Ocean RNA study doubles virus phyla

Ahmed Zayed and co-authors reported in Science on April 8, 2022 that a global survey of ocean RNA sequences identified 5,504 previously unknown marine RNA viruses and doubled the number of recognized RNA virus phyla from five to ten. The study drew on about 28 terabases of Global Ocean RNA sequences collected during the Tara Oceans expeditions, according to the paper summary and an AAAS release. The authors said the added diversity included groups that help fill gaps in the deep evolutionary tree of RNA viruses. ### Why are researchers talking about “doubling” virus phyla? The Science paper said the new sequences required “substantive revisions” to RNA virus taxonomy, including an increase in orthornaviran phyla from five to ten. In virus classification, a phylum is a high-level grouping, so the change was not a matter of adding a few species to an existing bucket. It altered the top-level map researchers use to organize RNA virus diversity. (eurekalert.org) The 5,504 viruses were found by screening ocean RNA datasets for genes encoding RNA-dependent RNA polymerase, or RdRp, an enzyme shared across RNA viruses and used as a marker for evolutionary relationships. The researchers then used computational methods to cluster and compare those sequences and place them on a phylogenetic tree. ### What exactly was sampled in the ocean? (eurekalert.org) The underlying material was not a set of clinical samples but a global database of RNA sequences from marine plankton collected across worldwide ocean surveys. Ohio State University, which highlighted the work in an institutional release, said the samples came from ocean water collected around the world. The AAAS release said the analysis spanned waters “from pole to pole.” (gavi.org) The Tara Oceans expeditions supplied the core dataset. The paper summary said the survey used nearly 28 terabases of Global Ocean RNA sequences, a scale that let the team search far beyond the small set of RNA viruses previously described from marine environments. ### Where does the “missing link” claim come from? AAAS said one of the newly described phyla, Taraviricota, appeared to represent a missing link in the evolutionary origins of RNA viruses with regard to retroelements. (news.osu.edu) The release said the finding suggested a common ancestor between Taraviricota and retroelements. Gavi’s summary of the paper said researchers viewed Taraviricota as a possible bridge between two known RNA virus branches that diverged in how they replicate. (eurekalert.org) The study also mapped the geographic distribution of the new phyla. Gavi said Taraviricota was abundant across temperate and tropical waters, while another newly described phylum, Arctiviricota, was abundant in the Arctic Ocean. ### Why did ocean data matter here? RNA viruses are widely known because of diseases in people, plants and animals, but the paper and accompanying releases said environmental RNA viruses have been much less studied than DNA viruses. (eurekalert.org) That left a large blind spot in marine ecology, where viruses can shape microbial communities and nutrient cycling. Jessica Labonté and Kathryn Campbell wrote in a related Science Perspective, cited in the AAAS release, that studies like this one create links between viral and cellular worlds and could support a more complete tree of life. (gavi.org) The authors of the main paper also said it remains difficult to determine exactly which organisms many of these newly identified viruses infect. ### What comes next for this line of research? The next step is host identification and deeper genomic characterization. (eurekalert.org) Gavi’s summary said the researchers regarded it as challenging to pinpoint which organisms these viruses infect, even after finding thousands of new sequences. That leaves follow-up work on matching viral genomes to marine hosts and refining the taxonomy built from these ocean datasets. The paper remains available in Science under the title “Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome,” with Ahmed Zayed listed as lead author in database and institutional records tied to the April 8, 2022 publication. (eurekalert.org) (gavi.org)