Assessment and application of GeneXpert rapid testing for respiratory viruses in school wastewater†

Schools are considered high-risk areas for the transmission of infectious respiratory diseases and thus could benefit from facility-level wastewater disease surveillance. This study assessed the quantitativeness, reproducibility, and feasibility of the rapid GeneXpert system for monitoring SARS-CoV-2, influenza A, influenza B, and RSV in school wastewater. We developed individual standard curves for each disease target using school wastewater spiked with known concentrations of target viruses to estimate viral concentrations in wastewater. Furthermore, we evaluated and compared the reproducibility of the GeneXpert system results against an established filtration-ddPCR workflow and compared the cost per sample of each method. Results show that the GeneXpert system can detect respiratory viruses in school wastewater. We used GeneXpert to perform daily wastewater monitoring for target respiratory viruses at four schools in Houston, TX, USA, over three months (from November 15, 2022, to February 15, 2023, n = 169). For SARS-CoV-2 and influenza A, we observed no significant differences between the positivity results (detection vs. not detected), and strong relationships between quantitative results from the two methods. The RSV detection using GeneXpert was less reproducible and sensitive, but overall consistent in terms of positive detections with the filtration-ddPCR workflow (90.5% consistent). The GeneXpert represents a cost-effective system for wastewater monitoring for respiratory viruses as compared to the filtration-ddPCR method, particularly when the number of samples is low. This study demonstrates the application of the GeneXpert system for facility-level wastewater surveillance and suggests that it represents an important technology for resource-constrained areas.