Unveiling the global urban virome through wastewater metagenomics
Nathalie Worp, David F. Nieuwenhuijse, Ray Izquierdo-Lara, Claudia M. E. Schapendonk, Christian Brinch, Emilie Egholm Bruun Jensen, Patrick Munk, René S. Hendriksen, Frederik Duus Møller, Thomas Nordahl Petersen, Jette Sejer Kjeldgaard, Christina Aaby Svendsen, Artan Bego, P.P. Power, Catherine A. Rees, Dionisia Lambrinidis, Elizabeth Heather Jakobsen Neilson, Karen Gibb, Kris Coventry, Peter Collignon, Susan Cassar, Franz Allerberger, Anowara Begum, Zenat Zebin Hossain, Carlon Worrell, Olivier Vandenberg, Ilse Y. Pieters, Victorien Dougnon, Angela Daniela Salazar Gutierrez, Freddy Soria, Vesna Rudić Grujić, Nataša Mazalica, Teddie O. Rahube, Carlos Alberto Tagliati, Dália dos Prazeres Rodrigues, Guilherme Oliveira, Larissa Camila Ribeiro de Souza, Ivan Ivanov, Bonkoungou Isidore Juste, Traoré Soumana Oumar, Thet Sopheak, Yith Vuthy, Antoinette Ngandjio, Ariane Nzouankeu, Ziem A. Abah Jacques Olivier, Christopher K. Yost, Pratik Kumar, Satinder Kaur Brar, Djim-adjim Tabo, Aiko D. Adell, Esteban Paredes-Osses, Maria Cristina Martinez, Sara Cuadros-Orellana, Changwen Ke, Huanying Zheng, Li Baisheng, Lok Ting Lau, Teresa Chung, Xiaoyang Jiao, Yongjie Yu, Zhao JiaYong, Johan F. Bernal Morales, María Fernanda Valencia, Pilar Donado-Godoy, Kalpy Julien Coulibaly, Jasna Hrenović, Matijana Jergović, Renáta Karpíšková, Zozo Nyarukweba Deogratias, Bodil Elsborg, Lisbeth Truelstrup Hansen, Pernille Erland Jensen, M. Abouelnaga, Mohamed A. Salem, Marliin Koolmeister, Mengistu Legesse, Tadesse Eguale, Annamari Heikinheimo, Soizick Le Guyader, Julien Schaeffer, José E. Villacís, Bakary Sanneh, Lile Malania, Andreas Nitsche, Annika Brinkmann, Sara Schubert, Sina Hesse, Thomas U. Berendonk, Courage Kosi Setsoafia Saba, Jibril Mohammed, Patrick Kwame Feglo, Regina Ama Banu, Charalampos Kotzamanidis, Efthymios Lytras, Sergio A. Lickes, Béla Kocsis, Norbert Solymosi, Thorunn R. Thorsteinsdottir, A. A. Mohamed Hatha, Mamatha Ballal
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.