ArticleScientific reports2022
The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 47 citations in OpenAlex.
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- Integrating Genomic Data into Test-negative Designs for Estimating Lineage-specific COVID-19 Vaccine Effectiveness.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Optimizing global genomic surveillance for early detection of emerging SARS-CoV-2 variants.Nature communications · 2026Article
- Finding the MissingAntibiotics (Basel, Switzerland) · 2025Article
- Determinants of SARS-CoV-2 outcomes in patients with cancer vs controls without cancer: a multivariable meta-analysis with genomic imputation.EClinicalMedicine · 2025Article
- Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein.Virus evolution · 2025Article
- Insights into Omicron: Genomic Characterization and Inpatient Risk Assessment at Single Tertiary Hospital in Indonesia.Journal of multidisciplinary healthcare · 2025Article
- The Clinical Anatomy of SARS-CoV-2 Variants of Concern in Central Greece During October 2020-July 2022.Microorganisms · 2024Article
- A program for real-time surveillance of SARS-CoV-2 genetics.Scientific reports · 2024Article
- Testing for SARS-CoV-2: lessons learned and current use cases.Clinical microbiology reviews · 2024Review
- The impact of health inequity on spatial variation of COVID-19 transmission in England.PLoS computational biology · 2024Article
- Rapid and Accurate Detection of the SARS-CoV-2 Omicron Variant with a CRISPR-Cas12a Reaction in the RT-qPCR Pot.ACS omega · 2024Article
- Article
- Diagnostic testing and the evolution of detection avoidance by pathogens.Evolution, medicine, and public health · 2024Article
- Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures.PloS one · 2024Article
- A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva.Biology methods & protocols · 2024Article
- SARS-CoV-2 Nucleocapsid Protein Mutations Found in Switzerland Disrupt N-Gene Amplification in Commonly Used Multiplex RT-PCR Assay.Pathogens (Basel, Switzerland) · 2023Article
- Multiplexed RT-qPCR Coupled with Whole-Genome Sequencing to Monitor a SARS-CoV-2 Omicron Variant of Concern in a Hospital Laboratory Setting in Latvia.Diagnostics (Basel, Switzerland) · 2023Article
- Assessing the importance of demographic risk factors across two waves of SARS-CoV-2 using fine-scale case data.PLoS computational biology · 2023Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4 and BA.5) variants of concern (VOC) share several mutations in their spike gene, including mutations resulting in the deletion of two amino acids at position 69 and 70 (del 69-70) in the Spike protein. Del 69-70 causes failure to detect the S gene target on a widely used, commercial test, the TaqPath SARS-CoV-2 RT-PCR (Thermo Fisher). The S gene target failure (SGTF) signature has been used to preliminarily infer the presence of Alpha and Omicron VOC. We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. The accuracy of the SGTF signature was high, making this genomic signature a rapid and accurate proxy for identification of these variants in real-world laboratory settings.
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