The evolutionary dynamics of pathogen emergence, spread and virulence

Extracted evolutionary and epidemiological information from pathogen genomes has grown into an important instrument across infectious disease research. By harnessing such information, molecular epidemiologists aim to shed light on the origin and epidemic history of pathogens, from reservoir dynamics to emergence in new hosts, including spatiotemporal spread and virulence evolution. However, despite the revolution in genome sequencing technologies and advances in statistical methodology, key questions about pathogen emergence and establishment in human populations remain unresolved for major viral epidemics. When confronted with new viral outbreaks, such as the devastating Ebola virus epidemic in West Africa or the pandemic spread of SARS-CoV-2 as the cause of COVID-19, it is also challenging to deploy these technologies in a systematic and concerted way. Finally, upon circulation in human populations, disease profiles may considerably vary among patients, but it is frequently unclear to what extent this can be attributed to viral genetic variation. In this project, I aim to make contributions on several fronts: i) elucidating reservoir dynamics of viral pathogens, ii) inferring historical pathogen emergence, iii) real-time tracking of pathogen spread and iv) increasing our understanding of virulence evolution.