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Original Research
Comparison of two polymerase chain reaction assays, DaAn Gene (DaAn Gene 2019-ncov) and Cepheid (Cepheid Xpert Xpress SARS-CoV-2) for Delta and Omicron variants of SARS-CoV-2 detection in Yaoundé, Cameroon
Submitted: 21 January 2025 | Published: 31 July 2025
About the author(s)
Martin Maidadi-Foudi, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon; and, Department of Microbiology, Faculty of Science, University of Yaoundé I, Yaoundé, CameroonMarie Atsama-Amougou, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Celestin Godwe, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon; and, Department of Biochemistry, Faculty of Science, University of Douala, Douala, Cameroon
Emilande Guichet, Translational Research on HIV and Endemic and Emerging Infectious Diseases (TransVIHMI), University of Montpellier/Institute of Research for Development (IRD), Montpellier, France
Nadine L. Boutgam, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Guy Roland Awoundza Metomo, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Oumarou Goni Hamadama, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Gilles-Fils Woguia, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Yannick F. Ngoume, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Dowbiss Meta Djomsi, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Roméo Brice D. Djounda, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Modeste Ngamaleu, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Hillary Tene, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Livo Esemu, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Joseph Fokam, Virology Laboratory, Chantal Biya International Reference Centre (CIRCB) for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon; and, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon; and, National AIDS Control Committee, Ministry of Public Health, Yaoundé, Cameroon
Marie-Claire Okomo, National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon
Boyomo Onana, Department of Microbiology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
Wilfred Mbacham, Biotechnology Centre of Nkolbisson (CBT), University of Yaoundé I, Yaoundé, Cameroon
Marcel Tongo, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Eric Delaporte, Translational Research on HIV and Endemic and Emerging Infectious Diseases (TransVIHMI), University of Montpellier/Institute of Research for Development (IRD), Montpellier, France
Martine Peeters, Translational Research on HIV and Endemic and Emerging Infectious Diseases (TransVIHMI), University of Montpellier/Institute of Research for Development (IRD), Montpellier, France
Ahidjo Ayouba, Translational Research on HIV and Endemic and Emerging Infectious Diseases (TransVIHMI), University of Montpellier/Institute of Research for Development (IRD), Montpellier, France
Charles Kouanfack, Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon
Abstract
Background: New severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may affect diagnostic test accuracy.
Aim: To evaluate the performance of two reverse transcription-polymerase chain reaction (RT-PCR) assays, DaAn Gene and Cepheid, for detecting Delta and Omicron variants.
Setting: Nasopharyngeal samples were collected in Yaoundé, Cameroon, between October 2021 and December 2022.
Methods: Nasopharyngeal samples were tested with both assays. Samples with a cycle threshold (CT) ≤ 28 were sequenced. Cohen’s kappa coefficient assessed assay agreement.
Results: We compared 294 samples. At CT ≤ 40, DaAn Gene showed a 59.2% (n = 174/294) positivity rate versus 57.8% (n = 170/294) for Cepheid (χ2 = 0.695, p = 0.4044). Agreement was 95.91% (n = 282/294) with κ = 0.95. DaAn Gene showed a 58.2% (n = 171/294) positivity rate versus 54.4% (n = 160/294) for Cepheid at CT ≤ 37 (p = 0.5058), with 95.6% agreement (κ = 0.95). At CT ≤ 33, DaAn Gene was 56.5% (n = 166/294) positive versus 54.1% (n = 159/294) for Cepheid (p = 0.6187), with 96.93% agreement (κ = 0.938). For 167 samples with CT ≤ 28, agreement was 97.0% (κ = 0.97) across variants. These RT-PCR assays effectively detected Delta and Omicron variants.
Conclusion: The emergence of Delta and Omicron variants did not significantly impact the diagnostic performance of these routine RT-PCR assays.
Contribution: This study confirms their continued effectiveness in detecting these variants in this setting.
Keywords
Sustainable Development Goal
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