Evaluation of RT-PCR assays for detection of SARS-CoV-2 variants of concern.
Sourav Dutta Dip, Shovon Lal Sarkar, Md Ali Ahasan Setu, Prosanto Kumar Das, Md Hasan Ali Pramanik, A S M Rubayet Ul Alam, Hassan M Al-Emran, M Anwar Hossain, Iqbal Kabir Jahid
Author Information
Sourav Dutta Dip: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Shovon Lal Sarkar: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Md Ali Ahasan Setu: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Prosanto Kumar Das: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Md Hasan Ali Pramanik: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
A S M Rubayet Ul Alam: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Hassan M Al-Emran: Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
M Anwar Hossain: Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
Iqbal Kabir Jahid: Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh. ikjahid_mb@just.edu.bd.
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 and RT-PCR assay was performed according to the instruction of the respective manufacturers. The specificity and sensitivity of Maccura kit was 81.8% and 82.5%, A*Star kit was 100% and 75.4%, Da An Gene kit was 100% and 68.4%, Sansure kit was 54.5% and 91.2% and TaqPath kit was 100% and 70.2% respectively. Our in house SYBR-Green method showed a consistent detection result with 90.9% specificity and 91.2% sensitivity. We also found that detection kits targeting more genes showed better accuracy which facilitates less false positive results (< 20%). Our study found a significant difference (p < 0.005) in Ct value reported for common target genes shared by the RT-PCR kits in relation with different variants of COVID-19 infection. Recent variants of concerns contain more than 30 mutations in the spike proteins including 2 deletion and a unique insertion mutation by which makes detection of these variants difficult and these facilitates the variants to escape from being detected.
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