Extraction free rapid detection of SARS-CoV-2 from oropharyngeal/nasopharyngeal swabs by real time PCR

Introduction: The emergence of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic has been troublesome particularly for developing countries that lack infrastructure and capacities to produce the kits locally. Simplification of the method can increase diagnostic efficiency which can benefit patients and help in infection control, consequently saving time and lives. Aim: To evaluate the diagnostic value of four methods (that omit extraction step) for detection of SARS-CoV-2 against the traditional extraction method. Materials and Methods: This was a cross-sectional analysis for evaluating diagnostic accuracy of four methods for detection of SARS-CoV-2 by real-time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR), conducted in the Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India, in October 2020. Ninety four SARS-CoV-2 RT-PCR positive samples and 20 negative samples were taken for this study. Automated extraction system was used for Ribonucleic Acid (RNA) extraction and four different approaches were compared to the traditional extraction method for detection of SARS-CoV-2 by RT-PCR. Results: The automated RNA extraction method was compared to the method of direct addition of samples with (Heat processed Direct Viral transport medium Sample (HDVS)) and without heating (Direct Viral transport medium Sample (DVS)), directs addition of diluted (1:5) sample with (Heat processed diluted VTM sample (HdVS)) and without heating (Diluted VTM sample (dVS)) as well as after addition of Proteinse K (PK) to the diluted samples that came either negative/invalid. Out of four methods, the HdVS method gave the best results, considering extraction with Perkin Elmer as standard, this method showed sensitivity of 96.74%, specificity of 100%. Conclusion: In current pandemic, molecular testing is critically challenged by the limited supplies of reagents of nucleic acid extraction alternative method like diluting and heating of Viral Transport Media (VTM) samples and using them directly as elutes serve as an easy, fast and inexpensive alternative.