Comparative analysis of the diagnostic performance of five commercial COVID-19 qRT PCR kits used in India

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.

The Comparative Analysis of Two RT-qPCR Kits for Detecting SARS-CoV-2 Reveals a Higher Risk of False-Negative Diagnosis in Samples with High Quantification Cycles for Viral and Internal Genes

“…For example, the Gerbion GmbH & Co. diagnostics kit showed a detection efficiency of 49%, while the kit from SolGent Co., Ltd. manufacturer showed a detection efficiency of 92% in SARS-CoV-2 detection [ 6 ]. On the other hand, a study in India showed differences of up to 21% between the RT-qPCR kits used for the COVID-19 diagnosis [ 7 ].…”

A systematic review and meta-analysis comparing the diagnostic accuracy tests of COVID-19

“…Sensitivity and specificity are reported as a mean (95% confidence limits). The forest plot represents the estimated sensitivity and specificity (black squares) and their 95% confidence limits (horizontal black line) [44][45][46][47][48][49][50][51][52][53][54][55][56][57][58]. Sensitivity and specificity are reported as a mean (95% confidence limits).…”

“…Positive Likelihood ratio, Negative likelihood ratio, and Diagnostic Odds ratio are reported with a mean (95% confidence limits). The Forest plot depicts the estimated sensitivity and specificity (black squares) and its 95% confidence limits (horizontal black line) [44][45][46][47][48][49][50][51][52][53][54][55][56][57][58]. For all outcomes, present, for each study: (a) summary statistics for each group (where appropriate) and (b) an effect estimate and its precision (e.g.…”

“…Reverse transcription-polymerase chain reaction Fifteen studies based on the RT-PCR technique were selected [44][45][46][47][48][49][50][51][52][53][54][55][56][57][58], in which a total of 6,902 subjects were studied. Sensitivity ranged from 36.8% to 99.2%, with a median of 94.5%, 95%CI (85.1, 98.0), while the test for equality of sensitivities presented a χ 2 = 577.02, df = 38, p-value = 2e -16 .…”

SARS-CoV-2 variants: Impact on biological and clinical outcome

“…The advent of the single-tube multiplex assays for SARS-CoV-2 proved advantageous with respect to time and labor. However, each commercial kit differed in its targets and sensitivities ( 76 – 78 ). Therefore, having multiple confirmatory genes served to compensate for the sensitivity and specificity of its targets.…”