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.
IF 0.8 Q4 PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH
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
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引用次数: 0
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.
期刊介绍：
The Journal of Public Health in Africa (JPHiA) is a peer-reviewed, academic journal that focuses on health issues in the African continent. The journal editors seek high quality original articles on public health related issues, reviews, comments and more. The aim of the journal is to move public health discourse from the background to the forefront. The success of Africa’s struggle against disease depends on public health approaches.
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