Real-time genetic cartography of viral epidemics

The ignition and rapid spread of viral pathogens such as HIV-1 and, more recently, Ebola virus in West Africa and Zika virus in the Americas, demonstrate the need for a better understanding of when and where outbreaks emerge and what determines how viruses spread at different geographic scales. Unfortunately, incomplete genetic surveillance efforts and problems with the current generation of analysis tools make it difficult to provide accurate predictions that can anticipate the spread of disease. New digital mapping approaches offer high-resolution insights into disease transmission risk, but these do not use the information about virus transmission history that is contained in virus genome sequences.

I will develop a new framework – genetic cartography – that brings together genetic, spatial and mobility data in order to inform and aid disease outbreak control. The goals of this fellowship are to find out what determines virus spread at local, regional and global scales using datasets containing thousands of HIV, Ebola and Zika virus genome sequences. I will also develop realistic computational models of virus spread at a high-resolution spatial scale that will predict future virus spread and disease burden.