Viral integrations

Similar to TEs, viruses can insert themselves into the genomic sequence of their host. Indeed, viruses are thought to be ancient precursors of some TE families, most notably endogenous retrovirus (ERV)s.

Integration can be an important step in the viral life cycle, for example the mechanism of HPV-associated cancers (nearly all cervical, and a majority of oralpharangeal) depends upon it. However, questions such as how often, how many, where, and when remain unanswered. Again, like TEs, detection of viral sequences will pose challenges to NGS technologies that rely on short sequence reads.

As part of the Oxford Biomedical Research Centre, I have developed viral detection algorithm. Viral integrations detected in WGS data collected from clinical samples and tissues can help to fill in the remaining gaps in our knowledge of viral dynamics in affected and healthy individual genomes.