Comparison of abbott Real Time SARS-COV-2 ASSAY, Genefinder™ Covid-19 plus realamp kit and Biomerieux Argene® SARS-COV-2 R-Gene® kit for the RT-PCR based detection of SARS-COV-2 from nasopharyngeal swabs

Early, rapid and reliable identification of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is crucial for successful control of coronavirus disease 2019 (COVID-19). The quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) assay is considered the gold standard for molecular diagnosis of SARS-CoV-2. The objective of this study was to compare the clinical performances of the three authorized tests - the Abbott Real Time SARS-CoV-2 (ACOV) assay (Abbott Molecular Inc., North Chicago, IL), GeneFinder? COVID-19 Plus RealAmp (GeneFinder) Kit (OSANG Healthcare Co., Ltd, Dongan-gu Anyang, Korea) and the Biomerieux ARGENE? SARS-COV-2 R-GENE? real-time detection (ARGENE) kit (bioM?rieux SA., Marcyl??toile, France) and to determine whether the selection of targeted genes has an impact on test's specificity. In this study, we included 155 nasopharyngeal swabs (NPS) from adult individuals with symptoms or suspected of COVID-19, aged from 17 to 91 years, previously tested by the ACOV and subsequently tested by the GeneFinder and the ARGENE. In this comparative analysis, we found that the GeneFinder assay detected the most cases of COVID-19 infection, followed by the ACOV assay, and then by ARGENE. Positive agreement ranged from 74.74% to 95.41%, with the strongest agreement observed between the GeneFinder and ACOV assays - 95.41% (95% confidence intervals (CI): 89.37%-98.36%) indicating an excellent agreement between these two tests and the lowest agreement between the GeneFinder and ARGENE assay - 74.74% (95% CI: 65.08%-81.41%). The negative percent agreement was 100% (GeneFinder/ACOV, GeneFinder/ARGENE and ACOV/ARGENE). Only 3.2% of cases were false-negative using the ACOV test, while 18.0% of samples were false-negative using the ARGENE assay to detect SARS-CoV-2. Combined usage of the Abbott SARS-CoV-2 and the GeneFinder assays can be applied to maximize SARS-CoV-2 detection accuracy.