Unveiling the global urban virome through wastewater metagenomics

Nathalie Worp, David F. Nieuwenhuijse, Ray W. Izquierdo-Lara, Claudia M. E. Schapendonk, Christian Brinch, Emilie Egholm Bruun Jensen, Patrick Munk, Rene S. Hendriksen, Frank Aarestrup, Bas B. Oude Munnink, Marion P. G. Koopmans and Miranda de Graaf ()
Additional contact information
Nathalie Worp: Erasmus University Medical Center, Department of Viroscience
David F. Nieuwenhuijse: Erasmus University Medical Center, Department of Viroscience
Ray W. Izquierdo-Lara: Erasmus University Medical Center, Department of Viroscience
Claudia M. E. Schapendonk: Erasmus University Medical Center, Department of Viroscience
Christian Brinch: Kgs, Research Group for Genomic Epidemiology, Technical University of Denmark
Emilie Egholm Bruun Jensen: Kgs, Research Group for Genomic Epidemiology, Technical University of Denmark
Patrick Munk: Kgs, Research Group for Genomic Epidemiology, Technical University of Denmark
Rene S. Hendriksen: Kgs, Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark
Frank Aarestrup: Kgs, Research Group for Genomic Epidemiology, Technical University of Denmark
Bas B. Oude Munnink: Erasmus University Medical Center, Department of Viroscience
Marion P. G. Koopmans: Erasmus University Medical Center, Department of Viroscience
Miranda de Graaf: Erasmus University Medical Center, Department of Viroscience

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017–2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.

Date: 2025
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DOI: 10.1038/s41467-025-65208-x

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