COMPARATIVE PERFORMANCE OF MANUAL VS. AUTOMATED RT-PCR AT MALAGASY MEDICAL ANALYSIS LABORATORY FOR SARS-COV-2 DETECTION: A STUDY BETWEEN TWO THERMO CYCLERS AND THE QIASTAT® DX ANALYZER-DX RESPIRATORY SARS-COV-2 PANEL

SARS-CoV-2, a single-stranded RNA virus with positive polarity belonging to the Betacoronavirus genus, is the etiological agent of the COVID-19 pandemic. Virological diagnosis primarily relies on the direct detection of the viral genome via real-time RT-PCR, which remains the gold standard due to its high sensitivity and specificity. This study aims to comparatively evaluate the analytical and clinical performance of two standard RT-PCR platforms (QuantStudio™ 7 Flex RealTime PCR System and Fluorocycler® XT) with that of a molecular syndromic diagnostic system, the QIAstat® Dx Analyzer (SARS-CoV-2 Respiratory Panel). A retrospective study was conducted in 2021 on a total of 60 nasopharyngeal samples. The positivity rate was 43.3% for QuantStudio™, 35% for Fluorocycler®, and 48% for QIAstat®. The concordance analysis between QIAstat® Dx and QuantStudio™ revealed a Kappa coefficient of 0.657 (substantial agreement), with a sensitivity of 76.9%, a specificity of 88.2%, a positive predictive value (PPV) of 83.3%, and a negative predictive value (NPV) of 83.9%. The Fluorocycler® XT showed near-perfect concordance with the QuantStudio™ (Kappa = 0.885), with a sensitivity of 90.9%, a specificity of 97.0%, a PPV of 90.9%, and a NPV of 97.0%. No significant differences were observed in the Ct values between the tested systems. Despite its multiplexing capability and automation, the QIAstat® Dx shows lower sensitivity, which limits its use as a first-line standalone test in clinical settings.