Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021

Subramoney, Kathleen; Mtileni, Nkhensani; Bharuthram, Avani; Davis, Ashlyn; Kalenga, Beauty; Rikhotso, Mikateko; Maphahlele, Mpho; Giandhari, Jennifer; Naidoo, Yeshnee; Pillay, Sureshnee; Ramphal, Upasana; Ramphal, Yajna; Tegally, Houriyah; Wilkinson, Eduan; Mohale, Thabo; Ismail, Arshad; Mashishi, Bonolo; Mbenenge, Nonhlanhla; Oliveira, Túlio de; Makatini, Zinhle; Fielding, Burtram C.; Treurnicht, Florette K.

doi:10.1002/jmv.27797

Cited by 30 publications

(30 citation statements)

References 23 publications

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“…A recent report from South Africa showed, similar to our study, that the TaqPath SGTF signature had high accuracy to identify Omicron BA.1 sublineage (97.5% confirmed by WGS). In that study, a genotypic assay targeting both the del 69-70 and a K417N was used as the gold standard for identifying Omicron BA.1 and ruling out of the Alpha and Beta variants with a subset of samples confirmed by WGS 22 . Given that the del 69-70 is present in VOC other than Omicron and Alpha, it is important to know the local prevalence of emerging variants for optimal application of the SGTF signature.…”

Section: Discussionmentioning

confidence: 99%

The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants

McMillen

Jani

Robilotti

et al. 2022

Sci Rep

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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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Section: Discussionmentioning

confidence: 99%

The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants

McMillen

Jani

Robilotti

et al. 2022

Sci Rep

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“…Caspase-8 has been discovered to be a master regulator of the three primary cell death pathways, including apoptosis, pyroptosis, and necroptosis. Previously, it was only recognized as an apoptotic caspase (9) . Recently, it was found that caspase-8 can function similarly to caspase-1 in processing pro-IL-1 and IL-18, releasing bioactive cytokines through either pyroptosis or necroptosis and triggering the generation of pro-inflammatory cytokines.…”

Section: Introductionmentioning

confidence: 99%

Relationship between Caspase-8 and SARS-CoV-2 Variants in a Sample of Iraqi Population

Ghazzi¹,

Fadhil²

2022

The Egyptian Journal of Hospital Medicine

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Background: Mutations started to accumulate in SARS-CoV-2 due to replication errors leading to emergence of variants. New variant appeared in December 2020. Caspase-8 can process pro-IL-1 and IL-18 causing the release of bioactive cytokines through immunogenic cell death that can kill virus-infected cells and activate the innate and adaptive immune systems. Objective: This study aimed to find the relationship between caspase-8 levels and wild-type, alpha, beta or gamma and omicron variants and its correlation with severity, CRP, and WBC. Materials and methods: 134 nasal swabs and blood samples were collected from COVID-19 patients and 48 healthy individuals. RNA was extracted and rRT-PCR assay to detect variants using a special kit. Caspase-8 levels were determined by ELISA. Results: There was a significant relationship (p < 0.001) in patients median caspase-8 than in control. Logistic regression analysis showed that odds ratio (OR) of unadjusted patients was 4.33 and with age-adjusted was 7.24. Caspase-8 levels showed a significant relationship with the severity of infection by COVID-19 (p < 0.01) and highly significant relation with variants of SARS-CoV-2 (p < 0.0001), as follows: Alpha, wild type, beta or gamma and omicron. Caspase-8 levels were significantly increased with increase of CRP levels (p < 0.05) making both of them good prognostic markers for infection progress. Observed negative Spearman correlation (rs = -0.27; p < 0. 01) were detected between caspase-8 and WBC. Conclusion:The most severe infections with SARS-CoV-2 appeared in wild type and alpha variant. Caspase-8 and CRP are excellent biomarkers for the progression of infection.

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“…One of those modified assays was the RT-qPCRbased SGTF assay because a Δ69-70 deletion in most sublineages of the Omicron (i.e., BA.1, BA.1.1, BA.3, BA.4, and BA.5) would hinder a detection of the spike gene but not of other genes. 35,36 However, this assay would not be able to differentiate between those sublineages of Omicron; 35 hence, the NGS facility was required to confirm the diagnosis.…”

Section: The Emergence and Hallmarks Of The Omicron Variantmentioning

confidence: 99%

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

Vidian¹,

Dikson²,

Litanto³

et al. 2022

Explor Res Hypothesis Med

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The world is now in the third year of the COVID-19 pandemic. As such, enormous volumes of virological, immunological, and epidemiological knowledge pertaining to the SARS-CoV-2 infection have been obtained during these years. The SARS-CoV-2 Omicron variant is currently causing the latest wave of infection globally presumably due to its ability to transmit with ease among individuals and to escape from the existing neutralizing antibodies. Fortunately, numerous treatment agents as well as prophylactic vaccines are now available, thus providing people with a better chance to control this infectious disease. This review will discuss the Omicron variant of concern as well as the available treatments and vaccines for COVID-19.

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Identification of SARS‐CoV‐2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021

Cited by 30 publications

References 23 publications

The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants

The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants

Relationship between Caspase-8 and SARS-CoV-2 Variants in a Sample of Iraqi Population

Emergence of the SARS-CoV-2 Omicron Variant: Current Treatments and Vaccines for COVID-19

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