Landscape phylogeography

Landscape phylogeography


Recent advances in genomics, mathematical modelling and computational biology have enabled evolutionary approaches to become a key component in studying of viral infectious diseases. The use of evolutionary approaches offers many advantages compared to traditional epidemiological methods; for example, they can reconstruct the demographic history of an entire epidemic even when surveillance data are sparse or non-existent, they require only a small number of sampled pathogens, and they can detect linkages among infections in time and space that may not be evident otherwise. Even over short time scales, viruses can accumulate significant diversity, resulting a genomic imprint of the ecological impact on transmission dynamics. By statistically analysing the genetic differences among viruses sampled from a population, we can reveal the underlying processes that govern viral transmission. Yet, a major challenge in this field is to develop methodologies to formally test the effect of environmental factors on pathogen transmission and evolution.

Ongoing work

We are currently developing tools in landscape phylogeography, a field at the interface between spatial and molecular epidemiology and that aims to relate phylogenetic informed movements to external/environmental factors. Specifically, we focus on new methods to investigate the impact of environmental factors on the dispersal history and dynamic of viral lineages (dispersal velocity, dispersal direction and dispersal frequency), as well as to assess potential intervention strategies in the context of viral epidemics. Besides methodological developments, we also apply new and existing methodologies to study several virus spreads in their environmental context: rabies virus in Asia, bluetongue virus in Europe, West Nile virus in North America, Lassa virus in Africa, and African swine virus in Belgium.


Our current research activities on this topic are performed in collaboration with the Evolutionary and Computational Virology lab of Philippe Lemey (KU Leuven) and the research team of Oliver Pybus (Department of Zoology, University of Oxford). We also have ongoing collaborations with the labs of Kristian Andersen at the Scripps Research Institute in San Diego, Roman Biek at the University of Glasgow, and Hervé Bourhy at the Pasteur Institute of Paris.

Related publications

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference — Application to H5N1 spread in the Mekong region
S. Dellicour, P. Lemey, J. Artois, T. T. Lam, A. Fusaro, I. Monne, G. Cattoli, D. Kuznetsov, I. Xenarios, G. Dauphin, W. Kalpravidh, S. Von Dobschuetz, F. Claes, S. H. Newman, M. A. Suchard, G. Baele, and M. Gilbert.
"Bioinformatics", Vol. 36, Issue 7, Pages 2098-2104, 2020.

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework
S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, O. G. Pybus, and P. Lemey.
"Nature Communications", Vol. 11, Pages 5620, 2020.

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa
M. Rakotomalala, B. Vrancken, A. Pinel-Galzi, P. Ramavovololon, E. Hébrard, S. Randrianangaly, S. Dellicour, Lemey P, and D. Fargette.
"Virus Evolution", Vol. 5, Issue 2, Pages vez023, 2019.

Using phylogeographic approaches to analyse the dispersal history, velocity, and direction of viral lineages – application to rabies virus spread in Iran
S. Dellicour, C. Troupin, F. Jahanbakhsh, A. Salama, S. Massoudi, M. K. Moghaddam, G. Baele, P. Lemey, A. Gholami, and H. Bourhy.
"Molecular Ecology", Vol. 28, Pages 4335-4350, 2019.

Identifying the patterns and drivers of Puumala hantavirus enzootic dynamics using reservoir sampling
L. Laenen, V. Vergote, B. Vanmechelen, K. Tersago, G. Baele, P. Lemey, H. Leirs, S. Dellicour, B. Vrancken, and P. Maes.
"Virus Evolution", Vol. 5, Issue 1, 2019.

On the importance of negative controls in viral landscape phylogeography
S. Dellicour, B. Vrancken, N. S. Trovão, D. Fargette, and P. Lemey.
"Virus Evolution", Vol. 4, Issue 2, 2018.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak
S. Dellicour, G. Baele, G. Dudas, N. R. Faria, O. G. Pybus, M. A. Suchard, A. Rambaut, and P. Lemey.
"Nature Communications", Vol. 9, Issue 1, Pages 2222, 2018.

Transmission dynamics of re-emerging rabies in domestic dogs of rural China
H. Tian, Y. Feng, B. Vrancken, B. Cazelles, H. Tan, M. S. Gill, Q. Yang, Y. Li, W. Yang, Y. Zhang, Y. Zhang, P. Lemey, O. G. Pybus, N. C. Stenseth, H. Zhang, and S. Dellicour.
"PLoS Pathogens", Vol. 14, Issue 12, Pages e1007392, 2018.

Using viral gene sequences to compare and explain the heterogeneous spatial dynamics of virus epidemics
S. Dellicour, R. Rose, N. R. Faria, L. F. P. Vieira, H. Bourhy, M. Gilbert, P. Lemey, and O. G. Pybus.
"Molecular Biology and Evolution", Vol. 34, Issue 10, Pages 2563-2571, 2017.

Spatio-temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium
L. Laenen, S. Dellicour, V. Vergote, I. Nauwelaers, S. De Coster, I. Verbeeck, B. Vanmechelen, P. Lemey, and P. Maes.
"Molecular Ecology", Vol. 25, Issue 23, Pages 5994-6008, 2016.

SERAPHIM: studying environmental rasters and phylogenetically informed movements
S. Dellicour, R. Rose, N. R. Faria, P. Lemey, and O. G. Pybus.
"Bioinformatics", Vol. 32, Issue 20, Pages 3204-3206, 2016.

Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
S. Dellicour, R. Rose, and O. G. Pybus.
"BMC Bioinformatics", Vol. 17, Issue 1, 2016.