Diagnostic Concordance of Two- and Three-Gene SARS-CoV-2 Molecular Assays in Cameroon: Implications for Efficient Pandemic Response in Low- and Middle-Income Countries

Background: The scale-up of molecular assays for diagnosing emerging pathogens has increased in low-and-middle-income countries (LMICs) since the advent of COVID-19. We herein evaluated the diagnostic concordance of three different assays for SARS-CoV-2 in Cameroon. Methods: A laboratory-based comparative study was performed on nasopharyngeal samples collected between March-2020 to March-2023 from the biobank of Chantal Biya International Reference Centre (CIRCB), Yaoundé-Cameroon. Samples were analyzed using DaAn Gene (N/ORF1ab-genes), ThermoFisher (N/ORF1ab/S-genes), and GeneXpert (N2/E-genes). Validated cycle thresholds (CT) for positivity were CT < 37 for DaAn Gene/ThermoFisher and CT < 40 for GeneXpert. Cohen's Kappa coefficient evaluated diagnostic concordance with DaAn Gene as reference. Results: We analysed 249 samples (55.8% males, median-age [IQR], 36 [27–50] years including 21.3% symptomatic participants). Overall positivity rates (median [IQR]) were 55.0% (CT: 30.6 [23.1–35.5]); 53.4% (CT: 26.6 [21.2–30.9]); 22.1% (CT: 32.7 [26.9–36.1]) for GeneXpert, DaAn Gene and ThermoFisher respectively. GeneXpert showed stronger concordance with DaAn Gene (83.1%; k = 0.66, 95% CI: 0.57–0.75) than ThermoFisher (67.9%; k = 0.38, 95% CI: 0.29–0.47). At validated thresholds, GeneXpert showed higher positive agreement with DaAn Gene (85.0%, 113/133) as compared to ThermoFisher (41.3%, 55/133), while maintaining comparable negative agreement (81.0% [GeneXpert] and 98.3% [ThermoFisher]). At low CTs (< 20) however, positive agreement with DaAn Gene was high for GeneXpert (100%, 15/15) and ThermoFisher (93.3%, 14/15). Conclusion: GeneXpert exhibits superiority over ThermoFisher in detecting cases of COVID-19. As expected, agreement between two- and three-genes assays at CT < 20 was excellent, suggesting interoperability of these platforms during outbreaks for high viral loads cases. However, two-genes assays may be decisive to guide decision-making for effective public health response while facing intermediate to low-level viral loads in LMICs.