Not only pandemic pathogens: The diversity of RNA viruses is far greater than previously thought, as revealed by the detection of thousands of previously unknown viruses in the ocean. They add five new strains and eleven classes to the family tree of RNA viruses, doubling the number of RNA virus strains. A new branch of these viruses might also prove to be a crucial link in virus evolution, as the researchers report in Science.
viruses are the oldest and most numerous beings on our planet. They are found almost everywhere and are perfectly adapted to reproduce in almost all forms of life. Alone in our body cavort billion this cell parasite. But so far only a tiny fraction of the total variety of viruses is known. Attempts to catalog the virosphere and their family tree to reconstruct are incomplete and incomplete.
Manhunt for viral RNA
This applies in particular to the RNA viruses – the group of viruses to which the Coronavirus SARS-CoV-2 and the causative agents of diseases such as Ebola, measles, mumps or hepatitis D. They are considered to be particularly original and, according to some theories, might even have existed before the first DNA-bearing cells. “RNA viruses are important to our world, but we mostly study only a tiny fraction of them: the few hundred species that infect humans, animals and plants,” explains lead author Matthew Sullivan from Ohio State University.
That’s why Sullivan and his colleagues conducted a large-scale virus hunt in one of the habitats that has so far hardly been examined for RNA viruses: the ocean. For their study, they analyzed the genetic data of more than 35,000 water samples from all of the world’s oceans that had been collected and sequenced as part of the Tara expedition. In order to recognize the RNA viruses, the researchers looked for a gene, RdRp, which is only found in these viruses and therefore represents a type of recognition signature.
In order to then assign the RdRp signatures to individual RNA virus types, the team developed a computer-aided, complex evaluation and comparison process. This helped them to catalog the approximately 44,000 RdRp-containing RNA sequences discovered in the water samples.
New Tribes, Classes and Species
The result revealed a huge number of previously completely unknown RNA viruses. “Almost every species we found was new,” says Sullivan. Some of these around 5,500 new species might be assigned to the already known five strains and 20 classes of RNA viruses. “But even among these viruses of known taxons identified in the ocean, 99.7 percent are new species,” the researchers report.
However, other RNA viruses might not be assigned to any of the known large groups – they represent five completely new strains, for which the team proposes the names Taraviricota, Pomiviricota, Paraxenoviricota, Wamoviricota and Arctiviricota. This means that the number of strains in the RNA virus family tree has doubled in one fell swoop. At least eleven new virus classes are added on the level below. The official family tree of the RNA viruses must now be extended accordingly. “The results thus change our ideas regarding the evolution and diversity of RNA viruses,” say Sullivan and his team.
The new finds also confirm that RNA viruses primarily use eukaryotic organisms as hosts – and thus higher organisms such as plants, animals and humans. Accordingly, four of the five new RNA virus strains and eight of the eleven new classes consist of such cell parasites that specialize in eukaryotes; only a small minority also infects prokaryotes such as bacteria.
Missing link in the family tree of life
One of the newly identified RNA virus strains might even shed new light on the evolution and emergence of viruses. Because the genome of the Taraviricota – a group of viruses found in all samples and oceans – proved to be particularly original. According to the researchers, the RdRp sequences of this virus strain indicate that the Taraviricota might be among the very first representatives of the Orthornaviruses – the RNA viruses in the narrower sense.
“Our analyzes suggest with high probability that the viruses of this newly proposed strain represent a missing link between retroelements and the orthonaviruses,” write Sullivan and his colleagues. Retroelements are gene sections that are also found in the DNA of all living beings and that can change their position and multiply using special mechanisms. They have therefore long been suspected of being relics of viral genomes that were integrated into the DNA at some point in the course of evolution.
“Studies like these uncover connections between the viral and cellular worlds,” write Jessica Labonté and Kathryn Campbell of Texas A&M University in an accompanying comment. “They open up the possibility of constructing a comprehensive family tree of life and understanding the origins and evolution of all life forms.” (Science, 2022; doi: 10.1126/science.abm5847)
Those: Ohio State University
