, 9470 Buchs, SwitzerlandDuring the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath<sup>TM</sup> COVID-19 CE-IVD RT-PCR Kit for large-scale routine diagnostic testing in Switzerland and the principality of Liechtenstein. The TaqPath Kit is a widely used multiplex assay targeting three genes (i.e., ORF1AB, N, S). With emergence of the B.1.1.7 (Alpha) variant, a diagnostic flaw became apparent as the amplification of the S-gene target was absent in these samples due to a deletion (ΔH69/V70) in the Alpha variant genome. This S-gene target failure (SGTF) was the earliest indication of a new variant emerging and was also observed in subsequent variants such as Omicron BA.1 and BA4/BA.5. The Delta variant and Omicron BA.2 did not present with SGTF. From September 2020 to November 2022, we investigated the applicability of the SGTF as a surrogate marker for emerging variants such as B.1.1.7, B.1.617.2 (Delta), and Omicron BA.1, BA.2, and BA.4/BA.5 in samples with cycle threshold (Ct) values < 30. Next to true SGTF-positive and SGTF-negative samples, there were also samples presenting with delayed-type S-gene amplification (higher Ct value for S-gene than ORF1ab gene). Among these, a difference of 3.8 Ct values between the S- and ORF1ab genes was found to best distinguish between “true” SGTF and the cycle threshold variability of the assay. Samples above the cutoff were subsequently termed partial SGTF (pSGTF). Variant confirmation was performed by whole-genome sequencing (Oxford Nanopore Technology, Oxford, UK) or mutation-specific PCR (TIB MOLBIOL). In total, 17,724 (7.4%) samples among 240,896 positives were variant-confirmed, resulting in an overall sensitivity and specificity of 93.2% [92.7%, 93.7%] and 99.3% [99.2%, 99.5%], respectively. Sensitivity was increased to 98.2% [97.9% to 98.4%] and specificity lowered to 98.9% [98.6% to 99.1%] when samples with pSGTF were included. Furthermore, weekly logistic growth rates (α) and sigmoid’s midpoint (t<sub>0</sub>) were calculated based on SGTF data and did not significantly differ from calculations based on comprehensive data from GISAID. The SGTF therefore allowed for a valid real-time estimate for the introduction of all dominant variants in Switzerland and Liechtenstein.https://www.mdpi.com/2076-2607/12/2/321S-gene target failurewhole-genome sequencingSARS-CoV-2surveillance |
| spellingShingle | Dominique Hilti Faina Wehrli Sabine Berchtold Susanna Bigler Thomas Bodmer Helena M. B. Seth-Smith Tim Roloff Philipp Kohler Christian R. Kahlert Laurent Kaiser Adrian Egli Lorenz Risch Martin Risch Nadia Wohlwend S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 Microorganisms S-gene target failure whole-genome sequencing SARS-CoV-2 surveillance |
| title | S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 |
| title_full | S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 |
| title_fullStr | S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 |
| title_full_unstemmed | S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 |
| title_short | S-Gene Target Failure as an Effective Tool for Tracking the Emergence of Dominant SARS-CoV-2 Variants in Switzerland and Liechtenstein, Including Alpha, Delta, and Omicron BA.1, BA.2, and BA.4/BA.5 |
| title_sort | s gene target failure as an effective tool for tracking the emergence of dominant sars cov 2 variants in switzerland and liechtenstein including alpha delta and omicron ba 1 ba 2 and ba 4 ba 5 |
| topic | S-gene target failure whole-genome sequencing SARS-CoV-2 surveillance |
| url | https://www.mdpi.com/2076-2607/12/2/321 |
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