Scientists have uncovered an enormous and largely unexplored diversity of RNA viruses in cities around the world. The findings suggest that urban environments contain far more viral genetic diversity than existing scientific databases currently document, revealing a vast microbial world that remains poorly understood.
Researchers examined material collected from subway handrails, hospital surfaces, soil, wastewater and other urban environments. They identified tens of thousands of viral sequences that had not previously been documented, although the discovery does not mean that these viruses pose a threat to human health.
Viruses are commonly associated with infectious diseases such as influenza, dengue and COVID-19. However, many viruses do not infect humans at all. Instead, they target bacteria, fungi, plants and other organisms, often playing important roles in ecosystems without directly causing human illness.
Global survey of city viruses
An international research consortium investigated the diversity of RNA viruses in urban and surrounding environments. The researchers analyzed 2,922 samples associated with 102 cities across 31 countries, covering locations with different climates, infrastructure and environmental conditions.
A substantial proportion of the samples came from the MetaSUB project, an international initiative studying microorganisms found in urban spaces. Between March and July 2020, researchers collected samples from public surfaces, including handrails, benches and ticket machines, using swabs to capture traces of genetic material.
The team also incorporated previously collected samples available through public databases. These included material from wastewater, surface water, sediments, soil and greenhouse crops, providing a broader picture of viral diversity in environments influenced by human activity.
Together, the samples contained more than 100 billion short genetic reads. Using computational methods to assemble and compare this material, the researchers identified 54,945 distinct viral sequences across the dataset.
Most viral sequences are unfamiliar
One of the study’s most striking findings was the limited overlap between the detected sequences and existing viral reference databases. Only 12,487 sequences, approximately 23 percent of the total, could be linked to previously documented viral genetic material.
The remaining 77 percent did not have identifiable counterparts in the available reference collections.
However, the researchers caution that these findings do not necessarily represent the discovery of an equivalent number of entirely new virus species. Many of the sequences are incomplete genetic fragments, and some may belong to viral groups that have already been described.
Nevertheless, the results reveal substantial gaps in scientific knowledge about environmental viruses, even in densely populated and extensively studied urban settings.
The researchers also observed that additional sampling continued to uncover previously unrecognized sequences. This pattern suggests that the diversity of RNA viruses associated with cities is considerably greater than current databases indicate.
The findings therefore point to an urban virosphere that is both remarkably diverse and only partially documented.
Tools and potential applications
To identify viral genetic material within complex environmental samples, the researchers used computational tools, including geNomad. This specialized software helps distinguish viral sequences from genetic material belonging to bacteria, plants and other organisms.
Importantly, identifying an unfamiliar viral sequence does not mean that researchers have discovered a new human pathogen. The team could predict a likely host for only about one-third of the identified viruses, highlighting the limitations of current reference databases and analytical methods.
More than half of the viruses within this subset were predicted to infect bacteria. Known as bacteriophages, these viruses can influence microbial communities by infecting bacteria and potentially affecting their abundance and distribution.
In urban environments, bacteriophages may help shape bacterial populations in wastewater systems, soils and other parts of the built environment.
These viruses are also attracting medical interest because of their potential applications in phage therapy, an approach that uses bacteriophages to target harmful bacteria. Such treatments are being investigated as antibiotic resistance becomes an increasingly serious global health challenge.
The researchers identified phages associated with bacteria belonging to the ESKAPE group, which includes several important hospital-associated pathogens. These bacteria are particularly concerning because they can develop resistance to multiple antibiotics and cause severe infections, especially in vulnerable patients.
Finding phages associated with ESKAPE bacteria could eventually help researchers identify candidates for new antibacterial treatments. However, the ability of individual phages to infect and destroy specific bacterial strains must be confirmed experimentally, and their safety and effectiveness require further investigation.
For now, the findings primarily expand the collection of viral sequences that scientists can examine for possible future applications.
Human and animal viruses detected
The analysis also identified genetic sequences associated with viruses that may infect humans or other mammals. However, detecting viral RNA in an environmental sample does not establish that infectious virus particles were present when the material was collected.
Viral genetic material can remain detectable after a virus has lost its ability to infect cells or replicate. Large environmental datasets may also contain low-level contamination, making careful interpretation essential.
The researchers therefore emphasize that the presence of viral sequences alone should not be interpreted as evidence of an immediate public health threat or an emerging outbreak.
Instead, broad environmental surveillance may provide a valuable way to monitor viral diversity and identify unusual changes over time. Such approaches could eventually help scientists recognize emerging patterns that warrant closer investigation.
The study, published in Nature Communications, demonstrates the capabilities of modern metagenomic analysis while highlighting the complexity of the largely invisible biological communities found throughout cities.
It also underscores the importance of expanding viral reference databases and maintaining environmental monitoring programs to improve understanding of these organisms.
As urban populations grow and climate change alters environmental conditions and ecological boundaries, understanding the viruses present in built environments may become increasingly important.
The findings reveal that even familiar public spaces contain a vast amount of viral genetic diversity that science has only begun to explore.
