Unveiling the global urban virome through wastewater metagenomics

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.

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Journal
Nature Communications
Published
2025-11-28
DOI
https://doi.org/10.1038/s41467-025-65208-x
Citations
4
Primary Topic
Bacteriophages and microbial interactions
Type
article
Field-Weighted Citation Impact
6.87

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article

Unveiling the global urban virome through wastewater metagenomics

Malcolm Vella Haber, Mala Rakoto‐Andrianarivelo, Mohamed A. Salem, Lisbeth Truelstrup Hansen et al.
4 citations
Nature Communications
Bacteriophages and microbial interactions
6.87
article

Unveiling the global urban virome through wastewater metagenomics

Malcolm Vella Haber, Mala Rakoto‐Andrianarivelo, Mohamed A. Salem, Lisbeth Truelstrup Hansen, Ibrahim Raufu Adisa, Norbert Solymosi, Célia M. Manaia, Aleksandar Vujacic, Matijana Jergović, Drew Capone, Patrick Munk, Stefan Örn, Teddie O. Rahube, Christian Brinch, Francis Ejobi, Marija Trkov, Aiko D. Adell, Zenat Zebin Hossain, D. G. Joakim Larsson, Alexandra Bastaraud, Thomas Ulrich Berendonk, Doan Minh Nguyen Tran, Elena Lavinia Diaconu, Cemil Kürekçi, Efthymios Lytras, Andreas Nitsche, Christopher K. Yost, Natalia Rigamonti, Marion Koopmans, Marcos Quintela‐Baluja, Sohan Rodney Bangera, Kristīna Tihomirova, Lok Ting Lau, Carlon Worrell, Ziem A. 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article en
4 citations

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.

Nature CommunicationsVol. 16(1)
Semmelweis University (HU), National Center for Disease Control and Public Health (GE), Universidade Federal de Minas Gerais (BR), University of North Carolina at Chapel Hill (US), Suez Canal University (EG), University of N'Djamena (TD), Aga Khan University (PK), Universitat Autònoma de Barcelona (ES), University of Copenhagen (DK), Ben-Gurion University of the Negev (IL), University of Medicine Tirana (AL), Université Joseph Ki-Zerbo (BF), Université Libre de Bruxelles (BE), Siriraj Hospital (TH), Norwegian Institute of Public Health (NO), University of Helsinki (FI), University of Ilorin (NG), University of Antananarivo (MG), University of Ghana (GH), Universidad Andrés Bello (CL), Hong Kong Polytechnic University (HK), University of Kelaniya (LK), Eastern Illinois University (US), Ifremer (FR), Universidad de San Carlos de Guatemala (GT), Baylor University (US), Korea Advanced Institute of Science and Technology (KR), University of Malawi (MW), University of Piura (PE), Central Michigan University (US), University of Iceland (IS), Vale (Brazil) (BR), Nanyang Technological University (SG), University of Banja Luka (BA), University of Zagreb (HR), University of Ibadan (NG), Ollscoil na Gaillimhe – University of Galway (IE), York University (CA), University of Regina (CA), Shiraz University of Medical Sciences (IR), Nanjing University of Information Science and Technology (CN), University of Washington (US), Melbourne Water (AU), Cochin University of Science and Technology (IN), University of Dhaka (BD), Botswana International University of Science and Technology (BW), University of Exeter (GB), Universidad de Buenos Aires (AR), Robert Koch Institute (DE), Mount Kenya University (KE), Universidade Católica Portuguesa (PT), Mahidol University (TH), Catholic University of the Maule (CL), Rashid Hospital (AE), Frederiksberg Hospital (DK), Warner Pacific College (US), Agriculture and Forestry University (NP), Kuwait Institute for Scientific Research (KW), Erasmus MC (NL), Canberra Hospital (AU), Kwame Nkrumah University of Science and Technology (GH), Kenya Medical Research Institute (KE), Swedish University of Agricultural Sciences (SE), Charles Darwin University (AU), Moldova State University (MD), AIMST University (MY), Shantou University (CN), University of Zambia (ZM), University of Sadat City (EG), Institut National de la Recherche Scientifique (CA), Gwangju Institute of Science and Technology (KR), National Institute of Infectious Diseases (JP), Institute of Public Health (AL), Institute of Food Safety, Animal Health and Environment “BIOR” (LV), Instituto de Salud Pública de Chile (CL), Water Services Corporation (Malta) (MT), Suratthani Rajabhat University (TH), Central University of Nicaragua (NI), Abu Dhabi Health Services (AE), Centre de Recerca en Sanitat Animal (ES), Malaysia Genome Institute (MY), Ministry of the Interior (EE), National Institute for Public Health and the Environment (NL), Instituto Nacional de Investigación en Salud Pública (EC), Federal Food Safety and Veterinary Office (CH), Public Health Authority of the Slovak Republic (SK), Luxembourg Institute of Science and Technology (LU), Centre Pasteur du Cameroun (CM), Manhiça Health Research Centre (MZ), Mangalore Institute of Oncology (IN), Water Research Institute (IT), Veterinary Research Institute (CZ), Université d'Abomey-Calavi (BJ), Caribbean Environmental Health Institute (LC), Shantou University Medical College (CN), National Veterinary Research Institute (PL), Instituto Nacional de Salud (PE), Indian Institute of Technology Jammu (IN), Public Health Institute of the Republic of Srpska (BA), Centre for Immunity, Infection and Evolution (GB), Colombian Corporation for Agricultural Research - AGROSAVIA (CO), National Laboratory of Health, Environment and Food (SI), Institut Pasteur de Madagascar (MG), Centre for Research and Technology Hellas (GR), Ministry for Health (MT), Institute of public health of Republic of Macedonia (MK), Institut Pasteur du Cambodge (KH), Forest Research Institute (BG), University of Veterinary Medicine (HU), Kilimanjaro Christian Medical Centre (TZ), Council for Scientific and Industrial Research (GH), Institut Pasteur de Dakar (SN), Andrija Stampar Teaching Institute of Public Health (HR), Ministerio de Salud Pública y Bienestar Social (PY), Institut Pasteur de Côte d'Ivoire (CI), Barbados Community College (BB), Universidad del Norte de Nicaragua (NI), Medical Research Institute (LK), Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana (IT), Águas de Portugal (Portugal) (PT), Institut Pasteur du Maroc (MA), Guangdong Provincial Center for Disease Control and Prevention (CN), Aquaplus (Belgium) (BE), Medical Developments International (Australia) (AU), Northumbrian Water Group (United Kingdom) (GB), Togolese Ministry of Health (TG), EYDAP (Greece) (GR), Partnerships in Environmental Management for the Seas of East Asia (PH), Ministry of Health and Social Welfare (GM), Henan Provincial Center for Disease Control and Prevention (CN), National Center of Infectious and Parasitic Diseases (BG), Austrian Agency for Health and Food Safety (AT), Laboratorio Tecnológico del Uruguay, Addis Ababa University (ET), Mustafa Kemal University (TR), Fundação Oswaldo Cruz (BR), The Ohio State University (US), Shahid Beheshti University of Medical Sciences (IR), University of Montenegro (ME), University of Agriculture Faisalabad (PK), University of Mauritius (MU), King Abdullah University of Science and Technology (SA), Makerere University (UG), Kasturba Medical College, Manipal (IN), Technische Universität Dresden (DE), University of Prishtina (XK), University of Otago (NZ), University for Development Studies (GH), Sokoine University of Agriculture (TZ), Newcastle University (GB), University of Gothenburg (SE), Erasmus University Rotterdam (NL), Technical University of Denmark (DK), American University of Beirut (LB), University of Edinburgh (GB)
European Commission, Nederlandse Organisatie voor Wetenschappelijk Onderzoek
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Bacteriophages and microbial interactions
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