Over 5,500 new viruses identified in the ocean – including a missing link in viral evolution

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Researchers have discovered that there are even more types of viruses in the ocean than previously thought.

An analysis of the genetic material in the ocean has identified thousands of previously unknown people RNA Viruses and doubled the number of phyla, or biological groups, of viruses thought to exist, according to a new study our team from researcher has published in the magazine Science.

RNA viruses are best known for the Diseases they cause in people ranging from the common cold to COVID-19. They also infect Plant and Animals important to people.

These viruses carry their genetic information in RNA instead DNS. RNA viruses develop much faster as DNA viruses. While scientists have catalogued Hundreds of thousands of DNA viruses In their natural ecosystems, RNA viruses are relatively unexplored.

RNA Viruses in Oceans

There are more RNA viruses in the oceans than previously thought. Photo credit: Guillermo Domínguez Huerta, CC BY-ND

Unlike humans and other cell-based organisms, viruses lack unique short stretches of DNA that could function as a genetic barcode, according to the researchers. Attempting to distinguish between different virus species in the wild without this barcode can be difficult.

We decided to find the gene that codes for a specific protein which allows a virus to replicate its genetic material to circumvent this limitation. It is the only protein that all RNA viruses have in common, as it plays an essential role in their replication. However, each RNA virus has small differences in the gene that codes for the protein that scientists can use to help distinguish one type of virus from another.

So we searched a global database of plankton RNA sequences collected over the four years Expeditions of the Tara Oceans global research project. Plankton are all aquatic organisms that are too small to swim against the current. They are an important part of the ocean food webs and frequent hosts for RNA viruses. Our screening eventually identified over 44,000 genes that code for the viral protein.

Organized diagram of five previously known phyla of RNA viruses

This diagram shows the five previously known phyla of RNA viruses automatically organized by our methods. Reprinted with permission from Zayed et al., Science Volume 376:156 (2022).

So our next challenge was to determine the evolutionary links between these genes. The more similar two genes were, the more likely viruses were closely related to those genes. Since these sequences had evolved so long ago (possibly before the first cell), the genetic guides that indicated where new viruses might have split from a common ancestor had been lost over time. However, a form of artificial intelligence called machine learning allowed us to organize these sequences in a systematic way and spot 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 strains from five to ten. Geographical mapping of these new sequences revealed that two of the new strains were particularly abundant in large oceanic regions, with regional preferences in both temperate and tropical waters (the Taraviricotanamed after the Tara Oceans Expeditions) or the Arctic Ocean (the arctiviricota).

we believe that Taraviricota may be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two distinct known branches of RNA viruses that differ in their replication.

Spread of RNA viruses across the ocean

This map shows the distribution of RNA viruses across the ocean. Wedge size is proportional to the average frequency of viruses present in that area and wedge color indicates virus strains. Source: Reprinted with permission from Zayed et al., Science Volume 376:156 (2022)

Why it matters

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 deadly diseases. But RNA viruses also play a role important role in ecosystems because they can infect a wide range of organisms, including microbes affect the environment and food webs at the chemical level.

Mapping where in the world these RNA viruses live can help clarify how they affect the organisms that power many of the ecological processes that govern our planet. Our study also provides improved tools that can help researchers catalog new viruses as genetic databases grow.


Viruses can cause more than just disease.

What is not yet known

Although so many new RNA viruses have been identified, it remains difficult to determine which organisms they infect. Researchers are also present limited to mostly fragments of incomplete RNA virus genomes, in part due to their genetic complexity and technological limitations.

Our next steps would be to find out 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.

Written by:

  • Guillermo Dominguez Huerta – Scientific Advisor in Microbiology, The Ohio State University
  • Ahmed Zayed – Research Scientist in Microbiology, The Ohio State University
  • James Wainaina – Postdoctoral Research Associate in Microbiology, The Ohio State University
  • Matthew Sullivan – Professor of Microbiology at Ohio State University

This article first appeared in The conversation.The conversation

For more information on this research, see 5,500 New RNA Virus Species Discovered in the Ocean.

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