The research, published in Nature Communications, emerged from MetaSUB, a decade-old international consortium studying microorganisms in urban settings.
Polish scientists from the Małopolska Centre of Biotechnology at Jagiellonian University were among the contributors, including Professor Paweł Łabaj, a MetaSUB co-founder who helped organize sample collection in Kraków.
Researchers examined nearly 3,000 samples from 102 cities in 31 countries, swabbing surfaces at bus stops, hospitals, banks and shops, and testing sewage, soil, water and sediment.
While earlier MetaSUB work focused on DNA-based microbes, this study targeted RNA viruses — a harder and more expensive category to analyze, since the samples had originally been prepared to detect SARS-CoV-2.
Bioinformatic analysis of the sequences identified roughly 55,000 distinct viral groups, each representing either a single virus or a cluster of closely related ones. Łabaj cautioned that this does not mean researchers discovered tens of thousands of new human pathogens — in most cases, they recovered only genome fragments rather than complete sequences.
"We are talking more about potential viruses. Only in isolated cases was there enough material and data to reconstruct nearly complete genomes", he said.
Viral diversity varied sharply by location. Soil, sediment and sewage samples showed the richest variety, while heavily human-altered sites such as transit stops and shops showed less, a pattern the authors say may reflect how human movement homogenizes urban microbial environments. Sewage stood out as especially diverse, reinforcing its potential as an early-warning tool for emerging outbreaks.
"Sewage has the greatest potential as a source of information about which viruses are currently circulating in the environment and what threats could emerge in the future. That's why monitoring it could form the basis of early-warning mechanisms", Łabaj said.
Among the study's more unexpected findings: of the roughly one-third of viruses whose likely hosts could be identified, most were bacteriophages that infect bacteria rather than viruses affecting humans or animals. Some of the bacteria linked to these phages included Clostridioides difficile and four species from the drug-resistant ESKAPE pathogen group, which are a major cause of hospital infections.
"This is a very important discovery at a time of growing drug resistance. Forecasts suggest that by 2050, millions of people could die each year from infections caused by antibiotic-resistant strains. Since phages attack and destroy bacteria, this opens up significant opportunities for new therapies", Łabaj said.
The analysis also hinted at gaps in current viral classification systems, identifying two distant genetic groups that could eventually be designated new virus types, plus one possible new class altogether. Findings suggest double-stranded RNA viruses may have evolved independently multiple times, meaning existing taxonomies may not fully capture their evolutionary history.
Łabaj said the consortium already holds tens of thousands of additional samples — including material collected in Kraków since 2020 — sitting frozen and unanalyzed for lack of funding to sequence them.
"We could examine, on a global scale, how the urban microbiome changes over time and space, and how pressure from urban development affects the evolution of bacteria, archaea, fungi and viruses; but funding for this is lacking", he said, noting that exploratory, data-driven research of this kind is often harder to finance than studies built around a single predefined hypothesis.
(jh)
Source: PAP