Global biogeography of airborne viruses in public transit systems and their host interactions
Year: 2025
Type: article
Abstract: BACKGROUND: There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses' taxonomy, functional potential, and microbial hosts were determined. The study also investigated correlations between virus and host abundances, the coevolution of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems and anti-CRISPR (Acr) proteins, and the potential impacts of auxiliary metabolic genes (AMGs) on hosts. RESULTS: Airborne viruses in global BEs exhibited biogeographical variations in diversity, composition, function, and virus-host interactions. Nearly half of the vOTUs analyzed were from the Caulimoviridae family, while 31.8% of them could not be taxonomically classified. Diverse functions were identified within the vOTUs, together with antimicrobial resistance genes with the potential to confer resistance to various antibiotics and antimicrobial agents. Strong correlations were observed between vOTU and host abundances, with clear distinctions between virulent and temperate viruses. However, there was limited co-evolution of CRISPR-Cas systems and Acr proteins, which was likely due to the oligotrophic and physical conditions in the BEs and the dominance of vOTUs with a virulent lifestyle. Phage-encoded AMGs appeared to have the potential to enhance host fitness. These findings highlight biogeographical variations in airborne viruses in BEs and that physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution. CONCLUSION: There are biogeographical variations in airborne viruses in BEs in global cities, as physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution. Moreover, the characteristics of airborne viruses in BEs are distinct from those of viruses found in other, more nutrient-rich ecosystems. Video Abstract.
Source: Microbiome
Authors: Huaxin Lei, Shicong Du, Xinzhao Tong, Wing Lam Chan, Marcus H. Y. Leung, Kari O. Bøifot, Daniela Bezdan, Daniel J. Butler, David C. Danko, David C. Green, Mark T. Hernandez, Frank J. Kelly, Alexander G. Lucaci, Cem Meydan, Marina Nieto-Caballero, Krista Ryon, Braden Tierney, Klas I. Udekwu, Benjamin G. Young, Christopher E. Mason, Marius Dybwad, Patrick K. H. Lee
Institutions: City University of Hong Kong, Xi’an Jiaotong-Liverpool University, Norwegian Defence Research Establishment, King's College London, Weill Cornell Medicine, MRC Centre for Environment and Health, Imperial College London, University of Colorado Boulder, University of Idaho, Swedish University of Agricultural Sciences, Cornell University, State Key Laboratory of Marine Pollution
Language: English
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,990
Awards: Development and Proof-of-Concept Implementation of the South Florida Miami RADx-rad SARS-CoV-2 Wastewater-Based Surveillance Infrastructure, Joan & Sanford I. Weill Medical College of Cornell University - to monitor the spread of antimicrobial resistance by generating a global map of bacterial species, resistance genes and markers, and modified bases..., Metagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantation
OpenAlex ID: W4413834883