ReservoirDOCs SIGNED
The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
Total Cost €
0EC-Contrib. €
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Project "ReservoirDOCs" data sheet
The following table provides information about the project.
| Coordinator |
KATHOLIEKE UNIVERSITEIT LEUVEN
Organization address contact info |
| Coordinator Country | Belgium [BE] |
| Total cost | 1˙810˙576 € |
| EC max contribution | 1˙810˙576 € (100%) |
| Programme |
1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC)) |
| Code Call | ERC-2016-COG |
| Funding Scheme | ERC-COG |
| Starting year | 2017 |
| Duration (year-month-day) | from 2017-08-01 to 2022-07-31 |
Partnership
Take a look of project's partnership.
| # | ||||
|---|---|---|---|---|
| 1 | KATHOLIEKE UNIVERSITEIT LEUVEN | BE (LEUVEN) | coordinator | 1˙311˙279.00 |
| 2 | THE UNIVERSITY OF EDINBURGH | UK (EDINBURGH) | participant | 350˙196.00 |
| 3 | THE REGENTS OF THE UNIVERSITY OF CALIFORNIA | US (OAKLAND CA) | participant | 149˙100.00 |
Map
Project 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.
Publications
| year | authors and title | journal | last update |
|---|---|---|---|
| 2019 |
Magda Bletsa, Marc A Suchard, Xiang Ji, Sophie Gryseels, Bram Vrancken, Guy Baele, Michael Worobey, Philippe Lemey Divergence dating using mixed effects clock modelling: An application to HIV-1 published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vez036 |
Virus Evolution 5/2 | 2020-03-13 |
| 2019 |
Daniel L Ayres, Michael P Cummings, Guy Baele, Aaron E Darling, Paul O Lewis, David L Swofford, John P Huelsenbeck, Philippe Lemey, Andrew Rambaut, Marc A Suchard BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics published pages: 1052-1061, ISSN: 1063-5157, DOI: 10.1093/sysbio/syz020 |
Systematic Biology 68/6 | 2020-03-13 |
| 2020 |
Qiqi Yang, Xiang Zhao, Philippe Lemey, Marc A. Suchard, Yuhai Bi, Weifeng Shi, Di Liu, Wenbao Qi, Guogang Zhang, Nils Chr. Stenseth, Oliver G. Pybus, Huaiyu Tian Assessing the role of live poultry trade in community-structured transmission of avian influenza in China published pages: 201906954, ISSN: 0027-8424, DOI: 10.1073/pnas.1906954117 |
Proceedings of the National Academy of Sciences | 2020-03-13 |
| 2020 |
Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography published pages: 182, ISSN: 1999-4915, DOI: 10.3390/v12020182 |
Viruses 12/2 | 2020-03-13 |
| 2019 |
Nuno R. Faria, Nicole Vidal, José Lourenco, Jayna Raghwani, Kim C. E. Sigaloff, Andy J. Tatem, David A. M. van de Vijver, Andrea-Clemencia Pineda-Peña, Rebecca Rose, Carole L. Wallis, Steve Ahuka-Mundeke, Jean-Jacques Muyembe-Tamfum, Jérémie Muwonga, Marc A. Suchard, Tobias F. Rinke de Wit, Raph L. Hamers, Nicaise Ndembi, Guy Baele, Martine Peeters, Oliver G. Pybus, Philippe Lemey, Simon Delli Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa published pages: e1007976, ISSN: 1553-7374, DOI: 10.1371/journal.ppat.1007976 |
PLOS Pathogens 15/12 | 2020-03-13 |
| 2019 |
Jade Vincent Membrebe, Marc A Suchard, Andrew Rambaut, Guy Baele, Philippe Lemey Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates published pages: 1793-1803, ISSN: 0737-4038, DOI: 10.1093/molbev/msz094 |
Molecular Biology and Evolution 36/8 | 2020-03-13 |
| 2018 |
Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 published pages: 901-904, ISSN: 1063-5157, DOI: 10.1093/sysbio/syy032 |
Systematic Biology 67/5 | 2020-03-13 |
| 2019 |
Alice Fusaro, Bianca Zecchin, Bram Vrancken, Celia Abolnik, Rose Ademun, Abdou Alassane, Abdelsatar Arafa, Joseph Adongo Awuni, Emmanuel Couacy-Hymann, M.’ Bétiégué Coulibaly, Nicolas Gaidet, Emilie Go-Maro, Tony Joannis, Simon Dickmu Jumbo, Germaine Minoungou, Clement Meseko, Maman Moutari Souley, Deo Birungi Ndumu, Ismaila Shittu, Augustin Twabela, Abel Wade, Lidewij Wiersma, Yao P. Akpeli, Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-019-13287-y |
Nature Communications 10/1 | 2020-03-13 |
| 2020 |
Mandev S Gill, Philippe Lemey, Marc A Suchard, Andrew Rambaut, Guy Baele Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction published pages: , ISSN: 0737-4038, DOI: 10.1093/molbev/msaa047 |
Molecular Biology and Evolution | 2020-03-13 |
| 2019 |
Marie-Angélique De Scheerder, Bram Vrancken, Simon Dellicour, Timothy Schlub, Eunok Lee, Wei Shao, Sofie Rutsaert, Chris Verhofstede, Tessa Kerre, Thomas Malfait, Dimitri Hemelsoet, Marc Coppens, Annemieke Dhondt, Danny De Looze, Frank Vermassen, Philippe Lemey, Sarah Palmer, Linos Vandekerckhove HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs published pages: 347-358.e7, ISSN: 1931-3128, DOI: 10.1016/j.chom.2019.08.003 |
Cell Host & Microbe 26/3 | 2020-03-13 |
| 2019 |
L. E. Kafetzopoulou, S. T. Pullan, P. Lemey, M. A. Suchard, D. U. Ehichioya, M. Pahlmann, A. Thielebein, J. Hinzmann, L. Oestereich, D. M. Wozniak, K. Efthymiadis, D. Schachten, F. Koenig, J. Matjeschk, S. Lorenzen, S. Lumley, Y. Ighodalo, D. I. Adomeh, T. Olokor, E. Omomoh, R. Omiunu, J. Agbukor, B. Ebo, J. Aiyepada, P. Ebhodaghe, B. Osiemi, S. Ehikhametalor, P. Akhilomen, M. Airende, R. Esumeh, E. Muoebonam, R. Giwa, A. Ekanem, G. Igenegbale, G. Odigie, G. Okonofua, R. Enigbe, J. Oyakhilome, E. O. Yerumoh, I. Odia, C. Aire, M. Okonofua, R. Atafo, E. Tobin, D. Asogun, N. Akpede, P. O. Okokhere, M. O. Rafiu, K. O. Iraoyah, C. O. Iruolagbe, P. Akhideno, C. Erameh, G. Akpede, E. Isibor, D. Naidoo, R. Hewson, J. A. Hiscox, R. Vipond, M. W. Carroll, C. Ihekweazu, P. Formenty, S. Okogbenin, E. Ogbaini-Emovon, S. Günther, S. Duraffour Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak published pages: 74-77, ISSN: 0036-8075, DOI: 10.1126/science.aau9343 |
Science 363/6422 | 2019-10-29 |
| 2018 |
Huaiyu Tian, Yun Feng, Bram Vrancken, Bernard Cazelles, Hua Tan, Mandev S. Gill, Qiqi Yang, Yidan Li, Weihong Yang, Yuzhen Zhang, Yunzhi Zhang, Philippe Lemey, Oliver G. Pybus, Nils Chr. Stenseth, Hailin Zhang, Simon Dellicour Transmission dynamics of re-emerging rabies in domestic dogs of rural China published pages: e1007392, ISSN: 1553-7374, DOI: 10.1371/journal.ppat.1007392 |
PLOS Pathogens 14/12 | 2019-10-29 |
| 2018 |
N. R. Faria, M. U. G. Kraemer, S. C. Hill, J. Goes de Jesus, R. S. Aguiar, F. C. M. Iani, J. Xavier, J. Quick, L. du Plessis, S. Dellicour, J. Thézé, R. D. O. Carvalho, G. Baele, C.-H. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. Obolski, L. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R. W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca Genomic and epidemiological monitoring of yellow fever virus transmission potential published pages: 894-899, ISSN: 0036-8075, DOI: 10.1126/science.aat7115 |
Science 361/6405 | 2019-10-08 |
| 2018 |
Simon Dellicour, Bram Vrancken, NÃdia S Trovão, Denis Fargette, Philippe Lemey On the importance of negative controls in viral landscape phylogeography published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vey023 |
Virus Evolution 4/2 | 2019-10-08 |
| 2017 |
Bram Vrancken, Marc A Suchard, Philippe Lemey Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vex028 |
Virus Evolution 3/2 | 2019-10-08 |
| 2018 |
Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken Recent advances in computational phylodynamics published pages: 24-32, ISSN: 1879-6257, DOI: 10.1016/j.coviro.2018.08.009 |
Current Opinion in Virology 31 | 2019-10-08 |
| 2018 |
Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 published pages: , ISSN: 2057-1577, DOI: 10.1093/ve/vey016 |
Virus Evolution 4/1 | 2019-10-08 |
| 2018 |
Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-03763-2 |
Nature Communications 9/1 | 2019-10-08 |
| 2018 |
Bert Vanmechelen, Magda Bletsa, Lies Laenen, Ana Rita Lopes, Valentijn Vergote, Leen Beller, Ward Deboutte, MiÅ¡a Korva, Tatjana AvÅ¡iÄ Å½upanc, Joëlle Goüy de Bellocq, Sophie Gryseels, Herwig Leirs, Philippe Lemey, Bram Vrancken, Piet Maes Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins published pages: , ISSN: 1471-2164, DOI: 10.1186/s12864-018-4995-0 |
BMC Genomics 19/1 | 2019-10-08 |
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