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 and adaptation to new hosts, and their spatiotemporal spread. 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, we also struggle to deploy these technologies in a systematic and concerted way despite a critical need to support public health interventions.
In this project, we aimed to unravel crucial steps in the emergence and establishment of key viral pathogens. We scrutinised the reservoir dynamics of HCV by sequencing complete hepacivirus genomes from infected samples emerging from a large-scale screening of African rodents, and analyzed the cross-species transmission history using novel evolutionary methods. To test hypotheses about the early establishment of HIV-1, we carved a genomic window into the past epidemic history of the virus by integrating molecular work on archival samples from Central Africa and on samples representative of the current HIV-1 diversity, using population dynamic models that incorporate epidemiological information. Finally, we took the Ebola epidemic in West Africa as a model to develop high-performance statistical approaches for extracting practical and timely epidemiological information from virus genome sequences during epidemics as they unfold. We further complemented these approaches with state-of-the-art visualisation tools.
