Cut-off Ct value of GeneXpert in comparison to gold standard RT-PCR for diagnosis of SARS-CoV-2: A retrospective study

ABSTRACT

<strong>BACKGROUND</strong> The novel coronavirus disease (COVID-19) has exposed the chinks in the armour of healthcare systems and has single-handedly literally brought the world to a standstill. Diagnostic testing for COVID-19 is critical for understanding epidemiology, contract-tracing, case management, and to control the transmission of the SARS-CoV-2. RT-PCR test, the gold standard test, involves fairly complex steps and take nearly 24–48 h for generating the results. GeneXpert is a rapid nucleic-acid-detection-based test approved by ICMR (Indian Council of Medical Research), which can shorten the turnaround time significantly.AIMThe aim of the study was to compare the performance of GeneXpert against the gold standard RT-PCR for SARS-COV-2. <strong>MATERIALS AND METHODS</strong> This retrospective study was conducted at a tertiary care centre from 25th March 2020 to 8th December 2020. The Nasopharyngeal/Oropharyngeal swabs that were sent to the Covid laboratory for testing of SARS COV-2 by GeneXpert (CBNAAT) were included for the study. The samples that gave a positive result were simultaneously tested for rRT-PCR. According to the manufacturer instructions, the cut-off value for GeneXpert is 45 whereas according to ICMR, cut-off value for RT-PCR to be taken is 35.RESULTSOut of 220 samples positive by GeneXpert , 102 (46%) showed negative results by RT-PCR. Among these 102 samples, 89% (91/102) samples were found to be positive by GeneXpert with Ct value >35 whereas 90% (96/107) positive GeneXpert samples had Ct value <35 which were also positive by RT-PCR. <strong>CONCLUSION</strong> The formulation of certain cut-off Ct values for the uniform results by both GeneXpert and RT-PCR should be implemented.