Most of the information that public health agencies and researchers have about emerging disease epidemics is obtained by on-the-ground epidemiology, that is, by asking infected people about where they went and who they contacted. Phylodynamics is an emerging area of research which aims to enrich this information using viral genomic data and bioinformatic methods. One application of phylodynamics is the identification of groups of epidemiologically related individuals, termed phylogenetic clustering. Here, we develop a novel clustering method which uses a Markov-modulated Poisson process, applied to a "family tree" of viruses, to identify parts of the population experiencing elevated transmission rates. We applied this method to anonymised viral genomic data sampled from almost 8000 HIV-infected individuals in British Columbia.
Rosemary McCloskey is a second year Master's student in the CIHR Strategic Training Program in Bioinformatics at UBC, working in Dr. Art Poon's lab at the BC Centre for Excellence in HIV/AIDS. She has an undergraduate degree in Mathematics from Simon Fraser University, and is the inaugural recipient of the Statistics Department Award in Data Science.