Evaluation of Sensitivity and Specificity of Three Commercial Real-Time Quantitative Polymerase Chain Reaction Kits for Detecting SARS-CoV-2 in Bangladesh

Background The coronavirus disease 2019 (COVID-19) pandemic has manifested into an unprecedented public health crisis. The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has facilitated reagent developers to customize and receive authorization for nucleic acid testing kits in a short period, which would have resulted in some shortcomings in the quality parameters of the kits. Consequently, in-house clinical validations of innovative real-time quantitative polymerase chain reaction (RT-qPCR) kits are required. This research aims to determine the sensitivity, specificity, and accuracy of various RT-qPCR kits available in Bangladesh. Methodology A total of 150 samples were obtained from patients with suspected COVID-19 infection when the delta variant was predominant, followed by RNA extraction performed using a nucleic acid isolation kit. Subsequently, three commercially available PCR kits named Sansure (China), STAT-NAT(Ⓑ) (Sentinel Diagnostics, Italy), and Roche Biochem (Switzerland) were applied to detect SARS-CoV-2. Results The results showed that the STAT-NAT(Ⓑ) kit is more sensitive than the other two, as indicated by the cycle threshold (Ct) values of respective genes. STAT-NAT(Ⓑ) RT-qPCR can detect the ORF1ab gene sensitively (p < 0.001) compared to Sansure. STAT-NAT(Ⓑ) was also capable of detecting E and RdRp genes more sensitively (p < 0.001) compared to Roche. Regarding specificity, STAT-NAT(Ⓑ )(95% confidence interval [Cl] = 92.29-99.73%). RT-qPCR showed more accuracy than Sansure (95% Cl = 90.77-99.32%) and Roche (95% Cl = 81.17-94.38%). The area under the curve for E, ORF1ab, and RdRp genes of the STAT NAT(Ⓑ) PCR kit was 0.952, 0.959, and 0.981, respectively. Conclusions This study concluded that STAT-NAT(Ⓑ) is a better diagnostic RT-qPCR kit compared to Sansure and Roche for detecting SARS-CoV-2.