RT-PCR test for the detection of SARS-CoV-2 in nasopharyngeal swabs: results of the Cepheid Xpert® Xpress SARS-CoV-2 assay versus the Thermo fisher TaqPath™ COVID-19 CE IVD

Introduction. In the response to the coronavirus pandemic, several PCR kits have been developed with varying performance. Aim. In this study, we compared the results of SARS-CoV-2 testing using the Xpert® Xpress SARS-CoV-2 (Cepheid EUA) Testing with the TaqPathTM -COVID-19 CE IVD kit. Methods. A total of 92 nasopharyngeal swab samples from patients during September to November 2021 at the National Public Health Laboratory in Ouagadougou, Burkina Faso. These samples were analyzed using both the Xpert Xpress SARS-CoV-2 assay and the TaqPath-COVID-19-CE IVD kit on the QuantStudio 5 thermal cycler after extraction with the ANDiS 350 automated extractor. Results. The majority of patients was male 68.48% (63/92) and female 31.52% (29/92). The mean age was 42.2 ± 13.76 years with extremes of 12 and 70 years. The Xpert Xpress SARS-CoV-2 kit showed positive agreement with a kappa coefficient of 93.35% [85.9; 100] compared to the TaqPath-COVID-19-CE IVD kit. It also showed a sensitivity of 100%, a specificity of 92.68 and negative and positive predictive values of 100% and 94.44% respectively. Conclusion. The Xpert Xpress test is a very simple assay that compares favorably with the TaqPath-COVID-19-CE IVD test and can be reliably used for the detection of SARS-CoV-2 in nasopharyngeal specimens.