Meta-transcriptomics and the evolutionary biology of RNA viruses

Abstract

Metagenomics is transforming the study of virus evolution, allowing the full assemblage of virus genomes within a host sample to be determined rapidly and cheaply. The genomic analysis of complete transcriptomes, so-called meta-transcriptomics, is providing a particularly rich source of data on the global diversity of RNA viruses and their evolutionary history. Herein we review some of the insights that meta-transcriptomics has provided on the fundamental patterns and processes of virus evolution, with a focus on the recent discovery of a multitude of novel invertebrate viruses. In particular, meta-transcriptomics shows that the RNA virus world is more fluid than previously realized, with relatively frequent changes in genome length and structure. As well as having a transformative impact on studies of virus evolution, meta-transcriptomics presents major new challenges for virus classification, with the greater sampling of host taxa now filling many of the gaps on virus phylogenies that were previously used to define taxonomic groups. Given that most viruses in the future will likely be characterized using metagenomics approaches, and that we have evidently only sampled a tiny fraction of the total virosphere, we suggest that proposals for virus classification pay careful attention to the wonders unearthed in this new age of virus discovery.

Biological species in the viral world

“…We find that biological species of viruses and bacteriophages can be associated with host tropism; however, the high incidence of host switching and uncertainties about primary host reservoirs, combined with the potential for recombination between very divergent genomes, contravenes the attachment of viral species' names to a particular host (65,66). Moreover, linking viruses to hosts has become particularly problematic in metagenomic studies, since sequences often originate from sources unrelated to host infection and many of the traits typically used for viral classification remain inaccessible (67,68). Although our analyses are currently restricted to fully sequenced genomes, there has been substantial progress in the recovery of identification and assembly of viral sequences from metagenomic datasets (69), thereby extending the applicability of our approach.…”

RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

“…Particularly, RNA based mNGS approach could simultaneously reveal the entire "infectome" (i.e. RNA viruses, DNA viruses, bacteria and eukaryotes) present within an organism, because all except for prion express RNA [2]. Furthermore, RNA sequencing goes beyond pathogen identification to reveal relevant data on pathogen abundance, genome sequence, and gene expression, providing important insight into the cause of disease such that it represents an avant-guard diagnostic tool in the information age.…”

Origins and Evolution of the Global RNA Virome

“…Recent revolutionary developments in virus metagenomics (metaviromics) dramatically expanded knowledge of the diversity of RNA viruses and provided an unprecedented amount of sequence data for informed investigation into RNA virus evolution (11,17,37). The foremost development was the massive expansion of the known invertebrate virome, which was achieved primarily through meta-transcriptome sequencing of various holobionts.…”