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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.
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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)

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KATHOLIEKE UNIVERSITEIT LEUVEN

Belgium

EU Contribution

€ 1 311 279,14

THE UNIVERSITY OF EDINBURGH

United Kingdom

EU Contribution

€ 350 196,86

THE REGENTS OF THE UNIVERSITY OF CALIFORNIA

United States

EU Contribution

€ 149 100

Project information

Grant agreement ID: 725422

Status

Ongoing project

  • Start date

    1 August 2017

  • End date

    31 July 2022

Funded under:

H2020-EU.1.1.

  • Overall budget:

    € 1 810 576

  • EU contribution

    € 1 810 576

Hosted by:

KATHOLIEKE UNIVERSITEIT LEUVEN

Belgium