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.
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.
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
Sullivan, PhD, a microbiologist at OSU and one of the study’s authors, told
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;
Between communities across several environments
of the global oceans, as well as study the driving forces behind all these
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