Unveiling the global urban virome through wastewater metagenomics

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. Rojas M.L.Z. Schill C.H. Gustafson N.W. Shakoor S. Hasan R. Mohsin M. Holmstad R. Ryrfors P. Wester A.L. Sørgaard A.-M. Fashae K. Odetokun I.A. Adisa I.R. Ahmed A.O. Vilchez S. Huete-Pιrez J. Mendoza F.P. Chambers S.T. Gemmell N. Jeunen G.-J. Passel M.V. Schmitt H. Pal P. Vubil D.C. Karraouan B. Bouchrif B. Djurovic D. Vujacic A. Santchurn S.J. Haber M.V. Spiteri D. Parimannan S. Rajandas H. Amin A. Banda D.L. Andrianarivelo M.R. Samison L.H. Collard J.-M. Rasolofoarison T. Bastaraud A. Penny C. Butrimaite-Ambrozeviciene C. Pereckienė A. Daoud Z. Matar G.M. Bartkevics V. Streikisa M. Kokina K. Avsejenko J. Bērziņš A. Alaati T. Fakhraldeen S.A. Jamil K. Raka L. Ng’eno E. Kiiyukia C. Shakenova Z. Kayama S. Sugai M. Kuroda M. Yu L. Hisatsune J. Alba P. Di Cesare A. Corno G. Diaconu E.L. Battisti A. Moran-Gilad J. Cormican M. O’Connor L. Morris D. Alebouyeh M. Fani F. Bangera S.R. Ballal M. Hatha A.M. Thorsteinsdottir T.R. Solymosi N. Kocsis B. Lickes S.A. Lytras E. Kotzamanidis C. Banu R.A. Feglo P.K. Mohammed J. Saba C.K.S. Berendonk T.U. Hesse S. Schubert S. Brinkmann A. Nitsche A. Malania L. Sanneh B. Villacis J.E. Schaeffer J. Le Guyader S. Heikinheimo A. Eguale T. Legesse M. Koolmeister M. Salem M.F. Abouelnaga M. Jensen P.E. Hansen L.T. Elsborg B. Deogratias Z.N. Karpíšková R. Jergović M. Hrenovic J. Coulibaly K.J. Donado-Godoy P. Valencia M.F. Bernal Morales J.F. JiaYong Z. Yu Y. Jiao X. Chung T. Lau L.T. Baisheng L. Zheng H. Ke C. Cuadros-Orellana S. Martinez M.C. Paredes-Osses E. Adell A.D. Tabo D.-A. Brar S.K. Kumar P. Yost C.K. Abah Jacques Olivier Z.A. Nzouankeu A. Ngandjio A. Vuthy Y. Sopheak T. Oumar T. Juste B.I. Ivanov I. Ribeiro de Souza L.C. Oliveira G. Rodrigues D. Tagliati C.A. Rahube T.O. Mazalica N. Grujić V.R. Soria F. Gutierrez A.D.S. Victorien D.T. Pieters I. Vandenberg O. Worrell C. Hossain Z.Z. Begum A. Allerberger F. Cassar S. Collignon P. Coventry K. Gibb K. Neilson E.H.J. Lambrinidis D. Rees C. Power P. Bego A. Svendsen C.A. Kjeldgaard J.S. Petersen T.N. Møller F.D. Aarestrup F. Oude Munnink B.B. Koopmans M.P.G. de Graaf M.
December 2025 Nature Research

Nature Communications
2025 #16 Issue 1

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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Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs, Lyngby, Denmark
Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
Institute of Public Health, Tirana, Albania
Universidad de Buenos Aires, Buenos Aires, Argentina
Melbourne Water Corporation, Melbourne, Australia
Charles Darwin University, Darwin, Australia
University of Copenhagen, Frederiksberg C, Denmark
Charles Darwin University, Darwin Northern Territory, Australia
Canberra Hospital, Canberra, Australia
ALS Water, Scoresby, Australia
Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
University of Dhaka, Dhaka, Bangladesh
Environmental Protection Department, St. Michael, Bridgetown, Barbados
Laboratoire Hos- pitalier Universitaire de Bruxelles (LHUB-ULB), Brussels, Belgium
AQUAFIN NV, Aartselaar, Belgium
Polytechnic School of Abomey-Calavi, Abomey- Calavi, Benin
Universidad Catσlica Boliviana San Pablo, La Paz, Bolivia
Public Health Institute of the Republic of Srpska, Faculty of Medicine University of Banja Luka, Banja Luka, Bosnia and Herzegovina
Public Health Institute of the Republic of Srpska, Banja Luka, Bosnia and Herzegovina
Botswana International University of Science and Technology, Palapye, Botswana
Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
Oswaldo Cruz Institute, Rio de Janeiro, Brazil
Vale Institute of Technology, PA, Belιm, Brazil
National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
University of Ouagadougou, Ouagadougou, Burkina Faso
Institut Pasteur du Cambodge, Phnom Penh, Cambodia
Centre Pasteur du Cameroun, Yaoundι, Cameroon
University of Regina, Regina, Canada
Eau Terre Environnement Research Centre (INRS-ETE), Quebec City G1K 9A9, Canada and Indian Institute of Technology, Jammu, India
Eau Terre Environnement Research Centre (INRS-ETE), Quebec City G1K 9A9, Canada and Lassonde School of Enginerring, York University, Toronto, Canada
University of N’Djamena, N’Djamena, Chad
Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
Institute of Public Health, Santiago, Chile
Universidad Catolica del Maule, Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile
Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
The Hong Kong Polytechnic University, Hong Kong
Shantou University Medical College, Shantou, China
Nanjing University of Information Science and Technology, Nanjing, China
Center for Disease Control and Prevention of Henan province, Zhengzhou, China
Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars, CI Tibaitatα, Corporaciσn Colombiana de Investigaciσn Agropecuaria (AGROSAVIA), Cundinamarca, Tibaitatα - Mosquera, Colombia
Institut Pasteur de Côte d’Ivoire, Abidjan, Cote dIvoire
University of Zagreb, Zagreb, Croatia
Andrija Stampar Teaching Institute of Public Health, Zagreb, Croatia
Veterinary Research Institute, Brno, Czech Republic
Centre de Recherche en Sciences Naturelles de Lwiro (CRSN-LWIRO), Bukavu, Democratic Republic Congo
BIOFOS A/S, Copenhagen K, Denmark
Technical University of Denmark, Kgs, Lyngby, Denmark
Suez Canal University, Ismailia, Egypt
University of Sadat City, Sadat City, Egypt
Ministry of Health, Environmental Micro- biology, Tallinn, Estonia
Addis Ababa University, Addis Ababa, Ethiopia
University of Helsinki, Helsinki, Finland
French Institute Search Pour L’ex- ploitation De La Mer (Ifremer), Nantes, France
Instituto Nacional de Investigaciσn en Salud Pϊblica-INSPI (CRNRAM), Galαpagos, Quito, Ecuador
National Public Health Laboratories, Ministry of Health and Social Welfare, Kotu, Gambia
National Center for Disease Control and Public Health, Tbilisi, Georgia
Robert Koch Institute, Berlin, Germany
Technische Universitδt Dresden, Institute of Hydrobiology, Dresden, Germany
University for Development Studies, Tamale, Ghana
University of Ghana, Accra, Ghana
Kwame Nkrumah University of Science and Technology, PMB, Kumasi, Ghana
Council for Scientific and Industrial Research Water Research Institute, Accra, Ghana
Veterinary Research Institute of Thessaloniki, Hellenic Agricultural Organisation- DEMETER, Thermi, Greece
Athens Water Supply and Sewerage Company (EYDAP S.A.), Athens, Greece
Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
Semmelweis University, Institute of Medical Microbiology, Budapest, Hungary
University of Veterinary Medicine, Budapest, Hungary
University of Iceland, Reykjavνk, Iceland
Cochin University of Science and Technology, Cochin, India
Kasturba Medical College, Manipal, India
Apollo Diagnostics, Mangalore, India
Shiraz University of Medical Sciences, Shiraz, Iran
Shahid Beheshti University of Medical Sciences, Tehran, Iran
National University of Ireland Galway, Galway, Ireland
Ben Gurion University of the Negev and Ministry of Health, Beer-Sheva, Israel
Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
CNR - Water Research Institute, Verbania, Italy
National Institute of Infectious Diseases, Tokyo, Japan
National Center of Expertise, Taldykorgan, Kazakhstan
Mount Kenya University, Thika, Kenya
Kenya Medical Research Institute, Nairobi, Kenya
University of Prishtina “Hasan Prishtina” & National Institute of Public Health of Kosovo, Pristina, Kosovo
Kuwait Institute for Scientific Research, Kuwait City, Kuwait
Institute of Food Safety, Riga, Latvia
American University of Beirut, Beirut, Lebanon
Central Michigan University & Michigan Health Clinics, Saginaw, MI, United States
National Food and Veterinary Risk Assessment Institute, Vilnius, Lithuania
Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
Institut Pasteur de Madagascar, Antananarivo, Madagascar
University of Antananarivo, Centre d’Infectiologie Charles Mιrieux, Antananarivo, Madagascar
University of Malawi, Blantyre, Malawi
Malaysian Genomics Resource Centre Berhad, Kuala Lumpur, Malaysia
AIMST University, COMBio, Kedah, Malaysia
Water Services Corporation, Luqa, Malta
Environmental Health Directorate, St. Venera, Malta
University of Mauritius, Reduit, Mauritius
Institute for Public Health Montenegro, Podgorica, Montenegro
Institut Pasteur du Maroc, Casablanca, Morocco
Centro de Investigaηγo em Saϊde de Manhiηa (CISM), Maputo, Mozambique
Agriculture and Forestry University, Kathmandu, Nepal
National Institute for Public, Health and the Environment (RIVM), Bilthoven, Netherlands
University of Otago, Dunedin, New Zealand
University of Otago, Christchurch, New Zealand
University of Central America, Managua, Nicaragua
Universidad Nacional Autσnoma de Nicaragua-Leσn, Leσn, Nicaragua
University of Ilorin, Ilorin, Nigeria
University of Ibadan, Ibadan, Nigeria
Norwegian Institute of Public Health, Oslo, Norway
VEAS, Slemmestad, Norway
University of Agriculture, Faisalabad, Pakistan
Aga Khan University, Karachi, Pakistan
Laboratorio Central de Salud Publica, Asuncion, Paraguay
Instituto Nacional de Salud, Lima, Peru
Universidad de Piura, Piura, Peru
WHO Environmental and Occupational Health, Manila, Philippines
Maynilad Water Services, Inc, Quezon City, Philippines
National Veterinary Research Institute, Pulawy, Poland
Uni- versidade Catσlica Portuguesa, CBQF - Centro de Biotecnologia e Quνmica Fina - Laboratσrio Associado, Escola Superior de Biotecnologia, Porto, Portugal
Aguas do Tejo Atlantico, Lisboa, Portugal
Gwangju Institute of Science and Technology, Gwangju, South Korea
Korea Advanced Institute of Science and Technology, Daejeon, South Korea
Institute of Public Health of the Republic of North Macedonia, Skopje, North Macedonia
State Medical and Pharmaceutical University, Chișinău, Moldova
National Agency for Public Health, Chișinău, Moldova
King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
University of Edinburgh, Scotland, Edinburgh, United Kingdom
Institut Pasteur de Dakar, Dakar, Senegal
Institute of Veterinary Medicine of Serbia, Belgrade, Serbia
Nanyang Technological University, Singapore, Singapore
Public Health Authority of the Slovak Republic, Bratislava, Slovakia
National Laboratory of Health, Environment and Food, Ljubljana, Slovenia
Independent consultant, Johannesburg, South Africa
Daspoort Waste Water Treatment Works, Pretoria, South Africa
Korea Advanced Institute of Science and Technology, Daejeon, South Korea
School of Veterinary Sciences, Lugo, Spain
Labaqua, Santiago de Compostela, Spain
IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autonoma de Barcelona, Bellaterra, Spain
University of Kelaniya, Ragama, Sri Lanka
Medical Research Institute, Colombo, Sri Lanka
Caribbean Public Health Agency, Catries, Saint Lucia
The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
Swedish University of Agricultural Sciences, Uppsala, Sweden
Federal Food Safety and Veterinary Office (FSVO), Bern, Switzerland
Ara Region Bern AG, Herrenschwanden, Switzerland
Centers for Disease Control, Taipei, Taiwan
Kilimanjaro Clinical Research Institute, Moshi, Tanzania
Sokoine University of Agriculture, Morogoro, Tanzania
Faculty of Science and Technology, Suratthani Rajabhat University, Surat Thani, Thailand
Faculty of Public Health, Mahidol University, Bangkok, Thailand
Faculty of Medicine Siriraj Hospital, Bangkok, Thailand
National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
National Institute of Hygiene, Lomι, Togo
Agence de Mιdecine Prιventive, Dapaong, Togo
Division of Integrated Surveillance of Health Emergencies and Response, Lomι, Togo
Public Health Institution of Turkey, Ankara, Turkey
Hatay Mustafa Kemal University, Hatay, Turkey
Makerere University, Kampala, Uganda
Abu Dhabi Public Health Center, Abu Dhai, United Arab Emirates
Dubai municipality, WWTP Al Aweer, Dubai, United Arab Emirates
Rashid Hospital, Dubai, United Arab Emirates
Northumbrian Water, Northumbria House, Abbey Road, Pity Me, Durham, United Kingdom
University of Exeter Medical School, Cornwall, United Kingdom
Newcastle University, Newcastle upon Tyne, United Kingdom
Brightwater Treatment Plant, Woodinville, WA, United States
Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
University of North Carolina, Chapel Hill, United States
University of Washington, Seattle, WA, United States
Baylor University, Waco, United States
Columbia Boulevard WWTP, Portland, United States
Eastern Illinois University, Charleston, United States
The Ohio State University, Columbus, OH, United States
Laboratorio Tecnolσgico del Uruguay, Montevideo, Uruguay
Institute of Public Health in Ho Chi Minh City, Ho Chi Minh, Viet Nam
University of Zambia, Lusaka, Zambia
Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden

Department of Viroscience
Research Group for Genomic Epidemiology
Research Group for Global Capacity Building
Institute of Public Health
Universidad de Buenos Aires
Melbourne Water Corporation
Charles Darwin University
University of Copenhagen
Charles Darwin University
Canberra Hospital
ALS Water
Austrian Agency for Health and Food Safety (AGES)
University of Dhaka
Environmental Protection Department
Laboratoire Hos- pitalier Universitaire de Bruxelles (LHUB-ULB)
AQUAFIN NV
Polytechnic School of Abomey-Calavi
Universidad Catσlica Boliviana San Pablo
Public Health Institute of the Republic of Srpska
Public Health Institute of the Republic of Srpska
Botswana International University of Science and Technology
Universidade Federal de Minas Gerais
Oswaldo Cruz Institute
Vale Institute of Technology
National Center of Infectious and Parasitic Diseases
University of Ouagadougou
Institut Pasteur du Cambodge
Centre Pasteur du Cameroun
University of Regina
Eau Terre Environnement Research Centre (INRS-ETE)
Eau Terre Environnement Research Centre (INRS-ETE)
University of N’Djamena
Escuela de Medicina Veterinaria
Institute of Public Health
Universidad Catolica del Maule
Guangdong Provincial Center for Disease Control and Prevention
The Hong Kong Polytechnic University
Shantou University Medical College
Nanjing University of Information Science and Technology
Center for Disease Control and Prevention of Henan province
Colombian Integrated Program for Antimicrobial Resistance Surveillance - Coipars
Institut Pasteur de Côte d’Ivoire
University of Zagreb
Andrija Stampar Teaching Institute of Public Health
Veterinary Research Institute
Centre de Recherche en Sciences Naturelles de Lwiro (CRSN-LWIRO)
BIOFOS A/S
Technical University of Denmark
Suez Canal University
University of Sadat City
Ministry of Health
Addis Ababa University
University of Helsinki
French Institute Search Pour L’ex- ploitation De La Mer (Ifremer)
Instituto Nacional de Investigaciσn en Salud Pϊblica-INSPI (CRNRAM)
National Public Health Laboratories
National Center for Disease Control and Public Health
Robert Koch Institute
Technische Universitδt Dresden
University for Development Studies
University of Ghana
Kwame Nkrumah University of Science and Technology
Council for Scientific and Industrial Research Water Research Institute
Veterinary Research Institute of Thessaloniki
Athens Water Supply and Sewerage Company (EYDAP S.A.)
Universidad de San Carlos de Guatemala
Semmelweis University
University of Veterinary Medicine
University of Iceland
Cochin University of Science and Technology
Kasturba Medical College
Apollo Diagnostics
Shiraz University of Medical Sciences
Shahid Beheshti University of Medical Sciences
National University of Ireland Galway
Ben Gurion University of the Negev and Ministry of Health
Istituto Zooprofilattico Sperimentale del Lazio e della Toscana
CNR - Water Research Institute
National Institute of Infectious Diseases
National Center of Expertise
Mount Kenya University
Kenya Medical Research Institute
University of Prishtina “Hasan Prishtina” & National Institute of Public Health of Kosovo
Kuwait Institute for Scientific Research
Institute of Food Safety
American University of Beirut
Central Michigan University & Michigan Health Clinics
National Food and Veterinary Risk Assessment Institute
Luxembourg Institute of Science and Technology
Institut Pasteur de Madagascar
University of Antananarivo
University of Malawi
Malaysian Genomics Resource Centre Berhad
AIMST University
Water Services Corporation
Environmental Health Directorate
University of Mauritius
Institute for Public Health Montenegro
Institut Pasteur du Maroc
Centro de Investigaηγo em Saϊde de Manhiηa (CISM)
Agriculture and Forestry University
National Institute for Public
University of Otago
University of Otago
University of Central America
Universidad Nacional Autσnoma de Nicaragua-Leσn
University of Ilorin
University of Ibadan
Norwegian Institute of Public Health
VEAS
University of Agriculture
Aga Khan University
Laboratorio Central de Salud Publica
Instituto Nacional de Salud
Universidad de Piura
WHO Environmental and Occupational Health
Maynilad Water Services
National Veterinary Research Institute
Uni- versidade Catσlica Portuguesa
Aguas do Tejo Atlantico
Gwangju Institute of Science and Technology
Korea Advanced Institute of Science and Technology
Institute of Public Health of the Republic of North Macedonia
State Medical and Pharmaceutical University
National Agency for Public Health
King Abdullah University of Science and Technology
University of Edinburgh
Institut Pasteur de Dakar
Institute of Veterinary Medicine of Serbia
Nanyang Technological University
Public Health Authority of the Slovak Republic
National Laboratory of Health
Independent consultant
Daspoort Waste Water Treatment Works
Korea Advanced Institute of Science and Technology
School of Veterinary Sciences
Labaqua
IRTA
University of Kelaniya
Medical Research Institute
Caribbean Public Health Agency
The Sahlgrenska Academy at the University of Gothenburg
Swedish University of Agricultural Sciences
Federal Food Safety and Veterinary Office (FSVO)
Ara Region Bern AG
Centers for Disease Control
Kilimanjaro Clinical Research Institute
Sokoine University of Agriculture
Faculty of Science and Technology
Faculty of Public Health
Faculty of Medicine Siriraj Hospital
National Institute for Public Health and the Environment (RIVM)
National Institute of Hygiene
Agence de Mιdecine Prιventive
Division of Integrated Surveillance of Health Emergencies and Response
Public Health Institution of Turkey
Hatay Mustafa Kemal University
Makerere University
Abu Dhabi Public Health Center
Dubai municipality
Rashid Hospital
Northumbrian Water
University of Exeter Medical School
Newcastle University
Brightwater Treatment Plant
Department of Environmental Sciences and Engineering
University of North Carolina
University of Washington
Baylor University
Columbia Boulevard WWTP
Eastern Illinois University
The Ohio State University
Laboratorio Tecnolσgico del Uruguay
Institute of Public Health in Ho Chi Minh City
University of Zambia
Centre for Immunity
Centre for Antibiotic Resistance Research (CARe)

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