Optimizing SARS-CoV-2 Detection: A Rapid, Cost-Effective Reverse Transcription Polymerase Chain Reaction (RT-PCR) Method Without RNA Extraction

Introduction In December 2019, the emergence of a novel coronavirus, SARS-CoV-2, led to the global COVID-19 pandemic. Early diagnostic efforts included molecular tests such as reverse transcription polymerase chain reaction (RT-PCR). However, testing faced challenges including RNA reagent shortages and prolonged processing times. Antigen card tests, though reliable for positive results, had limitations. Tata MD CHECK RT-PCR XF emerged as a versatile diagnostic assay, capable of detecting SARS-CoV-2 with or without RNA extraction. This facilitated efficient testing amid ongoing resource constraints. This study was planned to compare the diagnostic accuracy of the Tata MD CHECK RT-PCR XF kit, a direct RT-PCR assay that eliminates the RNA extraction step, with conventional RT-PCR incorporating RNA extraction for detecting SARS-CoV-2 RNA. The direct RT-PCR approach demonstrated a sensitivity of 93.9%, closely aligning with conventional RT-PCR results, and showed comparable performance in lower Ct ranges (0-30), though reduced detection was observed at higher Ct values. Methods A cross-sectional study was conducted in the Department of Microbiology, Santosh Medical College, Ghaziabad. Nasopharyngeal and oropharyngeal samples were collected in viral transport media (VTM). Samples were processed in duplicate: one underwent RNA extraction, while the other was directly tested, without RNA extraction, using the Tata MD CHECK RT-PCR XF kit. Results A total of 110 samples were evaluated, with 62.7% from males and 37.3% from females, primarily in the 21-40 age group. The Tata MD Direct PCR demonstrated high diagnostic accuracy, with a sensitivity of 93.9%, specificity of 100%, positive predictive value (PPV) of 100%, and negative predictive value (NPV) of 84.4%. Discussion This cost-effective and rapid method significantly reduced turnaround times compared to conventional RT-PCR.