Screening and analysis of ocean samples also identified a possible missing link in how the RNA viruses evolved

An international team of scientists has used genetic screening and machine learning techniques to identify more than 5,500 previously unknown species of marine RNA viruses and is proposing five new phyla (biological groups) of viruses. The latter would double the number of RNA virus phyla to 10, one of which may be a missing link in the early evolution of the microbes.

Though the newly-discovered viruses are not currently associated with human disease—and therefore do not drive any current medical laboratory testing—for virologists and other microbiologists, “a fuller catalog of these organisms is now available to advance scientific understanding of how viruses evolve,” said Dark Daily Editor-in-Chief Robert Michel.

“While scientists have cataloged hundreds of thousands of DNA viruses in their natural ecosystems, RNA viruses have been relatively unstudied,” wrote four microbiologists from Ohio State University (OSU) who participated in the study in an article they penned for The Conversation.

The OSU study authors included:

Zayed was lead author of the study and Sullivan led the OSU research team.

The researchers published their findings in the journal Science, titled, “Cryptic and Abundant Marine Viruses at the Evolutionary Origins of Earth’s RNA Virome.”

Matthew Sullivan, PhD
“RNA viruses are clearly important in our world, but we usually only study a tiny slice of them—the few hundred that harm humans, plants and animals,” explained Matthew Sullivan, PhD (above), Director, Center of Microbiome Science, in an OSU news story. Sullivan led the OSU research team. “We wanted to systematically study them on a very big scale and explore an environment no one had looked at deeply, and we got lucky because virtually every species was new, and many were really new,” he added. (Photo copyright: University of Ohio.)

RNA versus DNA Viruses

In contrast to the better-understood DNA virus, an RNA virus contains RNA instead of DNA as its genetic material, according to Samanthi Udayangani, PhD, in an article she penned for Difference Between. Examples of RNA viruses include:

One major difference, she explains, is that RNA viruses mutate at a higher rate than do DNA viruses.

The OSU scientists identified the new species by analyzing a database of RNA sequences from plankton collected during a series of ocean expeditions aboard a French schooner owned by the Tara Ocean Foundation.

“Plankton are any aquatic organisms that are too small to swim against the current,” the authors explained in The Conversation. “They’re a vital part of ocean food webs and are common hosts for RNA viruses.”

The team’s screening process focused on the RNA-dependent RNA polymerase (RdRp) gene, “which has evolved for billions of years in RNA viruses, and is absent from other viruses or cells,” according to the OSU news story.

“RdRp is supposed to be one of the most ancient genes—it existed before there was a need for DNA,” Zayed said.

The RdRp gene “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 propagate themselves. Each RNA virus, however, has small differences in the gene that codes for the protein that can help distinguish one type of virus from another,” the study authors explained.

The screening “ultimately identified over 44,000 genes that code for the virus protein,” they wrote.

Identifying Five New Phyla

The researchers then turned to machine learning to organize the sequences and identify their evolutionary connections based on similarities in the RdRp genes.

“The more similar two genes were, the more likely viruses with those genes were closely related,” they wrote.

The technique classified many of the sequences within the five previously known phyla of RNA viruses:

But the researchers also identified five new phyla—including two dubbed “Taraviricota” and “Arctiviricota”—that “were particularly abundant across vast oceanic regions,” they wrote. Taraviricota is named after the Tara expeditions and Arctiviricota gets its name from the Arctic Ocean.

They speculated that Taraviricota “might be the missing link in the evolution of RNA viruses that researchers have long sought, connecting two different known branches of RNA viruses that diverged in how they replicate.”

In addition to the five new phyla, the researchers are proposing at least 11 new classes of RNA viruses, according to the OSU story. The scientists plan to issue a formal proposal to the International Committee on Taxonomy of Viruses (ICTV), the body responsible for classification and naming of viruses. 

Studying RNA Viruses Outside of Disease Environments

“As the COVID-19 pandemic has shown, RNA viruses can cause deadly diseases. But RNA viruses also play a vital role in ecosystems because they can infect a wide array of organisms, including microbes that influence environments and food webs at the chemical level,” wrote the four study authors in The Conversation. “Mapping out where in the world these RNA viruses live can help clarify how they affect the organisms driving 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.”

This remarkable study, which was partially funded by the US National Science Foundation, will be most intriguing to virologists and microbiologists. However, clinical laboratories also should be interested in the fact that the catalog of known viruses has just expanded by 5,500 types of RNA viruses.

Stephen Beale

Related Information:

Researchers Identified Over 5,500 New Viruses in the Ocean, Including a Missing Link in Viral Evolution

Cryptic and Abundant Marine Viruses at the Evolutionary Origins of Earth’s RNA Virome

There’s More to RNA Viruses than Diseases

Differences Between DNA and RNA Viruses

Ocean Water Samples Yield Treasure Trove of RNA Virus Data

Global Survey of Marine RNA Viruses Sheds Light on Origins and Abundance of Earth’s RNA Virome

Scientists Find Trove of over 5,000 New Viruses Hidden in Oceans

Virologists Identify More than 5,000 New Viruses in the Ocean

;