In surveys of Earth’s microbial communities, the boom in newly discovered DNA viruses has expanded to the identification of RNA viruses. Still, compared with that of DNA viruses, the contribution of RNA viruses to global ecosystems is mostly unknown. In a new paper published in Cell, Uri Neri and colleagues perform a metatranscriptomics survey of entire microbial communities using bulk RNA sequencing. They identify previously undetected RNA viruses in a diverse range of habitats, increasing the number of known RNA virus clusters from 13,282 to 124,873. The newly described RNA viruses vary in their distribution across samples and habitats, and include several previously unrecognized bacteriophage-like lineages, suggesting a need to reorganize and add to the current taxonomy of RNA viruses. The researchers studied the diversity of the newly identified RNA viruses by comparing a protein most of them share: RNA-dependent RNA polymerase (RdRP). But the approach of looking at the phylogenetic tree of this ubiquitous protein comes with drawbacks: in some distant branches, RdRP may have heavily divergent sequence motifs, or it might be missed if split over multiple genomic units, leaving potentially large fractions of the RNA virome out of reach. Neri and colleagues also compared their analysis with other large-scale surveys of the RNA virome: those by the Serratus open-science collaboration and the Tara Oceans project. Notably, they found that the fraction of overlapping sequences across the different surveys was low, suggesting that the massive number of newly identified RNA viruses is just a glimpse of the true diversity of the global RNA virome.
Original reference: Cell https://doi.org/10.1016/j.cell.2022.08.023 (2022)
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