A groundbreaking Tel Aviv University study has discovered about 100,000 new types of previously unknown viruses – a ninefold increase in the number of RNA viruses known to science until now. These viruses were discovered in global environmental data from soil samples, oceans, lakes, and other ecosystems. This discovery may aid in the development of anti-microbial drugs and protect against agriculturally harmful fungi and parasites.

Study: Expansion of the global RNA virome reveals diverse clades of bacteriophages. Image Credit: Golden Wind / Shutterstock

Doctoral student Uri Neri led the study under the guidance of Prof. Uri Gophna of the Shmunis School of Biomedicine and Cancer Research in the Wise Faculty of Life Sciences at Tel Aviv University. The research was conducted in collaboration with the US-based research bodies NIH and JGI, as well as the Pasteur Institute in France. The study was published in the prestigious journal Cell and comprised data collected by more than a hundred scientists worldwide.

Viruses are genetic parasites, meaning they must infect a living cell to replicate their genetic information, produce new viruses, and complete their infection cycle. Some viruses are disease-causing agents that can cause harm to humans (such as the coronavirus). Still, the vast majority of viruses do not harm us and infect bacterial cells – some even live inside our bodies without us being aware.

Uri Neri says that the study used new computational technologies to mine genetic information from thousands of different sampling points worldwide (oceans, soil, sewage, geysers, etc.). The researchers developed a sophisticated computational tool that distinguished between the genetic material of RNA viruses and that of the hosts and used it to analyze the big data. The discovery allowed the researchers to reconstruct how the viruses underwent diverse acclimation processes throughout their evolutionary development to adapt to different hosts.

In analyzing their findings, the researchers identified viruses suspected of infecting various pathogenic microorganisms, thus opening up the possibility of using viruses to control them.

“The system we developed makes it possible to perform in-depth evolutionary analyses and to understand how the various RNA viruses have developed throughout evolutionary history. One of the key questions in microbiology is how and why viruses transfer genes between them. We identified a number of cases in which such gene exchanges enabled viruses to infect new organisms. Furthermore, compared to DNA viruses, the diversity and roles of RNA viruses in microbial ecosystems are not well understood. In our study, we found that RNA viruses are not unusual in the evolutionary landscape and, in fact, that in some aspects, they are not that different from DNA viruses. This opens the door for future research and a better understanding of how viruses can be harnessed for use in medicine and agriculture,” said Prof. Gophna

Overall, the results show a large expansion of the diversity of Orthornavira, especially that of RNA viruses associated with bacteria. In addition, they introduce relatively minor changes to the latest taxonomic scheme, supporting its overall robustness. Furthermore, RNA viruses are predicted to have multiple protein functions. This work generated a large number of sequences and derivatives, which can be accessed through the companion website (riboviria.org) or via the Zenodo deposit. Using this resource, researchers can gain meaningful context when describing new RNA viruses in future research. For example, by gaining insights into specific viral lineages’ ecological distributions or annotating their specific protein domains. Further, this resource may assist researchers in identifying key RNA virus genomes that can be further characterized experimentally.