Comparison of seven commercial RT-PCR kits with the NIV kit for the diagnosis of Covid-19

Abstract

Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread across the globe in an unprecedented manner and was declared a pandemic on March 11, 2020 by the World Health Organization (WHO). This study was carried out with the aim to compare the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and agreement of the eight different RT-PCR kits for the diagnosis of COVID-19. This observational cross-sectional study was carried out in the Department of Microbiology of a tertiary care hospital in Central Delhi from July to October 2021. A total of 45 nasopharyngeal and/or oropharyngeal swabs in Viral Transport Medium (VTM) from suspected COVID-19 patients were received in the laboratory for RT-PCR. These samples were tested by eight different Indian Council of Medical Research (ICMR)-approved RT-PCR kits with different gene targets. The comparison was made with the National Institute of Virology (NIV), the Pune COVID-19 RT-PCR kit. Statistical analysis: sensitivity, specificity, PPV, and NPV were calculated for each kit and compared using the McNemar test. Agreement of different kits was evaluated using Kappa analysis. The results of the 45 samples of suspected COVID-19 cases were recorded as per the cycle threshold (Ct) provided in the kit insert. Of these, 15 samples detected both E and RdRp genes and 30 were negative for both the genes of SARS CoV-2 by NIV, the Pune COVID-19 RT-PCR kit. All kits showed 100% sensitivity and had 100% NPV when compared with the NIV kit. However, specificity, PPV, and agreement were variable as compared to the NIV kit. The reporting should be carried out as per the manufacturer’s instructions. However, positive results with Ct values ≥ 36 showed variable results with different RT PCR kits and hence should be interpreted with caution.