A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

Fontana-Maurell, Marcela; Motta, Fernando do Couto; Arruda, Mónica; Cardoso, Pedro Henrique; Ribeiro, Marisa; Andrade, Elisabete; Godoy, Daniela Tupy de; Costa, Elaine; Rocha, Daniele; Siqueira, Marilda Agudo MT; Brindeiro, Rodrigo M.; Álvarez, Patrícia

doi:10.1590/0074-02760220202

Cited by 1 publication

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References 65 publications

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“…Many publications have evaluated different approaches to determining the accuracy and applicability of the SGTF in variant detection [ 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. In our study, the sensitivity and specificity values based on WGS VOC determination were in line with previously reported values [ 34 ]; our calculations based on variant-specific PCR, however, were consistently lower than for WGS, indicating a reduced accuracy in lineage classification.…”

Section: Discussionmentioning

confidence: 99%

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

Hilti,

Wehrli,

Berchtold

et al. 2024

Microorganisms

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During the SARS-CoV-2 pandemic, the Dr. Risch medical group employed the multiplex TaqPathTM 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.

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