Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been considered with great importance on correct screening procedure. The detection efficiency of recent variants of concern were observed by comparing 5 commercial RT-PCR kits and a SYBR-green method developed and validated in our laboratory. The RNA was extracted from nasopharyngeal samples from suspected COVID-19 patients as instructed by each manufacturer and RT-PCR was also done according to standard procedures according to manufacturers. We found that commercially available Maccura kit (sensitivity and specificity > 80%), TaqPath kit (sensitivity and specificity > 80%) and in house SYBR-Green method (sensitivity and specificity > 90%) showed a consistent detection result. We also found that detection kits targeting more genes show a better result than less target gene containing protocols which facilitates less false positive results ( 80%). Our study also showed a significant difference (sig. <0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants, specifically the Variants of Concerns (VOCs) tends to report a higher Ct value than wild type SARS-CoV-2 and suggests to detect with more target genes for better accuracy and better assessment of COVID-19 infection.