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Review
. 2018 Jan 2:243:83-90.
doi: 10.1016/j.virusres.2017.10.016. Epub 2017 Oct 27.

Meta-transcriptomics and the evolutionary biology of RNA viruses

Mang Shi  1 , Yong-Zhen Zhang  2 , Edward C Holmes  3
Affiliations
Review

Meta-transcriptomics and the evolutionary biology of RNA viruses

Mang Shi et al. Virus Res. .

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.

Keywords: Classification; Evolution; Meta-transcriptomics; Metagenomics; Phylogeny; Virosphere.

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Figures

Fig. 1
Fig. 1
Comparisons of virus enrichment and meta-transcriptomics approaches for RNA virus discovery. The workflow of a typical virus enrichment approach is marked in blue, whereas that of a meta-transcriptomics approach is marked in red.
Fig. 2
Fig. 2
Current taxonomy of RNA viruses in the context of the genetic diversity revealed by meta-transcriptomics. The phylogenies are based on RdRp amino acid sequences from a broader analysis as performed by Shi et al., 2016a, Shi et al., 2016b (and see this paper for a description of branch lengths and rooting schemes). The taxonomic groups (i.e. genus, family, and order) established by ICTV are shown to the left of each phylogeny.
See this image and copyright information in PMC

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