Endemic human coronaviruses (HCoV) cause seasonal peaks of respiratory disease. As infections with endemic coronaviruses are usually mild, symptoms-based surveillance may provide an incomplete characterisation of the circulation of these viruses. This study evaluates the efficacy of wastewater-based epidemiology as a tool to monitor the circulation of endemic human coronaviruses HCoV-229E, HCoV-NL63, and HCoV-HKU1 in Zurich, Switzerland.
A multiplex digital PCR assay was used to quantify viral RNA in wastewater samples collected between December 2021 and December 2024 in Zurich, Switzerland. Using EpiSewer, a Bayesian semi-mechanistic model, we estimated the effective reproduction number and characterized epidemic waves. The findings were compared against clinical data from the Swiss Sentinel reporting system (Sentinella).
Aggregated weekly flow-normalised viral concentrations correlated with the weekly number of clinical cases reported through the Sentinella surveillance system, although the overall reported number of weekly cases was low. Circulation generally peaked in the first quarter of the year, though peaks occurred later in the season compared to pre-pandemic trends observed in the literature. HCoV-NL63 showed increased activity in early 2023 and late 2024, while HCoV-229E and HCoV-HKU1 showed peaks in winter 2022, 2023, and 2024. HCoV-229E circulated even during periods of non-pharmaceutical interventions due to the SARS-CoV-2 pandemic.
In summary, we demonstrate that wastewater surveillance can offer a robust, population-level approach to tracking endemic coronaviruses independent of healthcare-seeking behavior and can provide critical insights into the evolving seasonality of respiratory viruses in the post-pandemic era.

Co-authors: Jolinda de Korne-Elenbaas, Nadine Hürlimann, Daniela Yordanova, Adrian Lison, Lara Jeworowski, Victor Corman, Timothy R. Julian, Tanja Stadler