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

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

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. S...

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Main Authors: 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
Format: Article
Language:English
Published: AOSIS 2025-07-01
Series:Journal of Public Health in Africa
Subjects:
mutations
severe acute respiratory syndrome coronavirus 2
reverse transcription-polymerase chain reaction
delta variant
omicron variant
cameroon.
Online Access:https://publichealthinafrica.org/index.php/jphia/article/view/1282
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Summary: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.
ISSN:2038-9922
2038-9930

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