Detection of SARS-CoV2 by a Commercial RNA Detection Kit: a Public Health Laboratory Experience

Abstract

Purpose: There is a critical shortage of the commercial SARS-CoV2 detection kits and a major problem for testing capacity in Bangladesh since December, 2019 to combat the Covid19 pandemic. So this study was aimed to assess SARS-CoV2 detection with a commercial RNA detection kit by the qualitative real time PCR from respiratory specimens (nasal or throat swab) of Covid19 suspected cases. Methods & Materials: This cross sectional study was done by convenience sampling from Munshiganj district and four different hospitals in Dhaka city from 28 November 2020 to 4 December 2020. Nasal or throat swab samples were collected from Covid19 suspected cases and sent to NIPSOM RT-PCR lab, National Institute of Preventive and Social Medicine (a public health laboratory), NIPSOM, Mohakhali, Dhaka, Bangladesh. A commercial kit [Adaltis MOLGen SARS-CoV-2 (3Genes) RealTime PCR, Italy] containing the primer and probe set in fluorimeter channel was used to detect three genes of SARS-CoV-2: RNA-dependent RNA polymerase (RdRp), envelope (E) and nucleocapsid (N) with endogenous internal control (IC). Threshold cycle (Ct) value was selected at ≤40 for each positive gene and detection of at least two different genes (RdRp and E gene or N gene) was interpreted as SARS-CoV2 positive. Results: A total of 1061 samples of Covid19 suspected cases within 4 to 98 years of age were included in this study and male female ratio was 1.33:1. Among 1061 samples, 299 (28.18%) were tested positive for SARS-CoV2 with mean age of 43.33 years and male was found predominantly. Of them, 94.98% were positive for RdRp, E and N genes whereas all (100%) were found positive for only RdRp and E gene. Here, the Ct value of IC ranged within <20 to 40 and 44.48% was found at Ct 30–35 followed by 36.79% at Ct 25–30 and 10.37% at Ct 35–40. For individual RdRp gene, E gene and N gene, highest Ct values were at 30–35 with 26.42%, 30.43% and 28.87% respectively. Conclusion: To address accurate and safely diagnosis of SARS CoV-2, this commercial RNA detection kit will help during the COVID-19 pandemic.