Comparative Performance Analysis of Commercial SARS-CoV-2 RNA Detection Assays: Implications for Sensitivity, Specificity, Accuracy, and Diagnostic Response Time

Background/Objectives: In 2020, the world found itself in the midst of the SARS-CoV-2 pandemic. The virus has spread globally, resulting in over 779 million cases worldwide. In response to this crisis, there arose a critical need for diagnostic techniques capable of meeting the overwhelming global demand, including RT-qPCR as the gold standard due to its high sensitivity and specificity. However, RT-qPCR has its limitations, including susceptibility to factors such as inadequate sample collection, variations in viral load, and insufficient clinical validation, all of which can lead to false negatives. Consequently, this study aims to evaluate the clinical performance of four commercial RT-qPCR kits for detecting SARS-CoV-2. Methods: The study utilized 200 nasopharyngeal swab samples collected in January 2022, comparing kits from Qiagen, Seegene, Bio-Manguinhos, and IBMP. Results: Results indicated significant differences in kit performance, with 66% of samples showing consistent results across all kits, and 34% showing discrepancies. Ct values were also analyzed, and statistical tests highlighted varying sensitivities among the kits, ranging from 100% to 86.82%. Conclusions: The study underscores how extraction and purification processes, kit quality, and target gene adequacy critically influence kit performance, influencing the occurrence of false positives and negatives.