An analysis of the genetic material in the ocean has identified thousands of previously unknown RNA viruses and doubled the number of phyla, or biological groups, of viruses thought to exist, according to one new study published in the journal science by a small team of researchers, Guillermo Dominguez Huertascientific advisor in microbiology, Ahmed Zayedresearcher in microbiology, James Wainainapostdoctoral researcher in microbiology e Matthew Sullivanprofessor of microbiology, all of Ohio State University.
RNA viruses are best known for the diseases they cause in people, ranging from the common cold to COVID-19 – which has brought humanity to its knees over the past two years – but they also infect plants and animals important to people. These viruses carry their genetic information in RNA rather than DNA, which is why RNA viruses evolve at much faster rates than viruses per second.
While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively little studied, and unlike humans and other organisms composed of cells, viruses nevertheless lack short, unique stretches of DNA that they could act like what researchers call a genetic barcodeWithout this barcode, trying to distinguish different virus species in nature can be difficult.
To get around this limitation, the study researchers decided to identify the gene that codes for a particular protein that allows a virus to replicate its own genetic material, and this is the only protein shared by all RNA viruses, because it plays an essential role in how they propagate. However, each RNA virus has small differences in the gene that codes for the protein that can help distinguish one type of virus from another.
Having said that, the researchers then examined a global database of RNA sequences from plankton, collected during the four-year global research project of the Tara Oceans Expeditions, but why the choice of plankton? Plankton are any aquatic organisms that are small to swim against the current, are a vital part of ocean food webs, and are common hosts for RNA viruses. Our screening ultimately identified over 44,000 genes that code for the viral protein.
Our next challenge, therefore, was to determine the evolutionary connections between these genes. The more similar two genes were, the more likely it is that viruses with those genes were closely related. Since these sequences had evolved long ago (perhaps before the first cell), the genetic signals indicating where the new viruses might have separated from a common ancestor had been lost in time. A form of artificial intelligence called machine learning, however, allowed us to systematically organize these sequences and detect differences more objectively than if the task were done manually.
We identified a total of 5,504 new marine RNA viruses and doubled the number of known RNA virus phyla from five to 10. Mapping these new sequences geographically revealed that two of the new phyla were particularly abundant in large ocean regions, with regional preferences in both temperate climates and tropical waters (the Taraviricota, named after the expeditions in the oceans of Tara) or the Arctic Ocean (the Arctiviricota).
We believe Taraviricota may be the missing link in the evolution of RNA viruses that researchers have long sought, linking two different known branches of RNA viruses that diverged in how they replicate.
These new sequences help scientists better understand not only the evolutionary history of RNA viruses, but also the evolution of early life on Earth.
As the COVID-19 pandemic has shown, RNA viruses can cause life-threatening diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide range of organisms, including microbes that affect environments and food webs on a chemical level.
Mapping where in the world these RNA viruses live can help clarify how they affect the organisms that drive many of the ecological processes that run our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.
Despite the identification of so many new RNA viruses, it remains difficult to identify which organisms they infect. Researchers are also currently limited primarily to fragments of incomplete RNA viral genomes, in part due to their genetic complexity and technological limitations.
Our next step would be to understand what types of genes might be missing and how they have changed over time. The discovery of these genes could help scientists better understand how these viruses work.
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