Survey of 102 cities reveals more than 40,000 new viruses
A study involving Brazilian researchers analyzed samples from subway stations, hospitals, bank branches, soil, and sewage in 31 countries. The researchers used genetic screening with a tool developed at the University of São Paulo.
A global mapping project revealed tens of thousands of previously unknown viruses circulating in environments with high human traffic, such as transit stations, hospitals, and sewage systems. The study, detailed in an article published in the journal Nature Communications, analyzed 2,922 samples collected in 102 cities across 31 countries, including São Paulo, Brazil. An international team, including Brazilian researchers, used this data to compile the UPVAtlas (Urban and Peri-urban RNA Virus Atlas), cataloging 54,945 viral species, 77% of which had never been described before. The study sheds light on vast, previously unknown biological diversity, revealing the complexity of microorganisms invisible in everyday city life.
The research focused on RNA viruses, which store their genetic instructions in RNA molecules rather than DNA. These viruses cause diseases such as dengue, Zika, the flu, yellow fever, and, most recently, COVID-19. Much of what is known about this group comes from studying these diseases.
“We were familiar with several disease-causing viruses, but we greatly underestimated viral diversity in nature. When you search for a virus based on a disease, there’s already a bias because all viruses that don’t cause disease end up being ignored. Once we’re able to analyze what’s present in a sample without that bias, we gain a broader view of viral diversity,” says Antônio Pedro Camargo, a professor in the Department of Biochemistry at the Institute of Chemistry of the University of São Paulo (IQ-USP) and one of the authors of the study. He is also a member of the Biology of Bacteria and Bacteriophages Research Center (RIDC B3), a Research, Innovation, and Dissemination Center supported by FAPESP.
Metatranscriptome
The MetaSUB consortium, which investigates the microbiome of urban environments, collected most of the material – 1,862 of the 2,922 samples. Between March and July of 2020, during the pandemic, the consortium collected the samples using a standardized protocol. A swab was rubbed against frequently touched surfaces, such as handrails, benches, and ticket machines. The remaining samples were retrieved from a public sequencing database and represent various aspects of the urban environment, including soil, sediment, freshwater, sewage, and greenhouses.
The materials were analyzed using metatranscriptomics, a technique that allows for the simultaneous sequencing of all RNA molecules present in a sample. “Imagine you pick up a handful of dirt. In there, you’ll find bacteria, bacterial viruses [bacteriophages], other microorganisms, insects – everything you can imagine,” Camargo explains. Rather than isolating each organism, the researchers extract and sequence the entire set of RNA from the sample.
The result is a large volume of unidentified fragments. “You’ll have a bunch of genome fragments, and at first, you won’t know what they are. They’re just sequences of letters. The challenge is figuring out what each piece of the genome corresponds to. Is it a bacterium? Is it a virus? If it’s a virus, what type?” the researcher explains.
This screening was performed using geNomad, a bioinformatics tool developed by Camargo. According to him, the program “allows us to process millions of genetic material sequence fragments and determine which correspond to viral genomes.”
To organize their findings, the researchers compared the sequences of an enzyme present in all RNA viruses, RdRP (RNA-dependent RNA polymerase), which is responsible for viral replication, and reconstructed the phylogenetic relationships among them. Some sequences were so different from anything previously described that the authors proposed creating new categories to accommodate them, including two phyla, a new class, and several unclassified groups. The proposal is preliminary. “This is all computational. You need more information to formally state that these are, in fact, completely new groups,” Camargo notes.
However, the survey revealed only a fraction of the actual microbial diversity. The accumulation curves, which measure the number of previously unknown viruses that appear with each new sample analyzed, did not stabilize in virtually any type of sample. This is a sign that the nearly 55,000 cataloged viruses represent only a fraction of what exists in these locations.
“There’s a very high level of viral diversity – greater than we previously knew. I think that’s the main point of the article,” says Camargo.
Hosts
This discovery does not mean that cities are teeming with new viruses capable of causing human disease. Only about one-third of the sequences had potential hosts identified, and more than half of those corresponded to viruses that infect bacteria.
However, a small portion has the potential to infect vertebrates. By cross-referencing the data with the Global Virome in One Network (VIRION) database, which compiles documented associations between viruses and vertebrates, the authors identified 60 viruses with a high probability of infecting humans and 47 that could infect other mammals. Of the 60 viruses, 19 were found in urban environments, and 34 were found in animal samples.
The study also identified 166 bacteriophages, which are viruses that specialize in attacking and destroying bacteria, with a history of infecting four strains from the ESKAPE group, which includes clinically significant microorganisms such as Staphylococcus aureus. According to the study, this finding could lead to research on using these viruses to combat these pathogens through a treatment known as phage therapy.
Surveillance
In general, urban surfaces, such as streets, banks, stations, and stores, exhibited lower viral diversity than natural environments, such as soil and sediment. According to the authors, this indicates that human activity tends to homogenize these communities. However, sewage was an exception, exhibiting one of the highest levels of diversity in the survey. This finding reinforces the potential of sewage for environmental monitoring.
Among hospital samples, São Paulo, Brazil, and Islamabad, Pakistan, had a higher abundance of vertebrate-pathogenic viruses than Baltimore, United States, and Seoul, South Korea. Camargo urges caution when interpreting these data: “It’s very difficult to infer any biological explanation from that. It may simply be a sampling issue.” The study itself acknowledges this limitation; some countries are represented by only one environment, making it impossible to separate the effect of location from that of the country.
UPVAtlas compiles sequences from different cities and environments into a single catalog, creating a starting point for future comparisons. It will be possible to compare a city’s current viral community with its future one and investigate how viral communities change depending on the environment and location.
Understanding this diversity is important to Camargo precisely because viruses are constantly evolving. “This process is closely related to their ability to infect organisms because viruses only survive if they can reproduce within host cells,” he says.
About São Paulo Research Foundation (FAPESP)
The São Paulo Research Foundation (FAPESP) is a public institution with the mission of supporting scientific research in all fields of knowledge by awarding scholarships, fellowships and grants to investigators linked with higher education and research institutions in the State of São Paulo, Brazil. FAPESP is aware that the very best research can only be done by working with the best researchers internationally. Therefore, it has established partnerships with funding agencies, higher education, private companies, and research organizations in other countries known for the quality of their research and has been encouraging scientists funded by its grants to further develop their international collaboration. You can learn more about FAPESP at www.fapesp.br/en and visit FAPESP news agency at www.agencia.fapesp.br/en to keep updated with the latest scientific breakthroughs FAPESP helps achieve through its many programs, awards and research centers. You may also subscribe to FAPESP news agency at http://agencia.fapesp.br/subscribe.
Journal
Nature Communications
Article Title
Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments
Newly discovered viruses reveal an evolutionary missing link
Using AI-powered tools and vast DNA databases, University of Miami researchers identified previously unknown viruses that offer new clues about the origins of life
image:
Abelardo Aguilar at work in the laboratory of Antoni Luque Santolaria.
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Credit: Ingrid Miranda/University of Miami
Researchers at the University of Miami have identified a group of previously unknown viruses that bridge an evolutionary gap between viruses and cellular protein compartments, a discovery with important implications for both biotechnology and scientists’ understanding of the origins of life.
The findings, published in Nature Communications, challenge the theory that these cellular compartments, called encapsulins, simply evolved from viruses. Instead, the researchers found evidence that viruses and encapsulins evolved from one another repeatedly over millions of years.
The researchers focused on a group of proteins that adopt a specific three-dimensional structure called the HK97-fold and assemble into protein shells. They are found in both viruses and encapsulins. The newly identified viruses—whose genomes are smaller and simpler than those of other viruses that form HK97-fold protein shells—share features with both viruses and encapsulins, making them a possible missing link between the two that could shed light on how complex biological systems first emerged.
“What makes the HK97-fold proteins so interesting is that they can form shells that enclose biochemical reactions in cellular lineages, archaea, and bacteria. But they also serve genetic purposes in viruses, storing and protecting their viral genome,” said Abelardo Aguilar, the first author and a Ph.D. student in the Department of Biology at the University of Miami College of Arts and Sciences. “These proteins build compartments with two different roles, which connects directly with the study of the origin of life and its early evolution because if you think about it, life at its core is about enclosing reactions and also enclosing information that can be inherited so those reactions can happen in the future.”
To identify these new viruses, Aguilar worked under the supervision of Antoni Luque Santolaria, an associate professor in the Department of Biology who has secondary appointments in the Department of Physics in the College of Arts and Sciences and the Department of Chemical, Environmental and Materials Engineering in the College of Engineering, and the senior author of the study, which included collaborators across different institutions. The team used bioinformatics tools, biophysical models, and AI-based tools, including protein language models and AlphaFold, to mine structural information from databases containing billions of DNA sequences. The sequences in the databases—which included IMG/M, a database affiliated with the U.S. Department of Energy’s Joint Genome Institute and the University of California, Berkeley—come from samples of soil, seawater, wastewater, the human gut, and other environments that were collected around the world.
“The majority of viruses cannot be grown in the lab. But now through sequencing, we have access to information on viruses for which we don’t know the host, that we can’t culture in the lab, but that are everywhere,” Luque explained. “That means there are multiple questions in relation to evolution and how viruses have adapted to the world that it’s now possible to explore bioinformatically.”
The Nature Communications article also outlines the potential molecular mechanism by which viruses and encapsulins may have evolved from one another. This mechanism shows how procapsids, which are immature viral protein shells (capsids), could allow evolutionary transitions and carry both genomic and metabolic roles.
“One implication of this research is the possibility that viral capsids could also facilitate biochemical reactions, which would open up the potential roles that capsids have in environments as a whole,” Aguilar explained.
These findings raise new questions about viruses that Aguilar and Luque said warrant further investigation.
Antoni Luque Santolaria Photo: Jenny Abreu/University of Miami
“When we’re looking at viruses, we tend to look only at the particles that are infective, and this study points out that we might need to start putting more emphasis on the non-infective versions of the virus and what other functions those viral-like particles may have that we have overlooked in the past.”
The research, which was supported by funding from the Gordon and Betty Moore Foundation and the U.S. National Science Foundation, demonstrates the potential of new AI-based bioinformatics tools to explore other unanswered questions about viruses.
“If you have the right question and you pair it with the right tools and physical insights, it gives researchers an opportunity to look at viruses in a way that we didn’t have an opportunity to do before,” Luque said. “There are evolution questions, but there are also questions about emerging pathogens or emerging viruses. The set of tools that we use can be moved forward in different contexts.”
Journal
Nature Communications
Method of Research
Data/statistical analysis
Article Title
Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids
Article Publication Date
14-Oct-2026
