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.
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 position, and dispersal frequency), as well as to assess potential intervention strategies in the context of viral epidemics. Over the last years, we have applied those novel methodologies to study several virus spreads in their environmental context such, for instance, Ebola virus during the 2014-16 western Africa outbreak, rabies virus in different regions of the world, West Nile virus in North America, Lassa virus in Africa, and Powassan virus in North America. Our methodological developments in landscape phylogeography have all been implemented in our toolbox “seraphim”, a R package hosted on GitHub.
Initiated within the research team of Oliver Pybus (Department of Zoology, University of Oxford), our current research activities on this topic are currently performed in collaboration with the Evolutionary and Computational Virology lab of Philippe Lemey (KU Leuven). We also have ongoing collaborations with, for instance, the labs of Nathan Grubaugh at the University of Yale (US), Houriiyah Tegally at Stellenbosch University (South Africa), and Hervé Bourhy at the Pasteur Institute (Paris).
Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
C. B. F. Vogels, D. E. Brackney, A. P. Dupuis, R. M. Robich, J. R. Fauver, A. F. Brito, S. C. Williams, J. F. Anderson, C. B. Lubelczyk, R. E. Lange, M. A. Prusinski, L. D. Kramer, J. L. Gangloff-Kaufmann, L. B. Goodman, G. Baele, R. P. Smith*, P. M. Armstrong*, A. T. Ciota*, S. Dellicour*, and N. D. Grubaugh*.
"Proceedings of the National Academy of Sciences USA",
Vol. 120,
Issue 16,
Pages e2218012120,
2023.
Combined phylogeographic analyses and epidemiologic contact tracing to characterize atypically pathogenic avian influenza (H3N1) epidemic, Belgium, 2019
S. Van Borm*, G. Boseret*, S. Dellicour*, M. Steensels, V. Roupie, F. Vandenbussche, E. Mathijs, A. Vilain, M. Driesen, M. Dispas, A. W. Delcloo, P. Lemey, I. Mertens, M. Gilbert, B. Lambrecht, and T. v. d. Berg.
"Emerging Infectious Diseases",
Vol. 29,
Issue 2,
Pages 351,
2023.
Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades
R. Klitting, L. E. Kafetzopoulou, W. Thiery, G. Dudas, S. Gryseels, A. Kotamarthi, B. Vrancken, K. Gangavarapu, M. Momoh, J. D. Sandi, A. Goba, F. Alhasan, D. S. Grant, S. Okogbenin, E. Ogbaini-Emovo, R. F. Garry, A. R. Smither, M. Zeller, M. G. Pauthner, M. McGraw, L. D. Hughes, S. Duraffour, S. Günther, M. A. Suchard, P. Lemey, K. G. Andersen, and S. Dellicour.
"Nature Communications",
Vol. 13,
Issue 1,
Pages 5596,
2022.
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.
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.
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.
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.
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.
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.