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Working from 35,000 worldwide water and plankton samples collected by the Tara Oceans Expeditions and sequenced by Genoscope (CEA-Jacob), an international team of researchers has identified 5,500 new RNA virus species and met the challenge of their phylogenetic classification. The team's work was published 7 April 2022 in Science.
DNA viruses are known to be abundant, diverse and important in a range of ecosystems. Conversely, RNA viruses have not been sufficiently studied outside of the setting of disease. To help address this dearth of knowledge, researchers from Genoscope and the Ohio State University's Department of Microbiology (USA) set their sights on analyzing sequences derived from 35,000 ocean-water and plankton samples collected from across the globe by the Tara Ocean consortium for its ongoing international study on the impact of climate change on the world's oceans.
The researchers looked at the gene sequences in those samples and systematically analyzed all RNA sequences carrying the code for viral RNA-directed RNA polymerase (RdRp), an enzyme that is obligatory for all RNA viruses but absent from other viruses and cells. RdRp is a very ancient enzyme. Its sequence has evolved and its position diverged numerous times over the eons. To take that multifold evolution into account and manage the billions of years of sequence divergence, the team used machine learning to align sequences based on conventional phylogenetic trees then validated the results via a precise classification of already-identified RNA virus sequences. This reproducible method ensured that the alignment of positions and sequences provided a reliable reflection of evolution.
That organization of 44,000 new sequences enabled the identification of 5,500 previously unknown viruses, only some of which belonged to the five existing phlya in the Orthornavirae kingdom, which groups mainly the pathogenic RNA viruses. To place the novel species phylogenetically, at least five additional phlya and 11 additional classes will be needed. A proposition for officialization is to be made to the International Committee on Taxonomy of Viruses. The team showed that the greatest abundancies of the newly-discovered species would fall within two of the novel phyla propositions, and particularly within one named Taraviricota, to honor the Tara Ocean Consortium.
The Genoscope researchers were able to trace the provenance of those two novel phyla and show that they are widespread across the planet's oceans and particularly in the Artic Ocean, where climate change is causing the largest effects.
According to the researchers, improved knowledge on viral diversity and abundance in the oceans will help explain the role of marine microbes in the adaptation of these bodies of water to climate change. The oceans absorb half of the atmosphere's carbon dioxide, and previous studies have suggested that marine viruses are the "handle" on a biological pump that affects carbon sequestration in the oceans. This Franco-American study thus furnishes fundamental knowledge that will be essential for the integration of RNA viruses in ecological and epidemiological models.
Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome I Science
CEA is a French government-funded technological research organisation in four main areas: low-carbon energies, defense and security, information technologies and health technologies. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world.