Seawater samples provide treasure trove of RNA virus data

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Seawater samples collected around the world have provided a treasure trove of new data on RNA viruses, expanding the possibilities for ecological research and reshaping our understanding of the evolution of these small but important submicroscopic particles.

By combining machine learning analyzes with traditional evolutionary trees, an international team of researchers has identified 5,500 new RNA virus species that represent the five known RNA virus phyla and suggest that there are at least five new phyla of RNA viruses needed to capture them.

The most abundant collection of newly identified species belongs to a phylum proposed by researchers named Taraviricotaa nod to the source of the 35,000 water samples that allowed the analysis: the Tara Oceans Consortium, a global study underway aboard the schooner Tara of the impact of climate change on the world’s oceans.

“There are so many new diversities here – and a whole phylum, the Taraviricota, have been found all over the oceans, suggesting they are ecologically important,” said lead author Matthew Sullivan, professor of microbiology at Ohio State University.

“RNA viruses are clearly important in our world, but we usually only study a tiny fraction of them – the few hundred that harm humans, plants and animals. We wanted to systematically study them on a very large scale and explore an environment that no one had examined in depth, and we were lucky because virtually all the species were new, and many were really new.

The study appears online today (April 7, 2022) in Science.

While microbes are essential contributors to all life on the planet, the viruses that infect or interact with them have various influences on microbial functions. These types of viruses are thought to have three main functions: killing cells, changing the way infected cells handle energy, and transferring genes from one host to another.

Learning more about the diversity and abundance of viruses in the world’s oceans will help explain the role of marine microbes in ocean adaptation to climate change, the researchers say. The oceans absorb half of the human-generated carbon dioxide in the atmosphere, and previous research from this group has suggested that marine viruses are the “knob” on a biological pump affecting the way carbon in the ocean is stored.

Ahmad Zayed

In taking on the challenge of classifying RNA viruses, the team entered waters still choppy from previous taxonomic categorization efforts that focused primarily on RNA viral pathogens. Within the biological kingdom Orthorshipsfive phyla were recently recognized by the International Committee on Taxonomy of Viruses (ICTV).

Although the research team identified hundreds of new RNA virus species that fit into these existing divisions, their analysis identified thousands of other species which they grouped into five proposed new phyla: Taraviricota, Pomiviricota, Paraxenoviricota, Wamoviricota and arcticiviricota, who, like Taraviricotaexhibits very abundant species – at least in the climate-critical waters of the Arctic Ocean, the region of the world where warming conditions are wreaking the most havoc.

Sullivan’s team has long cataloged DNA virus species in the oceans, increasing their numbers from a few thousand in 2015 and 2016 to 200,000 in 2019. For these studies, the scientists had access to virus particles to complete the analysis.

In these current efforts to detect RNA viruses, there were no virus particles to study. Instead, the researchers extracted sequences of genes expressed in organisms floating in the sea and narrowed the analysis to RNA sequences containing a signature gene, called RdRp, which evolved over billions of years in RNA viruses and is absent from other viruses or cells. .

The schooner Tara is a floating laboratory allowing the collection of samples around the world which are cataloged to better understand the invisible inhabitants of the ocean, from small animals to viruses and bacteria.  Copyright Maeva Bardy - Tara Ocean Foundation

Because RdRp’s existence dates back to when life was first detected on Earth, its sequence position diverged several times, meaning that traditional phylogenetic tree relationships were impossible to describe with sequences alone. . Instead, the team used machine learning to organize 44,000 new sequences in a way that could handle those billions of years of sequence divergence, and validated the method by showing that the technique could classify with precisely the sequences of RNA viruses already identified.

“We had to compare the known to study the unknown,” said Sullivan, also a professor of civil, environmental and geodetic engineering, founding director of the Center of Microbiome Science at Ohio State and a member of the management team of the EMERGE Biology Integration Institute.

“We’ve created a computationally reproducible way to align these sequences where we can be more confident that we’re aligning positions that accurately reflect evolution.”

Further analysis using 3D representations of structures and sequence alignment revealed that the group of 5,500 new species did not match the existing five phyla of RNA viruses classified in the Orthorships Kingdom.

“We compared our clusters to established and recognized taxa based on phylogeny, and that’s how we found that we had more clusters than existed,” said co-first author Ahmed Zayed, researcher in microbiology at Ohio State and research manager. at the EMERGE Institute.

Altogether, the results led the researchers to propose not only the five new phyla, but also at least 11 new orthornaviran classes of RNA viruses. The team is preparing a proposal to request the formalization of candidate phyla and classes by the ICTV.

Zayed said the breadth of new data on RdRp gene divergence over time leads to a better understanding of how early life may have evolved on the planet.

“RdRp is believed to be one of the oldest genes – it existed before there was a need for DNA,” he said. “So we’re not just tracing the origins of viruses, but also the origins of life.”

This research was supported by the National Science Foundation, Gordon and Betty Moore Foundation, Ohio Supercomputer Center, Ohio State’s Center of Microbiome Science, EMERGE Biology Integration Institute, Ramon-Areces Foundation, and Laulima Government Solutions/ NIAID. The work was also made possible by the unprecedented sampling and science of the Tara Oceans Consortium, the non-profit Tara Ocean Foundation and its partners.

Additional co-authors on the paper were co-lead authors James Wainaina and Guillermo Dominguez-Huerta, as well as Jiarong Guo, Mohamed Mohssen, Funing Tian, ​​Adjie Pratama, Ben Bolduc, Olivier Zablocki, Dylan Cronin, and Lindsay Solden , all of Sullivan. laboratory; Ralf Bundschuh, Kurt Fredrick, Laura Kubatko, and Elan Shatoff of Ohio State College of Arts and Sciences; Hans-Joachim Ruscheweyh, Guillem Salazar and Shinichi Sunagawa from the Institute of Microbiology and the Swiss Institute of Bioinformatics; Jens Kuhn of the National Institute of Allergy and Infectious Diseases; Alexander Culley of the Universitystar Laval; Erwan Delage and Samuel Chaffron from the Universitystar from Nantes; and Eric Pelletier, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain and Patrick Wincker from Genoscope.

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