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

Martin Maidadi-Foudi; Marie Atsama-Amougou; Celestin Godwe; Emilande Guichet; Nadine L Boutgam; Guy Roland Awoundza Metomo; Oumarou Goni Hamadama; Gilles-Fils Woguia; Yannick F Ngoume; Dowbiss Meta Djomsi; Roméo Brice D Djounda; Modeste Ngamaleu; Hillary Tene; Livo Esemu; Joseph Fokam; Marie-Claire Okomo; Boyomo Onana; Wilfred Mbacham; Marcel Tongo; Eric Delaporte; Martine Peeters; Ahidjo Ayouba; Charles Kouanfack

doi:10.4102/jphia.v16i1.1282

Retour

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

Article de revue

Avec comité de lecture

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

Martin Maidadi-Foudi, Marie Atsama-Amougou, Celestin Godwe, Emilande Guichet, Nadine L Boutgam, Guy Roland Awoundza Metomo, Oumarou Goni Hamadama, Gilles-Fils Woguia, Yannick F Ngoume, Dowbiss Meta Djomsi, …

Journal of public health in Africa, Vol.16(1), pp.1282-e8

31/07/2025

DOI: https://doi.org/10.4102/jphia.v16i1.1282

PMID: 40799375

Résumé

Cameroon

omicron variant

reverse transcription-polymerase chain reaction

mutations

delta variant

severe acute respiratory syndrome coronavirus 2

New severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may affect diagnostic test accuracy. To evaluate the performance of two reverse transcription-polymerase chain reaction (RT-PCR) assays, DaAn Gene and Cepheid, for detecting Delta and Omicron variants. Nasopharyngeal samples were collected in Yaoundé, Cameroon, between October 2021 and December 2022. Nasopharyngeal samples were tested with both assays. Samples with a cycle threshold (CT) ≤ 28 were sequenced. Cohen's kappa coefficient assessed assay agreement. We compared 294 samples. At CT ≤ 40, DaAn Gene showed a 59.2% ( = 174/294) positivity rate versus 57.8% ( = 170/294) for Cepheid (χ = 0.695, = 0.4044). Agreement was 95.91% ( = 282/294) with κ = 0.95. DaAn Gene showed a 58.2% ( = 171/294) positivity rate versus 54.4% ( = 160/294) for Cepheid at CT ≤ 37 ( = 0.5058), with 95.6% agreement (κ = 0.95). At CT ≤ 33, DaAn Gene was 56.5% ( = 166/294) positive versus 54.1% ( = 159/294) for Cepheid ( = 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. The emergence of Delta and Omicron variants did not significantly impact the diagnostic performance of these routine RT-PCR assays. This study confirms their continued effectiveness in detecting these variants in this setting.

Indicateurs

1 Consultations de la notice

Détails

Titre: 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
Créateurs - sans rôle: Martin Maidadi-Foudi - Department of Microbiology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
Marie 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 - 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 - 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
Détails de publication: Journal of public health in Africa, Vol.16(1), pp.1282-e8
Identifiants: 99148946409311
Unité académique: Recherches translationnelles sur le VIH et les Maladies Infect. Endém. émerg. - TransVIHMI
Langue: English
Type de ressource: Journal article