Unveiling the global urban virome through wastewater metagenomics

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Global Sewage Consortium - (Author)
  • Sina Hesse - , TUD Dresden University of Technology (Author)
  • D. G. Joakim Larsson - , University of Gothenburg (Author)
  • Chair of Limnology
  • Erasmus University Rotterdam
  • Technical University of Denmark
  • University of Edinburgh
  • University of Zambia
  • Institute of Public Health in Ho Chi Minh City
  • Technological Laboratory of Uruguay
  • Ohio State University
  • Eastern Illinois University
  • Columbia Boulevard Wastewater Treatment Plant
  • University of Washington
  • Baylor University
  • University of North Carolina at Chapel Hill
  • Brightwater Treatment Plant
  • University of Exeter
  • Newcastle University
  • Northumbrian Water
  • Dubai Hospital
  • Dubai Municipality
  • Abu Dhabi Public Health Center
  • Makerere University
  • Mustafa Kemal University
  • Ministry of Health, Turkey
  • Togo Ministry of Health (MOH)
  • Preventive Medicine Agency - Dapaong Office
  • Institut nationale d'Hygiène (INH)
  • National Institute of Public Health and the Environment

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.

Details

Original languageEnglish
Article number10707
JournalNature communications
Volume16
Issue number1
Publication statusPublished - 28 Nov 2025
Peer-reviewedYes

External IDs

PubMed 41315190
ORCID /0000-0002-9301-1803/work/203067748
ORCID /0000-0003-1054-8080/work/203071229