Eco-evolutionary virus-host relationships in mammals: a phylogenomic study of endogenous viral elements

Retroviruses have been infecting mammals for at least 100 million years, leaving descendants in host genomes known as endogenous retroviruses (ERVs). Additionally, although most endogenous viral elements (EVEs) found in host genomes are inactive 'viral fossils', an open reading frame is occasionally maintained in these sequences. This has lead to examples, such as the placentation gene syncitin, in which EVEs become co-opted by the host as virus-derived, functional genes (often with immune related functions). The increase in genomic and transcriptomic data for mammalian species allows for broader study of ERV features across this well-studied clade. This project will focus in particular on bats (order Chiroptera) which are the natural hosts of multiple zoonotic viruses of public health concern, including Ebola, Nipah, Hendra and SARS.

The order Chiroptera (bats), comprises >1200 species and encompasses some of the most extensive ecological and phenotypic radiation known among mammals, having adapted to a diverse multitude of ecological niches. This unique evolutionary history, combined with their ecological role as carriers of zoonotic viruses provides an ideal system in which to study the evolutionary relationship between mammals and their viruses through comparative genomic/transcriptomic approaches.

The project aims to create a computational pipeline for identifying endogenous viral elements (EVEs) in mammalian genomes/transcriptomes and to apply this to genome-scale sequence data obtained from tens of species of bats. Characterisation of EVEs across multiple species will allow a comparative analyses (e.g. phylogenomic selection analysis) to identify eco-evolutionary patterns in the relationship between viral and host lineages. Tissue specific transcriptome data will also be employed during the project in order to identify potentially functional EVEs by looking for EVE containing transcripts upregulated in immune tissues. These comparative analyses will hope to provide insight on, for example: the relative importance of co-evolution between host and virus compared with host ecology in determining the virus pathogen landscape; the roles of co-opted viral genes in host biology; and eco-evolutionary patterns of these co-opted viral genes.