Unveiling the Viral Dark Matter

A global study uncovers tens of thousands of previously unknown RNA viruses in cities, offering new clues about viral evolution and future public health threats.

Reading time: 5 min

When most people think about viruses, they think about disease. But viruses are everywhere: in oceans, soils, forests, wastewater, and on the surfaces we touch every day. In fact, there are an estimated 10³¹ viruses on the planet, of which only a tiny fraction has been identified.

This vast unknown viral diversity has been dubbed the “viral dark matter”. Thanks to recent advances in sequencing technologies, scientists are beginning to uncover the vast diversity of viruses present in soil, oceans, wildlife and other environments. One particularly fascinating study used samples from African army ants to characterise viral populations in a remote tropical forest in Gabon.  

Another remarkable study, this time focused not on forests but on cities globally, involved Xavier Rodó, ICREA researcher at ISGlobal. The study set out to map the diversity of RNA viruses across urban environments worldwide.

The hidden world of urban viruses

RNA viruses are of particular interest given their high mutation rates, which allow them to adapt quickly to new environments and hosts. Importantly, they account for two thirds of known human pathogens (HIV, influenza viruses, dengue, Ebola and SARS-CoV-2 are only some examples). Yet, few studies have looked at their diversity, especially in urban settings, where 56% of the world population now lives. 

The international MetaSUB consortium tackled this question by examining the diversity of RNA viruses in 102 cities and surrounding environments, across 31 countries. To do so, they analysed 2,922 genetic samples collected between March and July 2020, from a wide variety of urban and peri-urban environments: from handrails, benches or ticket machines in hospitals, banks and public transport stations, to nearby soils, green spaces and wastewater.

Key findings

These are some of the most noteworthy findings:

Thousands of previously unknown RNA viruses

The analysis uncovered 54,945 RNA viruses, 77% of which had not been previously reported. Two dominant classes of RNA viruses were observed across most countries, especially in environments closely associated with human activities. SARS-CoV-2 was also frequently observed, likely due to samples being collected during the pandemic.

Lower viral diversity in urban environments

Another clear finding was that viral diversity is lower in urban samples (streets, banks, subway stations) compared to those from peri-urban or natural environments, including sediment, soil or grasslands. This suggests that urbanization and human activity, whilst leaving a characteristic fingerprint, may “homogenize” viral communities. Wastewater also emerged as a major reservoir of viral populations, confirming its importance for viral monitoring.  But even in cities, the diversity remained huge- the analysis did not reach saturation, meaning that many more viruses likely remain undiscovered.   

New branches on the viral tree

The analysis also revealed evidence for two potentially new viral phyla, or major evolutionary branches, one new class and several previously unclassified groups. The study also found evidence that the emergence of double-stranded RNA genomes in the Duplornaviricote phylum may not have been a unique evolutionary event, as previously thought. Furthermore, by zooming in on a key viral enzyme (RNA-dependent RNA polymerase or RdRp), the researchers found evidence of directional selection, i.e. mutations that may provide the virus with selective advantages. Tracking these molecular signatures can help scientists understand viral evolution and adaptability, detect potentially pandemic strains, and guide vaccination strategies.

Urban viruses mostly infect bacteria

Most RNA viruses uncovered in the study are hosted by bacteria, fungi and plants, contrary to previous homocentric assumptions that RNA viruses mainly infect eukaryotes. In fact, more than half of the viruses for which a host could be identified were bacteriophages. This highlights the important ecological role these organisms play in shaping viral populations in cities and the complex eco-evolutionary dynamics that have shaped these relationships over time. Still, the researchers found over 100 viruses capable of infecting vertebrates, including families that contain well-known human pathogens such as rhinoviruses, polioviruses and enteroviruses. They also identified 166 RNA viruses associated with four major antibiotic-resistant bacteria known as ESKAPE pathogens: Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. These viruses could eventually open the door to virus-based therapies against antibiotic-resistant bacteria. In addition, the team uncovered viruses capable of infecting human gut bacteria such as Clostridia and Bacteroidia, two major components of our microbiota.

Socioeconomic factors may influence viral abundance

By correlating viral diversity with World Development Indicators, the study also found that urban areas in less developed countries tended to show a higher burden of vertebrate-associated viruses than those in more developed settings. For example, hospital samples from Islamabad and São Paulo showed higher viral abundance than those from Baltimore and Seoul.  

A call for viral discovery and monitoring

True, as the researchers caution, the study has important limitations. For example, sampling was uneven across countries and environments, making it difficult to determine whether observed differences reflect geography or simply differences in what was sampled (e.g. public transport stations in Poland versus greenhouses in France). Much more work lies ahead to investigate in full host-virus associations and the role this viral dark matter has in ecosystems and in human health.

Studies like this one will help improve our understanding of viral hosts and evolution, strengthen environmental surveillance, and support preparedness for future outbreaks.

Even so, the study is one of the most ambitious efforts to date to map the hidden world of RNA viruses in human-associated environments and sets a new standard for viral discovery by developing a robust pipeline for viral discovery, host prediction and phylogenetic analysis. It also provides one of the most comprehensive catalogues of environmental RNA viruses assembled to date (named UPVAtlas), providing a valuable resource for future research. Studies like this one will help improve our understanding of viral hosts and evolution, strengthen environmental surveillance, and support preparedness for future outbreaks.