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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

May 27, 2022 | Digital Pathology, Laboratory News, Laboratory Pathology, Molecular Diagnostics, Genetic Testing, Whole Gene Sequencing

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

$5 Million Federal Grant Funds Clinical Laboratory Scientist Training at San Jose State University

Oct 21, 2011 | Laboratory Hiring & Human Resources, Laboratory News, Laboratory Pathology

Local hospitals and biotech companies team up with San Jose State University to train more clinical laboratory scientists

Everyone is aware of the shortage of medical technologists (MT) and clinical laboratory scientists that plagues clinical laboratories in almost every region of the United States. It is widely-recognized that current training programs for MTs and CLSs fall short of providing adequate numbers of new workers to meet the demand by medical laboratories.

But it’s a different story in San Jose, California. That’s because San Jose State University (SJS) snagged a $5 million federal grant to fund its Clinical Laboratory Scientist (CLS) Training Program and similar work training programs for healthcare professionals.

(more…)

Biomedical and Molecular Diagnostics Firms Compete To Hire Already-Scarce Medical Laboratory Technologists

Sep 14, 2011 | Laboratory Hiring & Human Resources, Laboratory News, Laboratory Pathology

In Silicon Valley, biotech and molecular companies “raid” hospital laboratories to hire away MTs and CLSs

Competition for already hard-to-find medical technologists (MT) and clinical laboratory scientists (CLS) is heating up as biomedical and molecular development companies vie with hospitals and medical laboratories for these highly-prized workers. Growth in demand for MTs and CLSs by biotech companies means that clinical laboratories will face stiff competition when recruiting and hiring for these positions.

This competition for hiring MTs and CLSs was recently the topic of a story in the San Francisco Business Times (SFBT). Molecular development companies in the Bay Area want to hire qualified clinical laboratory professionals. The demand pressure from this emerging sector is driving up wages and further stressing the capacity of underfunded job-training programs, according to the article. (more…)

50 Years of Service in Clinical Laboratories Celebrating the Careers of Two Medical Technologists

Aug 31, 2011 | Laboratory Hiring & Human Resources, Laboratory News, Laboratory Pathology

In Connecticut and California, there are two medical technologists who have each put in 50 years on the job in their respective hospital laboratories

On opposite coasts of the United States, two medical technologists (MT) were each recognized by local newspapers for more than 50 years of service in clinical laboratories in their respective communities! As members of what is often called the “Greatest Generation”, these two long-serving med techs have much to teach the three younger generations now working in the nation’s medical laboratories.

For the last 51 years, Sandra Allard has worked in the laboratory at Waterbury Hospital, in Waterbury, Connecticut. The 69-year-old typically works in the blood bank, but pulls one night a week in chemistry, according to an article published by the Republican-American, a newspaper in Waterbury. Jeffrey Pinco, M.D., the Medical Director of the hospital laboratory, described Allard as an employee who cares about the hospital’s patients and brings old-fashioned values to her job. (more…)

In Alberta, Clinical Laboratories Adapt to One Integrated Province-Wide Health Services Administration Model

Jul 20, 2011 | Laboratory Management and Operations, Laboratory News, Laboratory Pathology

Pathologists and medical lab managers regularly challenged to provide high-quality cost-effective services with limited resources.

DATELINE: EDMONTON, ALBERTA, CANADA—Over the past decade and a half, this economically-prosperous province has re-aligned its healthcare regional bodies more than once in an effort to control costs while supporting clinical services that meet the expectations of its patients. In some cases, these realignments have subjected Alberta’s clinical laboratories to deep changes in their reporting structure and operational make-up.

Your Dark Daily editor was in Edmonton last week and had the opportunity to visit the Department of Laboratory Medicine and Pathology at the University of Alberta Hospital (UAH). The laboratory facility encompasses four different floors of one wing of the over 800 bed facility. It is the location of one of the two Provincial Laboratories for Public Health in Alberta and includes UAH’s Division of Medical Microbiology.

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