Climate change: more than 5,500 new viruses discovered in the ocean

Apart from their roles in human infectious diseases, we know relatively little about RNA viruses in the rest of the world. A better understanding of the diversity and abundance of viruses in the oceans is important to explain the role of microbes in the adaptation of the seas to climate change.

Optimized methods of discovery and classification in RNA sequence data carried out by the organization Tara Oceans have made it possible to duplicate the list of known RNA viruses.

An analysis of genetic material in the ocean has identified thousands of previously unknown RNA viruses and doubled the number of phyls, or biological clusters, of viruses believed to exist, according to a new study that a team of researchers at Ohio University in the United States just published in the journal Science.

The Tara Oceans Consortium is an ongoing global study on the impact of climate change on the world's oceans, aboard the schooner Tara.

RNA viruses are known for the diseases they cause in people, from the common cold to COVID-19. They also infect plants and animals important to humans. These viruses carry their genetic information in RNA, rather than DNA. They evolve at a much faster rate than DNA viruses. While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively little studied.

However, unlike humans and other cell-made organisms, viruses lack unique short stretches of DNA that could act as what researchers call a genetic barcode. Without this barcode, trying to distinguish different species of viruses in nature can be a challenge.

“To get around this limitation,” explained Guillermo Domínguez Huerta, scientific consultant in Microbiology at Ohio University, “we decided to identify the gene that codes for a particular protein that allows a virus to replicate its genetic material. It is the only protein that all RNA viruses share, because it plays an essential role in how they spread. However, each RNA virus has small differences in the gene that encodes the protein that can help distinguish one type of virus from another.”

So they examined a global database of plankton RNA sequences collected during the four-year global research project of the Tara Oceans expeditions.

Plankton gathers any aquatic organism that is too small to swim against the current. They are a vital part of the oceans' food webs and are common hosts of RNA viruses. “Our test eventually identified more than 44,000 genes that encode the virus's protein,” Dominguez Huerta said.

His next challenge, then, was to determine the evolutionary connections between these genes. The more similar two of them were, the more likely it was that viruses with those genes were closely related. Because these sequences had evolved a long time ago (possibly before the first cell), genetic signals indicating where the new viruses might have separated from a common ancestor had been lost over the years.

However, a form of artificial intelligence called machine learning made it possible 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 phylas from five to 10,” the specialist continued. Geographic mapping of these new sequences revealed that two of the new philes were particularly abundant in vast ocean regions, with regional preferences in temperate zones and tropical waters: the “Taraviricota” (named after the Tara Oceans expeditions) or the Arctic Ocean (the Arctiviricota).”

Researchers believe that Taraviricota could be the missing link in the evolution of RNA viruses that science has long sought, connecting two different known branches of RNA viruses that diverge in the way they replicate. These new sequences help to 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 diseases. But they also play a vital role in ecosystems because they can infect a wide range of organisms, including microbes that influence environments and food chains at the 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 make our planet work. These types of viruses are thought to have three main functions: killing cells, changing the way infected cells manage energy, and transferring genes from one host to another.

Despite identifying so many new RNA viruses, it remains a challenge to determine which organisms they infect. Currently, researchers are also mainly limited to fragments of genomes of incomplete RNA viruses, in part because of their genetic complexity and technological limitations.

“Our next steps,” the specialist concluded, “will be to find out what types of genes might be missing and how they changed over time. Discovering them could help scientists better understand how these viruses work.”

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