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

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.