Unveiling the global urban virome: insights from wastewater metagenomics

Understanding global viral dynamics is critical for public health1. Traditional infectious disease surveillance primarily focuses on individual pathogens and relies on the identification and reporting of symptomatic cases, which may not capture asymptomatic infections or newly emerging viruses, leading to delayed detection and response.2–4 Wastewater-based epidemiology has been used to track individual pathogens through targeted molecular approaches, but its reliance on predefined targets limits the ability to capture the full spectrum of circulating viruses.5–7 Here, we analyzed longitudinal and biannual wastewater samples from 62 major cities across six continents (2017-2019) using shotgun metagenomics and capture-based sequencing targeting viruses associated with gastrointestinal disease. Over 2,500 viral species spanning 122 families were detected, many with human, animal, or plant health relevance. The Bacteriophage families Microviridae and Virgaviridae dominated the metagenomic dataset, while in the enriched dataset Astroviridae and Picornaviridae were the most prevalent. Virus distributions were broadly similar across continents, but distinct city-level fingerprints emerged, reflecting spatiotemporal variation of viruses like astrovirus, and enterovirus. Global wastewater-based epidemiology enabled the early detection of several emerging viruses, including Echovirus E30 in Europe, and Tomato brown rugose fruit virus before agricultural outbreaks. These findings highlight the potential of wastewater metagenomics for early detection of emerging viruses and population-wide virome monitoring across diverse hosts.