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The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Objective

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 recent devastating Ebola virus epidemic, 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 propose to unravel crucial steps in the emergence and establishment of key viral pathogens. We will scrutinise the reservoir dynamics of HCV by sequencing complete hepacivirus genomes from infected samples emerging from a large-scale screening of African rodents, and analyze the cross-species transmission history using novel evolutionary methods that accommodate spatial and temporal variability in selective pressures. To test hypotheses about the early establishment of HIV-1, we will carve 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, with the development of ancestral recombination graphs that accommodate dated tips and spatial diffusion, as well as population dynamic models that incorporate epidemiological information. Finally, we will take the recent 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.

Field of science

  • /medical and health sciences/health sciences/public and environmental health
  • /natural sciences/biological sciences/genetics and heredity/genome
  • /humanities/history and archaeology/history

Call for proposal

ERC-2016-COG
See other projects for this call

Funding Scheme

ERC-COG - Consolidator Grant

Host institution

KATHOLIEKE UNIVERSITEIT LEUVEN
Address
Oude Markt 13
3000 Leuven
Belgium
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 1 311 279,14

Beneficiaries (3)

KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium
EU contribution
€ 1 311 279,14
Address
Oude Markt 13
3000 Leuven
Activity type
Higher or Secondary Education Establishments
THE UNIVERSITY OF EDINBURGH
United Kingdom
EU contribution
€ 350 196,86
Address
Old College, South Bridge
EH8 9YL Edinburgh
Activity type
Higher or Secondary Education Establishments
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
United States
EU contribution
€ 149 100
Address
Franklin Street 1111, 12 Floor
94607 Oakland Ca
Activity type
Higher or Secondary Education Establishments