Evolutionary Relationships between RNA Viruses and their Eucaryote Hosts

 

Fig 1: The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups (Koonin et al .2008). Picornaviruses are nonenveloped viruses that represent a large family of small, cytoplasmic, plus-strand RNA(~7.5kb) viruses, also responsibel for acture respiratory illness in humans. Compare main article fig 16b.

 

 

 

 

 

 

Fig 2: Evolution of the ebola single stranded RNA virus in the 2014 ebola epidamic. (A) Phylogenetic and temporal placement of 188 Liberian EBOV genomes relative to 734 sequences from Guinea, Mali, and Sierra Leone. Three distinct lineages are represented in the Liberian samples: GN1, SL1, and SL2. (B) Median-joining haplotype network including 175 Liberian sequences with ≥97% genome coverage and 466 sequences representative of lineages circulating elsewhere in Western Africa (Ladner et al. (2015).

 

 

 

 

Shi et al. (2018), using a large-scale meta-transcriptomic approach, we discover 214 vertebrate-associated viruses in reptiles, amphibians, lungfish, ray-finned fish, cartilaginous fish and jawless fish. The newly discovered viruses appear in every family or genus of RNA virus associated with vertebrate infection, including those containing human pathogens such as influenza virus, the Arenaviridae and Filoviridae families, and have branching orders that broadly reflected the phylogenetic history of their hosts. We establish a long evolutionary history for most groups of vertebrate RNA virus, and support this by evaluating evolutionary timescales using dated orthologous endogenous virus elements. We also identify new vertebrate-specific RNA viruses and genome architectures, and re-evaluate the evolution of vector-borne RNA viruses. In summary, this study reveals diverse virus–host associations across the entire evolutionary history of the vertebrates.

Phylogenetic positions of vertebrate-associated positive-sense and double-stranded RNA viruses within the broader diversity of RNA viruses. Phylogenies were estimated using a maximum likelihood method and midpoint-rooted for clarity only. Viruses discovered here are labelled with solid black circles. The name of the major clade (phylogeny) is shown at the top of each tree, and taxonomic names are shown to the right. The vertebrate associated virus diversity is shaded in grey. All horizontal branch lengths are scaled to the number of amino acid substitutions per site.

 

Phylogenetic positions of vertebrate-associated negative-sense RNA viruses within the broader diversity of RNA viruses. Phylogenies were estimated using a maximum likelihood method and midpoint-rooted for clarity only. Viruses discovered here are labelled with solid black circles. The name of the major clade (phylogeny) is shown at the top of each tree, and taxonomic names are shown to the right. The vertebrate associated virus diversity is shaded in grey. All horizontal branch lengths are scaled to the number of amino acid substitutions
per site.

 

References:

Koonin E et al. (2008) The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups Nature Reviews Microbiology 6 925-939.

Ladner J et al. (2015) Evolution and Spread of Ebola Virus in Liberia, 2014-2015 Cell Host & Microbe 18, 659–669 doi:10.1016/j.chom.2015.11.008.

Shi M et al. (2018) The evolutionary history of vertebrate RNA viruses Nature doi:10.1038/s41586-018-0012-7.