Long-Term Sewage Survey of SARS-CoV-2, Influenza A and Respiratory Syncytial Virus (RSV), and Correlation to Human Cases in a City with One Million Inhabitants

Wastewater-based epidemiology is a robust, scalable, cost-effective, and high-performing tool to monitor and predict SARS-CoV-2 trends. We aimed to investigate whether this approach could be applied to influenza A/B viruses and respiratory syncytial virus (RSV) in Marseille, southern France. Wastewater concentrations of SARS-CoV-2, influenza A/B viruses, and RSV in Marseille were monitored by qPCR between January 2021 and October 2024. These concentrations were compared with the diagnosis numbers for the three viruses collected at public hospitals in Marseille, using cross-correlation analyses. The Granger causality test was used to determine whether wastewater concentrations can predict the number of clinical cases. SARS-CoV-2 and influenza virus concentrations in wastewater preceded the rise in the incidence of patient diagnoses by a lag of five days and nine/ten days, respectively. In contrast, for RSV, the rise in incidence of clinical cases preceded that of wastewater concentrations. We conclude that wastewater-based epidemiology is a powerful tool to monitor the level of circulation of these viruses independently of tests carried out on people. It enables earlier alerts than monitoring patients for SARS-CoV-2 and influenza symptoms. However, for RSV, it does not provide an early warning, and clinical data-based surveillance appears to be more suitable.