Abstract :
Background and Objective: COVID-19 is the disease caused by infectious agent SARS-COV-2. Several mutations in 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 RT-PCR kit for SARS-CoV-2, fails to detect the Spike gene target due to Del 69–70. Alpha and Omicron VOCs have been inferred in part from the Spike Gene Amplification Failure (SGAF) marker.Materials and Methods: Samples of routine COVID-19 RT-PCR testing between January 2021 to August 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 executed by GraphPad Prism version 9.5.0.Results: 80 Samples were processed for NGS including 50 SGAF-detected samples. For the Alpha variant, the SGAF marker's sensitivity and specificity were 99.7% (95% CI 97.3–99.9%) and 99.4% (95% CI 97.4–99.7%), while for the Omicron variant, they were 99.2% (95% CI 98.7–98.9%) and 99.6% (95% CI 99.3–99.7%).Conclusion: The SGAF's positive predictive value was 100% for Omicron and 98% for Alpha. The high accuracy of the SGAF marker ensures a precise tool for identifying these variants in laboratory conditions. Furthermore, real-world data has demonstrated that SGAF testing aligns closely with genomic sequencing results, reinforcing its reliability as an early detection tool. New variants continue to emerge, integrating SGAF based approaches into routine laboratory workflows will remain an essential strategy for global surveillance and pandemic management.
Keyword :
SARS-CoV-2, STGF, Spike gene amplification failure, Alpha, Omicron, Taqpath RT-PCR, Next generation sequencing, VOC.