S Gene target failure analysis in Covid positive patienus using Taqpath Covid-19 Assay

Abstract

The evolution of SARS-COV-2 resulted in the emergence of various variants of concern. A deletion at positions 69 and 70 of the spike glycoprotein precursor gene (S-gene), is associated with S gene Target Failure (SGTF) in a commonly used three gene diagnostic RTqPCR assay and

is one of the mutations that characterize the omicron and alpha variants till now. The use of TaqPath COVID-19 CE-IVD RT-PCR kit with a non-detectable S gene target and Ct value≤37 for either the ORF1ab or N gene targets was classified as SGTF. In this study, nasopharyngeal swab samples of covid positive patients visiting TU Biotech Corona Laboratory were used. Of the total positive samples, 24.26% (304/1,253) of the samples with low cycle threshold (Ct) values were selected to access SGTF. The rate of SGTF detection was high in the end of January which slowly decreased towards the start of next month. Among the 304 samples, 16.11% (49/304) samples resulted in SGTF whereas 83.88% (255/304) samples showed non-SGTF. Highest number of SGTF was found in the sample having the Ct values in the range 30-35 for both N gene and ORF1ab. Therefore, Ct mean value of SGTF samples were found to be greater than that of non- SGTF samples. Among the SGTF samples, 69.38% (34/49) of them were male and 30.61% (15/49) were female. The mean age of SGTF individuals was 38.20 years ranging from 8 to 73 years old. In the study population highest number of SGTF cases 29/49 (59.18%) belonged to 25- 45 years age. Cough, fever and sore throat were the common symptoms in the SGTF patients. Among the SGTF samples the highest number of patients were vaccinated with Verocell followed by Covishield, Johnson and Pfizer vaccines. Detection of new variants of SARSCOV-2

with mutated spike protein through the SGTF approach helps in identifying circulating variants in the community.

Keywords: SARS-CoV-2, RT-qPCR, SGTF, non-SGTF, Ct value