Overall, my research is about combining genomic and non-genomic data to learn about how viruses spread in space and time. I do this by using the field of phylodynamics, the combination of evolution, epidemiology and immunology.
Developing phylodynamic approaches for disease control at emergence and elimination
Phylodynamics gives us extra information about unobserved processes with relatively small amounts of data. Emergence and elimination are stages of an outbreak where controlling individual transmission chains results in disprportionate impacts. But, many of our existing methods work best at endemicity and/or the peak of an epidemic. I’m interested in developing new ways of using existing frameworks to extract as much information out of hard-won genomes as possible. I’m especially interested in developing new ways of using imperfect genomic datasets (i.e. heavily biassed in space or time) so that we can all avoid simply writing a sentence in the Discussion and calling it a day.
Spatial spread of viruses
I spend much of my time doing phylogeographic analyses on large and small datasets. These analyses use sample locations to infer how location has evolved along a phylogeny over time: in other words, where and when did the virus move in the past? This can be done in a discrete way, using eg countries as the location, and non-genomic data can be included to find out what predicts movement between locations. Location can also change continuously, enabling a more accurate investigation of how a virus may spread within a country. Both can be used to identify source-sink dynamics and identify targetted non-pharmaceutical interventions.
Practical phylogenetics
Phylodynamics is great, but it’s slow and can be complicated to interpret. Condensing genomic information into easier to understand analyses with quick turnaround times has been an important part of my career so far. I was a co-developer on civet and grinch, both designed to make the huge amount of SARS-CoV-2 genomic data accessible and useable for data producers and the general public respectively. I’ve developed (along with a large global collaboration) a lineage system for Dengue virus (similar to the pango lineage system) to better describe global Dengue diversity, without the need to perform complex analyses. More information here