Abstract
To meet the unprecedented requirement of diagnostic testing for SARS-CoV-2, a large number of diagnostic kits were authorized by concerned authorities for diagnostic use within a short period of time during the initial phases of the ongoing pandemic. We undertook this study to evaluate the inter-test agreement and other key operational features of 5 such commercial kits that have been extensively used in India for routine diagnostic testing for COVID-19. The five commercial kits were evaluated, using a panel of positive and negative respiratory samples, considering the kit provided by National Institute of Virology, Indian Council of Medical Research (2019-nCoV Kit) as the reference. The positive panel comprised of individuals who fulfilled the 3 criteria of being clinically symptomatic, having history of contact with diagnosed cases and testing positive in the reference kit. The negative panel included both healthy and disease controls, the latter being drawn from individuals diagnosed with other respiratory viral infections. The same protocol of sample collection, same RNA extraction kit and same RT-PCR instrument were used for all the kits. Clinical samples were collected from a panel of 92 cases and 60 control patients, who fulfilled our inclusion criteria. The control group included equal number of healthy individuals and patients infected with other respiratory viruses (n = 30, in each group). We observed varying sensitivity and specificity among the evaluated kits, with LabGun COVID-19 RT-PCR kit showing the highest sensitivity and specificity (94% and 100% respectively), followed by TaqPath COVID-19 Combo and Allplex 2019-nCoV assays. The extent of inter-test agreement was not associated with viral loads of the samples. Poor correlation was observed between Ct values of the same genes amplified using different kits. Our findings reveal the presence of wide heterogeneity and sub-optimal inter-test agreement in the diagnostic performance of the evaluated kits and hint at the need of adopting stringent standards for fulfilling the quality assurance requirements of the COVID-19 diagnostic process.
Highlights
The ongoing COVID-19 pandemic has spread globally infecting approximately 90 million individuals and has led to 1.9 million deaths within a year since the first declaration of the outbreak in Wuhan, China on 31st December 20191,2
These kits included Allplex 2019–nCOV assay, Lab Gun COVID-19 RT-PCR Kit, TaqPath COVID-19 combo kit, BGI Real Time Fluorescent RT-PCR Kit and TRUPCR SARS-CoV-2 RT qPCR KIT assays and their performance was compared with 2019-nCoV Kit, provided by National Institute of Virology (NIV) under the aegis of Indian Council of Medical Research (ICMR)
Since the study was done on anonymized samples after they have been used for routine diagnostic processing; involved less than minimal risk to the participants as there was no additional sampling involved; was integrated with the quality audit of the institute and the programmatic requirement of evaluating the operational performance of the commercial diagnostic kits, it qualified for exemption from ethical review and waiver of informed consent according to ICMR’s “National Ethical Guidelines for Biomedical and Health Research involving Human Participants”
Summary
The ongoing COVID-19 pandemic has spread globally infecting approximately 90 million individuals and has led to 1.9 million deaths within a year since the first declaration of the outbreak in Wuhan, China on 31st December 20191,2. The availability of whole genome sequencing of the SARS-CoV-2 virus, within 2 weeks of the declaration of the outbreak, enabled the development of a wide range of RT-qPCR kits by several commercial manufacturers within a relatively short span of time To cope with this urgency and huge demand for testing, regulatory agencies like United States Food and Drug Administration (USFDA) adopted the procedure of Emergency Use Authorization (EUA) for clinical use of these kits in contrast to the customary process of granting full approval or clearance for diagnostic a ssays[5,6].
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