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Publications

Journal Article Epublish

PubMed: 40799375 DOI: 10.4102/jphia.v16i1.1282

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.

J Public Health Afr 16(1):1282

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

Affiliations

  • Centre for Research on Emerging and Re-emerging Diseases (CREMER), Institute of Medical Research and Medicinal Plants Studies (IMPM), Yaoundé, Cameroon.
  • Department of Microbiology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon.
  • Department of Biochemistry, Faculty of Science, University of Douala, Douala, Cameroon.
  • Translational Research on HIV and Endemic and Emerging Infectious Diseases (TransVIHMI), University of Montpellier/Institute of Research for Development (IRD), Montpellier, France.
  • Virology Laboratory, Chantal Biya International Reference Centre (CIRCB) for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon.
  • Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon.
  • National AIDS Control Committee, Ministry of Public Health, Yaoundé, Cameroon.
  • National Public Health Laboratory (NPHL), Ministry of Public Health, Yaoundé, Cameroon.
  • Biotechnology Centre of Nkolbisson (CBT), University of Yaoundé I, 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 (χ 2 = 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.

MeSH

Genes, Sars-Cov-2, Polymerase Chain Reaction, Severe Acute Respiratory Syndrome-Related Coronavirus, Mutation