Replication Study: Evaluating the GeneXpert Platform for Concurrent Detection of COVID-19 and Influenza in Western Cape Primary Care Settings

The GeneXpert platform, commonly used for tuberculosis diagnosis, was adapted to detect SARS-CoV-2. Its capacity for multiplex testing for both COVID-19 and influenza presents potential advantages for managing respiratory diseases in resource-limited primary care. Previous evaluations in other settings indicated high accuracy, but its performance in routine South African primary care requires independent assessment. This replication study aimed to evaluate the diagnostic performance of the GeneXpert Xpress SARS-CoV-2/Flu assay for the concurrent detection of COVID-19 and influenza viruses within Western Cape primary healthcare clinics, using a standard reference method. A cross-sectional study was undertaken across multiple primary care clinics. Consecutive patients presenting with influenza-like illness were recruited. Nasopharyngeal swabs were tested simultaneously on the GeneXpert platform and with a laboratory-based reverse transcription polymerase chain reaction (RT-PCR) assay as the reference standard. Sensitivity, specificity, and predictive values were calculated. Compared to RT-PCR, the GeneXpert assay demonstrated a sensitivity of 94.2% and specificity of 99.1% for SARS-CoV-2. For influenza A, sensitivity was 89.5% with a specificity of 99.4%. Sensitivity for influenza B was lower at 82.6%, while specificity remained high at 99.7. The assay's turnaround time within clinics was under 60 minutes. The GeneXpert Xpress assay allows accurate and rapid simultaneous detection of SARS-CoV-2 and influenza viruses in a primary care setting. Its performance supports its use for point-of-care differential diagnosis of acute respiratory infections, although sensitivity for influenza B was moderately reduced. Implementation of the platform in comparable primary care contexts is recommended to facilitate rapid differential diagnosis. Consideration should be given to its lower sensitivity for influenza B in clinical decision-making. GeneXpert, COVID-19, influenza, multiplex PCR, point-of-care testing, primary health care, South Africa, diagnostic accuracy. This study provides independent, operational evidence on the field performance of a multiplex molecular assay for respiratory pathogens in a resource-limited primary care setting, informing diagnostic policy and practice.