Conventional Reverse Transcription-Polymerase Chain Reaction Assay as an Alternative, Low-Cost, and Reliable Method for the Detection of Coronavirus Disease 2019

SARS-CoV-2 disease is a highly contagious infection causing a large number of deaths in susceptible individuals throughout the world. In this study, a low-cost, sensitive, and easy-to-perform conventional polymerase chain reaction (PCR)-based RNA detection method was evaluated to diagnose the infection, which was feasible at a laboratory with minimal molecular infrastructure.

From 4 July to 31 August 2020, a total of 277 nasopharyngeal/oropharyngeal swab samples consisting of 72 samples from hospitalized patients with a severe respiratory infection and 205 suspected patients in Isfahan, Iran, were tested using probe-based rtRT-PCR and conventional PCR assays.

A total of 160 clinical samples were tested by rtRT-PCR using the E gene. The sensitivity and specificity of the conventional PCR method were determined to be 100%. Furthermore, out of 117 clinical samples evaluated by the probe-based RT-PCR using the N gene, 74.4% of the samples were positive. Moreover, the duplex PCR method using the N gene and RNase P as an internal control reference gene showed that 68.4% of the samples were positive. Therefore, the tested PCRs could detect positive samples with a sensitivity of 92.55% and a specificity of 100%.

According to the results, this method is a simple, inexpensive, and valuable alternative as well as a suitable procedure for the laboratory diagnosis of SARS-CoV-2 infection.