Publication date: Jul 04, 2025

Wastewater-based epidemiology (WBE) is a valuable tool for surveillance of infectious diseases like COVID-19, yet balancing prediction accuracy with practical deployment remains challenging, particularly in low-resource, low-prevalence, and early warning contexts. We analyzed a two-and-a-half-year dataset from Athens-Clarke County, Georgia (USA) to compare approaches for predicting COVID-19 cases from SARS-CoV-2 wastewater data. We evaluated the effects of extraction replicates and use of quantitative versus detection frequency data on model performance using random forest and linear models. Results show that two extraction replicates generally suffice for reliable prediction, supporting efficient resource use. Combined viral load and detection frequency produced the strongest models, but detection frequency alone predicted new COVID-19 cases more accurately than viral load alone and was less sensitive to RT-qPCR instrumentation changes, making it a practical alternative when quantification is unreliable/infeasible. Linear models predicted new cases more accurately than random forest models, offering a resource-efficient option for monitoring wastewater trends. Following declines in clinical testing in spring 2022, wastewater-based models estimated substantially higher case counts than were reported, underscoring WBE’s role for ongoing surveillance of COVID-19 and other infectious diseases. These findings provide practical guidance for optimizing WBE implementation, particularly where early warning and resource constraints are significant factors.

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