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

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

doi:10.3390/microorganisms12020321

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. 2024 Feb 3;12(2):321. doi: 10.3390/microorganisms12020321.

Authors

Dominique Hilti^{1

2}, Faina Wehrli¹, Sabine Berchtold¹, Susanna Bigler¹, Thomas Bodmer¹, Helena M B Seth-Smith³, Tim Roloff³, Philipp Kohler⁴, Christian R Kahlert⁵, Laurent Kaiser^{6

7}, Adrian Egli³, Lorenz Risch^{1

2}, Martin Risch^{1

5}, Nadia Wohlwend¹

Affiliations

¹ Laboratory Dr. Risch, 9470 Buchs, Switzerland.
² Institute of Laboratory Medicine, Private University in the Principality of Liechtenstein (UFL), 9495 Triesen, Liechtenstein.
³ Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland.
⁴ Zentrallabor, Kantonsspital Graubünden, 7000 Chur, Switzerland.
⁵ Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, 9007 St. Gallen, Switzerland.
⁶ Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland.
⁷ Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland.

Abstract

During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPath^TM 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 (t₀) 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.

Keywords: S-gene target failure; SARS-CoV-2; surveillance; whole-genome sequencing.

Grants and funding

This research received no external funding.