Validation of the Cepheid Xpert® Xpress SARS-CoV-2 using upper and lower respiratory tract specimens

This study validated the performance of the reverse transcriptase-polymerase chain reaction (rRT-PCR) based Cepheid Xpert® Xpress SARS-CoV-2 assay against the TIB MOLBIOL E-gene/EAV, a standard laboratory rRT-PCR SARS-CoV-2 assay. Upper and lower respiratory tract samples (nasopharyngeal and nasal swabs, bronchoalveolar lavage, and tracheal aspirate) were obtained from patients suspected to have contracted COVID-19. Results from the Xpert® Xpress and standard rRT-PCR assays were compared for positive and negative agreement and analyzed for precision, reproducibility, 95% confidence intervals, and coefficients of variation. The Xpert® Xpress assay demonstrated 100% agreement with the standard lab rRT-PCR for both upper and lower respiratory tract samples. Both the Xpert® Xpress and lab rRT-CPR identified weakly positive (Ct values 35-39) sample replicates with 100% reproducibility and showed 100% precision in identifying triplicates of upper respiratory tract samples. The single-cartridge Xpert® Xpress system has a short turnaround time and can be employed to improve patient management and hospital bed allocation. Further verification of the system is required before implementation and consideration must be paid to its higher cost and impracticality for high-throughput use.