Wastewater as an Early Warning System: What 2 Years of SARS-CoV-2 Surveillance in Warsaw Reveal

Even before COVID-19 transitioned from crisis to an endemic threat, wastewater-based epidemiology (WBE) was recognized as a powerful tool for detecting pathogen transmission. Now, WBE is invaluable for detecting silent SARS-CoV-2 transmission and for anticipating future waves. A new 2-year study from Warsaw, published in Scientific Reports, demonstrates how long-term, granular wastewater surveillance can reveal infection dynamics that clinical testing alone may miss.

“Routine monitoring and wastewater-based bio-surveillance represents a strong supporting tool for following and understanding SARS-CoV-2 endemicity or epidemic dynamics in society,” the authors write. By tracking viral RNA across four wastewater treatment plants and multiple subcatchments, including housing estates, health care facilities, military areas, and transportation hubs, the research team created one of the most detailed urban WBE datasets to date.

Between April 2023 and December 2024, researchers analyzed 2,184 wastewater samples using RT-qPCR and next-generation sequencing. The average cumulative viral load across the system reached “3.5 × 10⁵ genomic copies per litre,” with the highest concentrations detected at wastewater inflows and healthcare facilities. Notably, viral levels in sewage frequently exceeded what would be predicted from official case counts, suggesting “a higher number of undiagnosed COVID-19 infections within the community.”

“COVID-19 case data, in reference to the SARS-CoV-2 presence in wastewater, were presented as “raw” without any corrections or “normalised” and reported as cases per 10,000 people,” the authors wrote.

This gap between clinical surveillance and environmental signals is one of WBE’s greatest strengths. As the authors explain, wastewater data can detect viral circulation before individuals seek testing or develop symptoms, offering “epidemiological support during the preepidemic period.” In Warsaw, SARS-CoV-2 levels began to rise weeks before each of the 2 documented COVID-19 waves, reinforcing the value of wastewater as an early warning system.

The study also highlights how infection signals differ across urban infrastructure. Viral loads varied significantly between housing estates, health care units, and transportation hubs, with communicable-disease health care facilities showing the highest concentrations. According to the authors, this confirms that “health care units [were] identified as the primary source of the viral load in the area,” an insight with implications for occupational health, facility design, and wastewater handling practices.

Beyond detection, the team performed genomic sequencing to track viral evolution in sewage. Samples segregated into 11 distinct clades, allowing researchers to differentiate between the 2023 and 2024 COVID-19 waves. “The obtained genotypes segregated within 11 clades (21I to 24F), making ‘23 and ‘24 waves distinguishable,” the authors report. Variants such as JN.1 and BA.2.86, known for immune escape, were identified in wastewater before they were fully reflected in clinical surveillance.

Crucially, this work aligns with new European regulatory priorities. The authors emphasize that their methodology supports the requirements of “Directive (EU) 2024/3019,” which mandates enhanced urban wastewater surveillance for public health protection. They argue that standardized sampling locations, coordinated governance, and collaboration between public health authorities and wastewater utilities are essential for scaling WBE across Europe.

In their conclusion, the researchers underscore the broader importance of environmental hygiene: “By focusing on the biological factors in the load of wastewater outflow, this approach is vital for environmental hygiene and early epidemic detection, helping to safeguard communities and promote a healthier future.”

For infection preventionists, public health leaders, and environmental services professionals, the message is clear: What flows beneath our cities may offer the clearest view of what lies ahead.

Korzekwa, K., Lepionka, T., Bisak, A. et al. Long-term biological surveillance of SARS-CoV-2 in critical points for municipal sewage catchment in light of wastewater-based epidemiology, public health, and environmental hygiene. Sci Rep 15, 43320 (2025). https://doi.org/10.1038/s41598-025-27171-x