Assessment of\nRapid and Conventional RT-qPCR-Based\nSystems for Wastewater Surveillance

Conventional wastewater surveillance (WS) relies on highly\ntrained\npersonnel, advanced instrumentation, and significant resources, making\nthe development and use of simple, rapid, and sensitive alternative\ntechnologies valuable for reducing costs, time, and labor intensity.\nFor the first time, this study investigated the use of two well-developed\nrapid systems, including the GeneXpert and LuminUltra, in parallel\nwith a conventional WS reference methodology for the assessment of\nsevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in three\ncities: Saskatoon, Prince Albert, and North Battleford, Saskatchewan,\nCanada. RNA extractions from wastewater samples were carried out for\nthe conventional reference and LuminUltra methods, while GeneXpert\nwas used for both raw and concentrated wastewater samples. Bland–Altman\nplots showed a combination of systematic bias and random error between\nthese real-time reverse transcription-quantitative polymerase chain\nreaction (RT-qPCR)-based systems. Additionally, results indicated\nthe reasonable performance of GeneXpert in viral detection with a\nsensitivity rate of >98%, as compared to the conventional reference\nmethodology of 100% and LuminUltra with >65%. A Spearman correlation\ntest showed meaningful relationships between the GeneXpert and conventional\nreference methodology viral level results across all cities, indicating\nGeneXpert’s reliability for accurate viral detection and disease\nprevalence determination, specifically in limited-resource communities,\nwith a shorter processing time and cost-effectiveness in analysis.