Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments

RNA viruses are major zoonotic threats driving infectious disease outbreaks across hosts, including humans. However, the ecosystem of RNA viruses in urban areas remains largely unexplored. This study analyzed the 3,326 metatranscriptome samples from 102 cities in 31 countries, including urban built and non-built environments, uncovering 54,945 RNA viral units, 77% of which are previously unseen. Two new phyla were discovered (urv.p.001 and urv.p.002), enhancing our understanding of the RNA virome’s phylogenetic diversity. Our research also supports Duplornaviricota’s polyphyletic nature and identifies 104 amino acid sites in RNA polymerase affecting viral function. A distinct biogeographical pattern of RNA viruses was observed, showing significant clustering of different environmental types, with soil environment being central and indicating its potential role in mediating environmental viral exchange. Interactions between RNA viruses and ESKAPE pathogens, highlighting urban areas as significant reservoirs for RNA viruses. These findings underscore the value of continuous surveillance and mapping of urban environments to track RNA virus prevalence and dynamics for the future of public health.