ArticleJournal of clinical laboratory analysis2026
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.
Article in Journal of clinical laboratory analysis, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundThe 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.
methodsA 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.
resultsWe 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).
conclusionGeneXpert 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.
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