A distinctive genomic feature, the spike gene S Gene Target Failure (SGTF), enables accurate detection of the Alpha and Omicron SARS-CoV-2 variants of Gujarat region.

Authors: NILAY HARSHADKUMAR DAVE, Neeraj Arora, Dr Chetana Roat

Keywords: SARS-Cov-2, STGF, Spike Gene Target Failure, Alpha, Omicron, Taqpath RT-PCR, Next Generation Sequencing, VOC

Abstract: SARS-COV-2 is the infectious agent that causes COVID-19. Several mutations in the spike gene are shared by the Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4, and BA.5) variants of concern (VOC). The TaqPath SARS-CoV-2 RT-PCR kit, fails to detect the S gene target due to Del 69–70. Alpha and Omicron VOCs have been inferred in part from the S gene target failure (SGTF) marker. Samples of routine COVID-19 RT-PCR testing between December 2020 to July 2022 were considered in this study. RNA was extracted and subjected to RT-PCR by Taqpath kit as well NGS by Ion AmpliSeq SARS-CoV-2 Research Panel. FASTA files were analysed by nextstrain database and statistical analysis were performed using GraphPad Prism version 8.4.2. Samples (n=80) were sequenced including 50 SGTF-positive samples. For the Alpha variant, the SGTF marker's sensitivity and specificity were 99.6% (95% CI 96.1–99.9%) and 98.6% (95% CI 99.2–99.8%), while for the Omicron variant, they were 99.6% (95% CI 98.9–99.9%) and 99.8% (95% CI 99.4–99.9%).The SGTF's positive predictive value was 100% for Omicron and 98% for Alpha. The high accuracy of the SGTF marker ensures a precise tool for identifying these variants in laboratory conditions. Furthermore, real-world data has demonstrated that SGTF testing aligns closely with genomic sequencing results, reinforcing its reliability as an early detection tool. New variants continue to emerge, integrating SGTF-based approaches into routine laboratory workflows will remain an essential strategy for global surveillance and pandemic management.