Scientists have identified more than 42,000 previously unknown viruses circulating in cities around the world, on surfaces in subway stations, park benches and hospitals, and in sewage networks, according to a study published in July in the journal Nature Communications, a peer-reviewed publication from Springer Nature.
The research team analyzed 2,922 biological samples collected in 102 cities across 31 countries, including São Paulo, Brazil. From that material, the scientists built what they call the Atlas of Urban and Peri-urban RNA Viruses, cataloguing 54,945 species of RNA viruses, the group of pathogens that includes the causes of dengue fever, Zika, influenza, yellow fever and COVID-19.
About 77% of those species, more than 42,000 viruses, had never before been described by science.
How the viruses were collected
Most of the material, 1,862 samples, was gathered by the international MetaSUB consortium between March and July 2020, during the peak of the COVID-19 pandemic. MetaSUB is a global research network that studies the microorganisms found on mass-transit systems and other public surfaces in cities worldwide.
Researchers used sterile swabs to wipe surfaces that people touch constantly, including stair handrails, benches in plazas and transit stations, and public transport ticket machines.
Beyond urban surfaces, the study incorporated sequences drawn from public databases covering the areas surrounding cities, including soil, sediment, fresh water, agricultural greenhouses and sewage systems.
All the material was processed using metatranscriptomic sequencing, a technique that extracts and decodes the RNA of every organism present in a sample, including viruses, bacteria, fungi and insects, at the same time, without the need to isolate them individually.
The scientists cautioned that the nearly 55,000 viruses catalogued so far represent only the "tip of the iceberg." They said further collection is likely to uncover thousands more previously unknown species.
Is the public at risk?
Despite the scale of the numbers, the researchers said the discovery does not point to a health threat for people living in cities. Most of the newly identified viruses, they said, are not capable of infecting humans.
Researchers were able to estimate a host for only about a third of the sequences mapped. Of that group, more than half were bacteriophages, viruses that infect and destroy bacteria exclusively and are harmless to human or other animal cells.
After cross-checking the data against the global VIRON database, the team found that 60 of the viruses are likely capable of infecting humans. Of that group, only 19 were collected from urban surfaces.
Caution with the data
The study reported that samples taken from hospitals in São Paulo and Islamabad, Pakistan, showed a higher presence of viruses from families known to be pathogenic to vertebrate animals, compared with samples from hospitals in Seoul, South Korea, and Baltimore, in the United States.
Antônio Pedro Carmago, a professor in the biochemistry department at the University of São Paulo's Institute of Chemistry and one of the study's authors, said the finding needs to be interpreted with caution.
He said it was very difficult to draw any biological explanation from the pattern and that it could simply reflect differences in sampling. The scientific article itself noted that in certain countries only one specific type of environment was analyzed, which limits direct geographic comparisons.
