Hey, I'm Jon

I am a 3rd year Ph.D. student in the Virus Evolution Lab under the supervision of Prof Edward Holmes at the University of Sydney, Australia.

Overview

I completed my Bachelor of Advanced Science in Biology at Macquarie University in 2018, followed by a Master of Research in early 2021. My master's thesis, under Assoc Prof Rachael Gallagher and Prof Jemma Geoghegan, focused on exploring the plant virosphere using transcriptome data.

Since beginning my Ph.D. in June 2021, I have dabbled in three main areas:

  1. Reconstructing the Evolutionary History of Virus Families: Much of this work has focused on expanding largely unexplored areas of the virosphere. Taxa like the ‘basal metazoans’ are vastly understudied and may provide insights into the long-term evolutionary history of virus families. The decreasing cost of metagenomic sequencing has broadened the species diversity in transcriptome studies. The secondary analysis of existing transcriptome data, known as transcriptome mining, can circumvent challenges like securing funding for virus discovery in less economically prioritized taxa. This approach has significantly contributed to the rapid expansion of our knowledge regarding virus biodiversity. We have recently used this method to explore the Flaviviridae.

  2. Using Protein Structural Prediction to Reconstruct Virus Evolution: In collaboration with Dr. Joe Grove we have begun exploring how protein structural information, particularly from non-polymerase proteins (e.g., envelope) can be used to detect deep homology between the Flavivirdae clades that would be missed using sequence based comparisons alone. We then combined this structural information with phylogenetics to greatly enhance our evolutionary history reconstructions of the Flaviviridae.


  3. Identifying Potential Viral Etiological Agents in Wildlife: Wildlife serve as natural reservoirs and potential vectors of infectious diseases. Understanding the viruses they harbor is essential for wildlife health and zoonotic disease prevention. Metatranscriptomic sequencing not only characterises the viruses in a sample but gives a picture of the “total infectome”, thereby allowing for more informed decisions about potential etiological agents. In a recent study, we employed this method alongside traditional veterinary diagnostic techniques to discover a novel papillomavirus in a New Zealand fur seal with clinically and histologically confirmed oral papilloma-like lesions.

Outside of this, I have an interest in artifical intelligence and developing tools for virus discovery and phylogenetics.

Feel free to get in touch if you are after collaboration in any of these areas.