Analysis of genetic material in the oceans has identified thousands of previously unknown RNA viruses and doubled the number of phyla, or biological groups of viruses thought to exist.
According to a new study published by a research team in the journal Science, RNA (ribonucleic acid) viruses are the viruses best known for the illnesses they cause in humans, from the common cold to COVID-19. They also infect plants and animals that are important to humans.
These viruses carry their genetic information in RNA, not DNA. RNA viruses develop at a much faster rate than DNA viruses. While hundreds of thousands of DNA viruses in their natural ecosystems have been cataloged by scientists, RNA viruses are relatively unstudied.
However, unlike humans and other organisms made up of cells, viruses do not have a unique short DNA that can act as what researchers call a genetic barcode. Without these barcodes, trying to differentiate between different viral species in the wild can be challenging.
Quoted from Science Alert, Friday (4/8/2022) to overcome this limitation, they decided to identify the gene that codes for a particular protein that allows the virus to replicate its genetic material.
It is the only protein shared by all RNA viruses, as it plays an important role in how they propagate themselves. Each RNA virus, however, has small differences in the genes that code for proteins that can help distinguish one type of virus from another.
So researchers sifted through a global database of planktonic RNA sequences collected during the four-year Tara Oceans global research project. Plankton are aquatic organisms that are small enough to swim against the current.
"They are an important part of marine food webs and are common hosts for RNA viruses. Our screening eventually identified more than 44,000 genes encoding viral proteins," the researchers said.
Their next challenge was to determine the evolutionary relationship between these genes. The more similar the two genes, the more likely the viruses with those genes are closely related.
Because this sequence has evolved for so long (perhaps predating the first cell), genetic cues indicating where a new virus may have split off from a common ancestor have been lost over time.
A form of artificial intelligence called machine learning, however, allows them to systematically organize this sequence and detect differences more objectively than if the task was 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," the researchers said.
Mapping of this new sequence geographically revealed that two of the new phyla were highly abundant over large oceanic regions, with regional preferences in either temperate and tropical waters (Taraviricota, named after the Tara Oceans expedition) or the Arctic Ocean (Arctiviricota).
"We believe that the Taraviricota may be the missing link in the evolution of RNA viruses that researchers have long sought, linking two distinct branches of RNA viruses that differ in the way they replicate."
They say this finding is important because the new sequence helps 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 deadly disease. But RNA viruses also play an important role in ecosystems because they can infect a wide variety of organisms, including microbes that affect the environment and food webs on a chemical level.