Long-term wastewater surveillance of SARS-CoV-2: a 5.5-year study reveals correlation with public health indicators and early warning potential during and after the pandemic

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Background While wastewater surveillance (WS) is a validated tool for SARS-CoV-2 monitoring, its long-term reliability and forecasting accuracy remain debated. This study, spanning a 65-month period (5.5 years), evaluates the dynamics of SARS-CoV-2 in municipal wastewater across multiple epidemiological shifts, including vaccination rollouts, variant emergence, and change in testing policies. Materials and methods Inlet wastewater from a large metropolitan area in southern France (450,000 inhabitants) was monitored weekly or twice weekly. SARS-CoV-2 RNA (IP4 target) was quantified by Reverse Transcription digital PCR (RT-dPCR) in 345 samples and compared to 15 regional public health indicators (virological, hospital-based, and syndromic) using Spearman correlation coefficients ( r s ). The time lags in days that maximized r s were calculated using a lag-based association analysis to evaluate the early warning capacity of WS. Results Overall, the SARS-CoV-2 RNA load in wastewater was consistently correlated with specific virological indicators such as incidence rate, and non-specific syndromic indicator such as emergency procedures. WS of SARS-CoV-2 RNA demonstrated significant early warning capabilities, preceding hospital admissions by 8 to 12 days and mortality by up to 30 days during the pandemic phase. However, the strength of the correlations and the early warning capacity varied across epidemiological phases, the outbreak wave, the variants circulating and the population’s vaccination rate. Crucially, in the post-pandemic period, WS remained a robust proxy and could provide arguments about the virus causing an increase in syndromic indicators. Conclusion This 5.5-year longitudinal study provides one of the most comprehensive datasets of SARS-CoV-2 environmental dynamics. It advocates for the permanent implementation of WS to monitor respiratory and emerging infectious threats in a post-pandemic world.