Current research
My research focuses on understanding trends in the evolution of viruses, how they have impacted our evolution and their ability to jump between species. Major research themes are listed below:
Paleovirology
Paleovirology is the study of viral fossils in the DNA of host organisms. Viral fossils have been identified in every known vertebrate, and can provide a record of past infections for an organism. Using these fossils, called endogenous viral elements (EVEs), we can trace the evolution of viral families, and identify when and how frequently viruses jumped between different species.
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One current project focuses on finding, characterising and classifiying EVEs in vertebrates as a starting point for many paleovirological investigations. This involves developing bioinformatic workflows to screen genomic and transcriptomic data for viral sequences and reconstructing degraded remnants of ancient viral genes.
Are viral fossils helping us?
EVEs are ubiquitous throughout animal genomes, many of which are "accidental" remnants of infections that serve no clear purpose. However, we are beginning to understand that some EVEs have drastic impacts on their hosts - some can protect us from viral infection, some have contributed to our own genes (eg. placenta formation) and some are extraordinarily conserved but their function is unclear.
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One current project in this area involves identifying co-opted EVEs - EVEs that used to be a virus but are now cellular genes that help us - and predicting their function. This work involves bioinformatics like structural protein prediction (eg. AlphaFold), sequence analysis and phylogeny as well as lab experiments with animal cells and infection.
Expanding the global virome
Almost all studies of viruses are based on either human viruses, or animals humans have close contact with, for example livestock and pets. However, this is only a tiny percentage of all the viruses in the world.
Aside from discovering new viruses to study the evolution of viruses, it is also important to understand what viruses are circulating in an ecosystem to prevent zoonosis and future pandemics, and help with conservation of endangered species.
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One project involves assessing the diversity of viruses in different animal species, both to understand what viruses are circulating, but also which animal species are likely to host the next pandemic virus. This involves molecular lab techniques like DNA extractions and PCR as well as bioinformatic techniques, coding and workflow development.
