Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments
Year: 2026
Type: article
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).
Source: Nature Communications
Authors: Zihao Gao, Jun Wu, Alexander G. Lucaci, Jian Ouyang, Lan Wang, Lan Wang, Krista A. Ryon, Eran Elhaik, Alexander J. Probst, Xavier Rodó, Thirumalaisamy P. Velavan, Anastasia Chasapi, Christos A. Ouzounis, Manuela Oliveira, Emmanuel Dias-Neto, Olayinka Osuolale, Michael Poulsen, Dmitry Meleshko, Malay Bhattacharyya, Juan A. Ugalde, Alba Tull, Kathleen H. Rubins, Maria A. Sierra, Braden T. Tierney, Bharath Prithiviraj, Nitesh Kumar Sharma, Viorel Munteanu, Serghei Mangul, Kubra Can Kurt, Masayuki Ushio, Natalia Mazur-Panasiuk, Katarzyna Kopera, Kamila Marszałek, Michał Kowalski, Rodolfo Brizola Toscan, Wojciech Branicki, Krzysztof Pyrć, Paweł P. Łabaj, Balakrishnan Subramanian, Alina Frolova, Joshua G. Burkhart, Youping Deng, Klas I. Udekwu, Lynn M. Schriml, Nur Hazlin Hazrin-Chong, Haruo Suzuki, Patrick K. H. Lee, Antonio Pedro Camargo, Nikos C. Kyrpides, Di Liu, Lin-Fa Wang, Lin-Fa Wang, Christopher E. Mason, Tieliu Shi, Jacqueline Proszynski, Daniel Brennan, Chris K. Deng, Andrew Wan, Masaki Nasu, Andre Kahles, Eduardo Castro-Nallar, Paula Quiroga, Mariana Massó, Harleen Kaur, Angela Ivask
Institutions: East China Normal University, Weill Cornell Medicine, Tongji University, SingHealth, National University of Singapore, SingHealth Duke-NUS Academic Medical Centre, Duke-NUS Medical School, Lund University, University of Duisburg-Essen, Institució Catalana de Recerca i Estudis Avançats, Barcelona Institute for Global Health, Duy Tan University, Universitätsklinikum Tübingen, Vietnamese - German Center of Excellence in Medical Research, University of Tübingen, Centre for Research and Technology Hellas, Aristotle University of Thessaloniki, Universidade do Porto, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rutgers Cancer Institute, Elizade University, University of Copenhagen, Indian Statistical Institute, Universidad Andrés Bello, Carnegie Mellon University, University of Pittsburgh, Reckitt Benckiser (United States), University of Southern California, Technical University of Moldova, Ştefan cel Mare University of Suceava, Jagiellonian University, Mohamed bin Zayed University of Artificial Intelligence, Hong Kong University of Science and Technology, Pomeranian Medical University, University of Białystok, Kyiv Academic University, Institute of Molecular Biology and Genetics, University of Hawaiʻi at Mānoa, University of Hawaii System, University of Idaho, Swedish University of Agricultural Sciences, University of Maryland, Baltimore, National University of Malaysia, Keio University, Keio University Shonan Fujisawa, City University of Hong Kong, Lawrence Berkeley National Laboratory, Universidade de São Paulo, Joint Genome Institute, Chinese Academy of Sciences, Wuhan Institute of Virology, ETH Zurich, University of Talca, Universidad de Buenos Aires, University of Tartu
Language: English
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: U.S. Department of Energy, University of Southern California, Natural Science Foundation of Shanghai, Rutgers Cancer Institute of New Jersey, City University of Hong Kong, University of Pittsburgh, Carnegie Mellon University, University of Hawai'i, Joint Genome Institute, Trường Đại học Duy Tân, Ministerul Cercetării, Inovării şi Digitalizării, Keio University, Fundação de Amparo à Pesquisa do Estado de São Paulo, National Natural Science Foundation of China, East China Normal University, Tongji University, Sveriges Lantbruksuniversitet, Universiti Kebangsaan Malaysia, Ministry of Education, India, National Academy of Sciences of Ukraine, Hong Kong University of Science and Technology, Universidade do Porto, Zayed University, Pomorski Uniwersytet Medyczny W Szczecinie, Indian Statistical Institute, Directorate for Biological Sciences, Office of Science, Weill Cornell Medical College, National Key Research and Development Program of China
OpenAlex ID: W7169036500