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

• DOI: 10.1099/acmi.0.000643.v2
• Publication Date: 2024-08-07T09:26:32Z
• Authors: Ashish William; Yogita Rai; Deepti Rawat; Sanjib Gogoi; Megh Singh Dhakad; Manoj Jais; Ravinder Kaur
• Keywords: Radiology, Nuclear Medicine and Imaging; Gold standard (test); GeneXpert MTB/RIF; Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); Pcr test; RT-PCR; Mycobacterium tuberculosis; Infectious disease (medical specialty); FOS: Health sciences; Applications of Deep Learning in Medical Imaging; Diagnostic Methods for COVID-19 Detection; Gene; Biochemistry; Polymerase chain reaction; Coronavirus disease 2019 (COVID-19); Infectious Diseases; Virology; Health Sciences; Pathology; Medicine; Tuberculosis; Disease; Internal medicine; Biology

Background The novel coronavirus disease (COVID-19) has highlighted vulnerabilities in healthcare systems and has single-handedly literally brought the world to a standstill. Diagnostic testing for COVID-19 is critical for understanding epidemiology, contact-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. Aim The aim of the study was to compare the performance of GeneXpert against the gold standard rRT-PCR for SARS-CoV-2.

Materials and methods 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 VRDL laboratory for testing of SARS-CoV-2 by GeneXpert (CBNAAT) were included for the study. A total 220 samples positive and 50 samples negative for SARS-CoV-2 by GeneXpert were simultaneously tested for rRT-PCR. rRT-PCR was considered as gold standard test (reference) for calculating the sensitivity and specificity of GeneXpert (CBNAAT) test. Results Out of 220 samples positive for COVID-19 by GeneXpert, 118 (53.64%) were also positive by rRT-PCR while 102 (46.36%) showed negative results by rRT-PCR. However, 50 GeneXpert negative samples showed 100% agreement with rRT-PCR i.e. they were also negative by rRT-PCR. The GeneXpert sensitivity and specificity for COVID-19 was seen to be 100% (95% CI: 96.92 to 100%) and 32.89% (95% CI: 25.50 to 40.97%) respectively as compared to gold standard RT-PCR test. The positive predictive value (PPV) and negative predictive value (NPV) of GeneXpert for COVID-19 was found to be 53.64% and 100% respectively. Conclusion This study highlights that the GeneXpert test is highly sensitive and found to be helpful in emergency and challenging situations, where it can be useful in the early diagnosis and management of COVID-19 infection and thus, prevention of morbidity and mortality.