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Researchers Use Machine Learning to Identify Thousands of New Marine RNA Viruses in Study of Interest to Microbiologists and Clinical Laboratory Scientists

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

Ohio State University Scientists Discover Nearly 200,000 Unknown Viruses in Ocean Depths; Could Lead to Biotechnology Breakthroughs

Pole-to-pole sampling of marine life leads researchers to conclude the world’s oceans could hold the key to many scientific and biotechnological advancements

Virologists and microbiologists will be intrigued to learn that scientists at Ohio State University (OSU) have identified nearly 200,000 previously unknown viruses living deep in the oceans. The catalog of 195,728 viruses could serve as a “road map” to a better understanding of ecosystems within the world’s oceans and the role they play in maintaining the health of the planet.

Though the research was not specifically directed at developing useful insights for clinical care, it could one day lead to new diagnostic assays or therapies. For clinical laboratories and anatomic pathology groups, this study demonstrates how understanding and knowledge about viruses and other organisms continue to grow.

The researches published their findings in the journal Cell

Viruses Are Tiny but Important

The OSU researchers led a 24-member team’s effort to expand the catalog of ocean viruses and draw the first global map of viral diversity.

“Viruses tend to steal genes and do really interesting things with them. So, someone who’s savvy in biotechnology can mine this data set to find new enzymes that can help us in our everyday lives, whether that’s cosmetic products or creating a new thermocycler or some sort of engineering process,” Matthew Sullivan, PhD, a microbiologist at OSU and one of the study’s authors, told CNN.

“Viruses are these tiny things that you can’t even see, but because they’re present in such huge numbers, they really matter,” Matthew Sullivan, PhD, a microbiologist at Ohio State University and one of the study’s authors, said in a new release. “We’ve developed a distribution map that is foundational for anyone who wants to study how viruses manipulate the ecosystem. There were many things that surprised us about our findings.” These new discoveries could someday form the basis for new medical laboratory tests and therapeutic drugs. (Photo copyright: Ohio State University.)

According to the news release, “The samples were collected during the unprecedented three-year Tara Oceans Expedition, in which a team of more than 200 experts took to the sea to catalog and better understand the unseen inhabitants of the ocean, from tiny animals to viruses and bacteria.”

“What was really exciting was now being able to study these viruses at two important levels—the population level and by looking at genetic variation within each population, which tells us about evolution,” Ann Gregory, PhD, co-lead author of the study, said in an OSU news release. “We have expanded the number of known viral populations more than tenfold and this new map will help us understand the impact of ocean viruses on a global level,” she added.

A news release from Tara Ocean Foundation notes that prior ocean surveys had identified 16,000 viral species.

Massive Quest for Knowledge

The OSU scientists studied ocean life from varying ocean depths, stretching from pole to pole, using samples collected during the Tara Oceans expeditions, which took place from 2009-2013. The Tara Ocean Foundation has backed 11 scientific expeditions and collected more than 60,000 samples that have been the basis for more than 70 scientific publications.

The team of researchers split the viruses into five ecological zones: all depths of the Arctic and Antarctic and three distinct depths of the Temperate and Tropical regions, noted the OSU study.

By developing new methods to sequence viruses in planktonic populations, the OSU research team, according to the Tara Ocean press release, was able to understand genetic variations:

  • Between individuals within each population;
  • Between populations within each viral community; and
  • Between communities across several environments of the global oceans, as well as study the driving forces behind all these variations.

In its news release, Tara Ocean Foundation pointed out one surprise was the “cradle of viral diversity” found in the Arctic Ocean, which had not been part of earlier studies of ocean life.

“This research has significant implications for understanding how ocean micro-organisms affect the atmosphere,” Sullivan said in the Cell Press news release, which goes on to note that, “The investigators say that having a more complete picture of marine viral distribution and abundance will help them to determine which viruses they should be focusing on for further studies.”

“Previous ocean ecosystem models have commonly ignored microbes, and rarely included viruses, but we now know they are a vital component to include,” said Sullivan.

At this time, the OSU study offers little that clinical laboratories can use other than a deeper awareness of how viruses impact our world and environment. However, further study of the ocean depths may yield surprises that also expand medical knowledge and lead to new therapies and diagnostic tests.

—Andrea Downing Peck

Related Information:

The World’s Oceans Have Nearly 200,000 Viral Species–about 12 Times More than Previously Known

Researchers Detail Marine Viruses from Pole to Pole

Marine DNA Viral Macro- and Micro-Diversity from Pole to Pole

The Arctic Ocean, Cradle of Viral Biodiversity

Pole-to-Pole Study of Ocean Life Identifies 200,000 Marine Viruses