Unveiling the global urban virome through wastewater metagenomics
2
Issued Date
2025-12-01
Resource Type
eISSN
20411723
Scopus ID
2-s2.0-105023334380
Pubmed ID
41315190
Journal Title
Nature Communications
Volume
16
Issue
1
Rights Holder(s)
SCOPUS
Bibliographic Citation
Nature Communications Vol.16 No.1 (2025)
Suggested Citation
Worp N., Nieuwenhuijse D.F., Izquierdo-Lara R.W., Schapendonk C.M.E., Brinch C., Jensen E.E.B., Munk P., Hendriksen R.S., Larsson D.G.J., Berglund F., Woolhouse M., Bunnik B.v., Kwenda G., Do Phuc N., Tran D.M.N., Van C.D., Baklayan P., Rigamonti N., Wittum T.E., Kang S., Lilienthal R., Truong P., Sukapanpatharam P., Beck N.K., Davis M., Sobsey M.D., Meschke J.S., Brown J., Sozzi E., Capone D., Lefor B., Gaze W.H., Zhang L., Bunce J.T., Graham D.W., Leonard A., Moore A., Jassim L.M., Obaidi O., Thomsen J., Kalule J.B., Ejobi F., Kurekci C., Levent B., Nikiema-Pessinaba S.C., Njanpop-Lafourcade B.M., Bidjada B., de Roda Husman A.M., Thamlikitkul V., Suthienkul O., Chonsin K., Hounmanou Y.M.G., Mdegela R.H., Kumburu H.H., Hong Y.P., der Heijden T.V., Boss R., Örn S., Norrgren L., Rutgersson C., Charlemagne K., Pathirage S., Premasiri H.I., Bandara N.K.B.K.R.G.W., Perera R.R.D.P., Cerdà-Cuéllar M., Lopez M.G., Quintela-Baluja M., Song M.J., Esterhuyse K., Keddy K., Trkov M., Truska P., Pastuchová K., Gavačová D., Wuertz S., Zuniga-Montanez R., Tay M.Y.F., Radosavljevic V., Gassama A., Perry M.R., Hong P.Y., Burduniuc O., Cojocaru R., Kochubovski M., Bosevska G., Yoon S., Hur H.G., Shin H., Di Yoong Wen D., Álvaro P., Martins J., Rocha J., Manaia C., Wasyl D., Yauce F.C., Sibulo R., Catangcatang K., Magtibay B.B., Velasquez J.E. Unveiling the global urban virome through wastewater metagenomics. Nature Communications Vol.16 No.1 (2025). doi:10.1038/s41467-025-65208-x Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/113555
Title
Unveiling the global urban virome through wastewater metagenomics
Author(s)
Worp N.
Nieuwenhuijse D.F.
Izquierdo-Lara R.W.
Schapendonk C.M.E.
Brinch C.
Jensen E.E.B.
Munk P.
Hendriksen R.S.
Larsson D.G.J.
Berglund F.
Woolhouse M.
Bunnik B.v.
Kwenda G.
Do Phuc N.
Tran D.M.N.
Van C.D.
Baklayan P.
Rigamonti N.
Wittum T.E.
Kang S.
Lilienthal R.
Truong P.
Sukapanpatharam P.
Beck N.K.
Davis M.
Sobsey M.D.
Meschke J.S.
Brown J.
Sozzi E.
Capone D.
Lefor B.
Gaze W.H.
Zhang L.
Bunce J.T.
Graham D.W.
Leonard A.
Moore A.
Jassim L.M.
Obaidi O.
Thomsen J.
Kalule J.B.
Ejobi F.
Kurekci C.
Levent B.
Nikiema-Pessinaba S.C.
Njanpop-Lafourcade B.M.
Bidjada B.
de Roda Husman A.M.
Thamlikitkul V.
Suthienkul O.
Chonsin K.
Hounmanou Y.M.G.
Mdegela R.H.
Kumburu H.H.
Hong Y.P.
der Heijden T.V.
Boss R.
Örn S.
Norrgren L.
Rutgersson C.
Charlemagne K.
Pathirage S.
Premasiri H.I.
Bandara N.K.B.K.R.G.W.
Perera R.R.D.P.
Cerdà-Cuéllar M.
Lopez M.G.
Quintela-Baluja M.
Song M.J.
Esterhuyse K.
Keddy K.
Trkov M.
Truska P.
Pastuchová K.
Gavačová D.
Wuertz S.
Zuniga-Montanez R.
Tay M.Y.F.
Radosavljevic V.
Gassama A.
Perry M.R.
Hong P.Y.
Burduniuc O.
Cojocaru R.
Kochubovski M.
Bosevska G.
Yoon S.
Hur H.G.
Shin H.
Di Yoong Wen D.
Álvaro P.
Martins J.
Rocha J.
Manaia C.
Wasyl D.
Yauce F.C.
Sibulo R.
Catangcatang K.
Magtibay B.B.
Velasquez J.E.
Nieuwenhuijse D.F.
Izquierdo-Lara R.W.
Schapendonk C.M.E.
Brinch C.
Jensen E.E.B.
Munk P.
Hendriksen R.S.
Larsson D.G.J.
Berglund F.
Woolhouse M.
Bunnik B.v.
Kwenda G.
Do Phuc N.
Tran D.M.N.
Van C.D.
Baklayan P.
Rigamonti N.
Wittum T.E.
Kang S.
Lilienthal R.
Truong P.
Sukapanpatharam P.
Beck N.K.
Davis M.
Sobsey M.D.
Meschke J.S.
Brown J.
Sozzi E.
Capone D.
Lefor B.
Gaze W.H.
Zhang L.
Bunce J.T.
Graham D.W.
Leonard A.
Moore A.
Jassim L.M.
Obaidi O.
Thomsen J.
Kalule J.B.
Ejobi F.
Kurekci C.
Levent B.
Nikiema-Pessinaba S.C.
Njanpop-Lafourcade B.M.
Bidjada B.
de Roda Husman A.M.
Thamlikitkul V.
Suthienkul O.
Chonsin K.
Hounmanou Y.M.G.
Mdegela R.H.
Kumburu H.H.
Hong Y.P.
der Heijden T.V.
Boss R.
Örn S.
Norrgren L.
Rutgersson C.
Charlemagne K.
Pathirage S.
Premasiri H.I.
Bandara N.K.B.K.R.G.W.
Perera R.R.D.P.
Cerdà-Cuéllar M.
Lopez M.G.
Quintela-Baluja M.
Song M.J.
Esterhuyse K.
Keddy K.
Trkov M.
Truska P.
Pastuchová K.
Gavačová D.
Wuertz S.
Zuniga-Montanez R.
Tay M.Y.F.
Radosavljevic V.
Gassama A.
Perry M.R.
Hong P.Y.
Burduniuc O.
Cojocaru R.
Kochubovski M.
Bosevska G.
Yoon S.
Hur H.G.
Shin H.
Di Yoong Wen D.
Álvaro P.
Martins J.
Rocha J.
Manaia C.
Wasyl D.
Yauce F.C.
Sibulo R.
Catangcatang K.
Magtibay B.B.
Velasquez J.E.
Author's Affiliation
University of Washington
The Ohio State University
The University of North Carolina at Chapel Hill
The University of Edinburgh
Nanyang Technological University
Göteborgs Universitet
Newcastle University
Technical University of Denmark
Korea Advanced Institute of Science and Technology
Erasmus MC
Mahidol University
Sveriges lantbruksuniversitet
King Abdullah University of Science and Technology
Sahlgrenska Akademin
Baylor University
Gwangju Institute of Science and Technology
Rijksinstituut voor Volksgezondheid en Milieu
Makerere University
Charles Darwin University
Institut de Recerca I Technologia Agroalimentaries
Mustafa Kemal Üniversitesi
University of Exeter Medical School
University of Zambia
Faculty of Medicine Siriraj Hospital, Mahidol University
Sokoine University of Agriculture
Department of Environmental Sciences and Engineering
University of Kelaniya
Eastern Illinois University
Państwowy Instytut Weterynaryjny - Państwowy Instytut Badawczy
Escola Superior de Biotecnologia da Universidade Católica Portuguesa
University of Belgrade Faculty of Veterinary Medicine
Nicolae Testemitanu State University of Medicine and Pharmacy
Institut Pasteur de Dakar
Taiwan Centers for Disease Control
Rashid Hospital
Universidad de Piura
Kilimanjaro Clinical Research Institute
Medical Research Institute Colombo
Suratthani Rajabhat University
Dubai Municipality
Federal Food Safety and Veterinary Office
The World Health Organization Regional Office for the Western Pacific philippines
Northumbrian Water Group Limited
Public Health Institution of Turkey
Institute of Public Health of the Republic of North Macedonia
Abu Dhabi Public Health Centre
Institute of Public Health in Ho Chi Minh City
Labaqua S.A.U
A Águas do Tejo Atlântico, S.A
National Laboratory of Health
National Agency for Public Health
Independent Consultant
National Institute of Hygiene
Daspoort Waste Water Treatment Works
Maynilad Water Services, Inc.
School of Veterinary Sciences
Public Health Authority of the Slovak Republic
Agence de Mιdecine Prιventive
Caribbean Public Health Agency
Columbia Boulevard WWTP
Laboratorio Tecnolσgico del Uruguay
Brightwater Treatment Plant
Ara region bern ag
Division of Integrated Surveillance of Health Emergencies and Response
The Ohio State University
The University of North Carolina at Chapel Hill
The University of Edinburgh
Nanyang Technological University
Göteborgs Universitet
Newcastle University
Technical University of Denmark
Korea Advanced Institute of Science and Technology
Erasmus MC
Mahidol University
Sveriges lantbruksuniversitet
King Abdullah University of Science and Technology
Sahlgrenska Akademin
Baylor University
Gwangju Institute of Science and Technology
Rijksinstituut voor Volksgezondheid en Milieu
Makerere University
Charles Darwin University
Institut de Recerca I Technologia Agroalimentaries
Mustafa Kemal Üniversitesi
University of Exeter Medical School
University of Zambia
Faculty of Medicine Siriraj Hospital, Mahidol University
Sokoine University of Agriculture
Department of Environmental Sciences and Engineering
University of Kelaniya
Eastern Illinois University
Państwowy Instytut Weterynaryjny - Państwowy Instytut Badawczy
Escola Superior de Biotecnologia da Universidade Católica Portuguesa
University of Belgrade Faculty of Veterinary Medicine
Nicolae Testemitanu State University of Medicine and Pharmacy
Institut Pasteur de Dakar
Taiwan Centers for Disease Control
Rashid Hospital
Universidad de Piura
Kilimanjaro Clinical Research Institute
Medical Research Institute Colombo
Suratthani Rajabhat University
Dubai Municipality
Federal Food Safety and Veterinary Office
The World Health Organization Regional Office for the Western Pacific philippines
Northumbrian Water Group Limited
Public Health Institution of Turkey
Institute of Public Health of the Republic of North Macedonia
Abu Dhabi Public Health Centre
Institute of Public Health in Ho Chi Minh City
Labaqua S.A.U
A Águas do Tejo Atlântico, S.A
National Laboratory of Health
National Agency for Public Health
Independent Consultant
National Institute of Hygiene
Daspoort Waste Water Treatment Works
Maynilad Water Services, Inc.
School of Veterinary Sciences
Public Health Authority of the Slovak Republic
Agence de Mιdecine Prιventive
Caribbean Public Health Agency
Columbia Boulevard WWTP
Laboratorio Tecnolσgico del Uruguay
Brightwater Treatment Plant
Ara region bern ag
Division of Integrated Surveillance of Health Emergencies and Response
Corresponding Author(s)
Other Contributor(s)
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.