Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments

RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments—including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings — across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health. RNA viruses are well-known pathogens that can cause zoonotic spillover and threaten human health. Here, the authors have compiled samples collected from urban and surrounding environments across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas).

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Journal
Nature Communications
Published
2026-07-16
DOI
https://doi.org/10.1038/s41467-026-73605-z
Primary Topic
Plant and Fungal Interactions Research
Type
article
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article

Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments

Klas I. Udekwu, Angela Ivask, Katarzyna Kopera, Haruo Suzuki et al.
Nature Communications
Plant and Fungal Interactions Research
article

Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments

Klas I. Udekwu, Angela Ivask, Katarzyna Kopera, Haruo Suzuki, Patrick K. H. Lee, Serghei Mangul, Jacqueline Proszynski, Chris Deng, Christos Ouzounis, Nikos C. Kyrpides, Alexander J. Probst, Olayinka Osuolale, Braden Tierney, Nur Hazlin Hazrin-Chong, Wojciech Branicki, Paweł P. Łabaj, Masayuki Ushio, Viorel Munteanu, Malay Bhattacharyya, Emmanuel Dias‐Neto, Natalia Mazur-Panasiuk, Youping Deng, А.В. Фролова, Alexander G. Lucaci, Tieliu Shi, Bharath Prithiviraj, Lin‐Fa Wang, Antônio Pedro Camargo, Eduardo Castro-Nallar, Kamila Marszałek, Krista Ryon, Kübra Can Kurt, L Wang, Eran Elhaik, Thirumalaisamy P. Velavan, Nitesh Kumar Sharma, Krzysztof Pyrć, Balakrishnan Subramanian, Michael Poulsen, Xavier Rodó, André Kahles, Joshua Burkhart, Manuela Oliveira, Kathleen Rubins, Anastasia Chasapi, Christopher E. Mason, Rodolfo Brizola Toscan, Lynn M. Schriml, Jun Wu, Jian Ouyang, Zihao Gao, Andrew Wan, Masaki Nasu, Alba Tull, Juan A Ugalde, Mariana Massó, Dmitry Meleshko, Maria A. Sierra, Di Liu, Paula Quiroga, Daniel Brennan, Harleen Kaur, Michał Kowalski
article en

Abstract

RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments—including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings — across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health. RNA viruses are well-known pathogens that can cause zoonotic spillover and threaten human health. Here, the authors have compiled samples collected from urban and surrounding environments across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas).

Nature CommunicationsVol. 17(1)
Rutgers, The State University of New Jersey (US), Tongji University (CN), University of Southern California (US), University of Hawaiʻi at Mānoa (US), Ştefan cel Mare University of Suceava (RO), University of Copenhagen (DK), Jagiellonian University (PL), University of Maryland, Baltimore (US), Hawaii Department of Health (US), University of Talca (CL), Universidad Andrés Bello (CL), Lawrence Berkeley National Laboratory (US), University of Idaho (US), SingHealth (SG), City University of Hong Kong (HK), University of Pittsburgh (US), Duy Tan University (VN), Technical University of Moldova (MD), Universidade de São Paulo (BR), Universidade do Porto (PT), Lund University (SE), Joint Genome Institute (US), Hong Kong University of Science and Technology (HK), National University of Computer and Emerging Sciences (PK), Cornell University (US), Aristotle University of Thessaloniki (GR), Universidad de Buenos Aires (AR), University of Białystok (PL), New York University Shanghai (CN), Swedish University of Agricultural Sciences (SE), Elizade University (NG), ETH Zurich (CH), Universitätsklinikum Tübingen (DE), SingHealth Duke-NUS Academic Medical Centre (SG), Tri-Institutional PhD Program in Chemical Biology (US), Veterinarians Without Borders (US), Wuhan Institute of Virology (CN), IPO Porto (PT), Life Services (United States) (US), Mohamed bin Zayed University of Artificial Intelligence (AE), Kyiv Academic University (UA), Reckitt Benckiser (United States) (US), Duke-NUS Medical School (SG), Centre for Research and Technology Hellas (GR), Shanghai Tongji Urban Planning and Design Institute (CN), Keio University Shonan Fujisawa (JP), Vietnamese - German Center of Excellence in Medical Research (VN), Barcelona Institute for Global Health (ES), i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto (PT), Weill Cornell Medicine (US), Rutgers Cancer Institute (US), University of Tartu (EE), University of Duisburg-Essen (DE), Indian Statistical Institute (IN), East China Normal University (CN), Institute of Molecular Biology and Genetics (UA), Carnegie Mellon University (US), Pomeranian Medical University (PL), National University of Malaysia (MY)
Sustainable cities and communities
Openalex Percentile: Top 9%
Plant and Fungal Interactions Research
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