Comparative genomics decoding of virus – host interactions

The purpose of this research is to generate new knowledge about virus-host interactions and evolution by investigating the endogenous retrovirus (ERV) record.

Retroviruses convert their RNA genome to proviral DNA, which integrates permanently into the host nuclear DNA to produce new viruses. Germline infections over millions of years have left numerous heritable ERVs.

These ERVs represent retrovirus diversity at the time of insertion and thus provide a genomic record of past virus-host interactions. By examining these ERVs, we can obtain a better understanding of the long-term association between viruses and hosts.

This investigation exploits the fast-growing catalog produced by state-of-the-art genome sequencing for developing computational analyses to characterize ERVs in individuals and across populations.

We examine to what extent structural genomic variations involving the ERV record differs between individuals and different populations for conclusions regarding virus transmission history and virus-host co-evolution.

We further explore role of ERV structural variations in host biology by aligning these with genome annotations to reveal ERVs that were repurposed by the host, for example as novel genes, defense against infections, and as protein docking platforms for gene expression in health and disease.

Results are expected to generate new broad research directions integrating viruses with host biology for improved understanding in many areas of biology and biomedicine.