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

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.

Epidemiological Surveillance Reveals the Rise and Establishment of the Omicron SARS-CoV-2 Variant in Brazil

“…The SGTF samples identified before epidemiological week 49 possibly indicate the presence of the Alpha VOC, as previously described [28]. The Omicron (sublineages BA.1, BA.4, and BA.5) and Alpha VOCs share the 69-70 deletion in the Spike protein that prevents the oligonucleotide probe from binding to its target sequence, leading to what has been termed SGTF [25]. Due to the high accuracy of the SGTF method, this strategy was widely used for monitoring these variants [8,25].…”

“…The positive samples were grouped by sex (male and female) and age cluster (0 to 9 years; 10 to 19 years; 20 to 29 years; 30 to 39 years; 40 to 49 years; 50 to 59 years; and ≥60 years). The SARS-CoV-2 variant genotyping in this study was performed according to the SGTF detection method [25]. SGTF were considered only in samples with CT values < 26 for any other viral gene (N or ORF1ab) to exclude samples with SGTF profiles due to lower viral input in primary samples.…”

“…One of the main mutations is the 69-70 deletion, which prevents the oligonucleotide probe in some RT-qPCR kits from binding to its target sequence, leading to what has been called S gene target failure (SGTF). The SGTF is a marker for Omicron and Alpha detection, but it is absent in the Delta VOC [25]. Nowadays, several Omicron sublineages have been detected, including BA.1, BA.1.1, BA.2, BA.3, BA.2.12.1, BA.4, and BA.5.…”

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

“…The deletions ΔH69/V70 are reported to enhance infectivity through increased spike incorporation into virions, to increase replication, and to even compensate for immune escape mutations that reduce infectivity [ 71 , 80 ]. Additionally, the ΔH69/V70 S gene mutations have been linked to the failure of tests used for detection of SARS-CoV-2 (S gene target failure) [ 81 ]. A second mutation, which also independently emerged in other lineages, is N439K.…”

Evaluation of a multiplexed oligonucleotide ligation assay for SARS-CoV-2 variant identification

“…Though WGS provides the most detailed information of available methods, turnaround time remains suboptimal, with surveillance data typically delayed by two to four weeks. As a complementary, more rapid approach, TaqPath spike gene target failure and mutation-specific RT-qPCR assays have also been utilized to identify known variants and help prioritize samples for WGS [7] , [8] , [9] . There is limited literature, however, on intermediate methods that have the potential to provide more comprehensive mutation coverage than RT-qPCR and more timely results than WGS.…”