Omicron Plus India: Trends Observed in S-gene Target Failure Detection Rate

Praveenkumar Ganesan1, Chaitali Nikam2, *, Caesar Sengupta3, Riyaj Ahmad1, Darshak Patil1, Prince Sharma1, Kumar K. Kallathi3
1 Molecular Biology, Thyrocare Technologies Limited, Navi Mumbai 400703, India
2 Infectious Diseases, Thyrocare Technologies Limited, Navi Mumbai 400703, India
3 Thyrocare Technologies Limited, Navi Mumbai 400703, India

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© 2023 Ganesan et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Infectious Diseases, Thyrocare Technologies Limited, Navi Mumbai 400703, India; E-mail:



COVID-19 is an infectious disease caused by SARS-COV-2. As the world eagerly awaits the transition of the COVID-19 pandemic to an endemic, the ever-evolving virus has a new variant of concern, as announced by WHO on November 26th, 2021. The Omicron variant, B.1.1.529, was first reported to WHO on November 24th, 2021. The variant has a large number of mutations in the S-gene and has caused a detrimental change in COVID-19 epidemiology. The efficient management of COVID-19 depends on early diagnosis and treatment. This new chain of new variants of concern has always posed a challenge to the accurate diagnosis of COVID-19.


In this study, we studied the S-gene target failure of positive cases of COVID-19 from December 2nd, 2021, to January 1st, 2022. Moreover, we checked this trend per month for two months after that by accumulating positives. All positive samples detected for COVID-19 by ICMR approved kit (target selections N and ORF1ab) were re-run using another ICMR-approved kit with three targets (S, N, and ORF1ab). The absence of S-gene in the target, i.e., S-gene target failure (SGTF), can be considered an indication of an Omicron variant as per the advisory policy. In continuation with this, considering the next wave in China, we tested SGTF for the next two months, and as expected, a reduction in SGTF percentage was observed.


A total of 53,276 samples were received in December 2021, of which 4848 samples showed a positive result for SARS-CoV-2. Out of this, 2119 (43.70%) samples showed SGTF. To analyze this trend, we tested 156 samples from February, 2022 and 118 samples from March, 2022, which resulted in only 8 (5.1%) and 3(2.5%) samples showing SGTF.


The study sheds light on the doubling rate of infection of COVID-19 in India and SGTF, indicating the spread of the Omicron variant. The infection can be controlled by accurately diagnosing variants of concern (VOC), but all positive samples cannot be screened for sequencing. In this case, kits with multiple targets that show the SGTF can be used as a proxy screening test, and for further confirmation, whole genome sequencing can be done.

Keywords: S-gene target failure, SGTF, Omicron, Variant B.1.1.529, COVID-19, Infectious disease, Pandemic.