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ReservoirDOCs SIGNED

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

Total Cost €

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EC-Contrib. €

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Partnership

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 ReservoirDOCs project word cloud

Explore the words cloud of the ReservoirDOCs project. It provides you a very rough idea of what is the project "ReservoirDOCs" about.

molecular    shed    diffusion    models    hepacivirus    central    archival    epidemiologists    concerted    epidemiological    accommodate    dated    outbreaks    window    health    instrument    carve    statistical    tips    populations    dynamics    epidemic    hiv    questions    recombination    critical    unresolved    population    incorporate    sequencing    grown    emergence    performance    evolutionary    pressures    methodology    reservoir    harnessing    rodents    representative    unravel    variability    interventions    temporal    extracted    practical    spread    human    history    ebola    analyze    graphs    infected    west    confronted    hcv    deploy    devastating    transmission    ancestral    establishment    systematic    complete    pathogens    model    struggle    disease    integrating    technologies    cross    extracting    samples    unfold    selective    screening    origin    hosts    scrutinise    sequences    viral    africa    african    diversity    infectious    pathogen    spatiotemporal    despite    spatial    hypotheses    virus    light    species    public    dynamic    revolution    genome    genomes    epidemics    genomic   

Project "ReservoirDOCs" data sheet

The following table provides information about the project.

Coordinator
KATHOLIEKE UNIVERSITEIT LEUVEN 

Organization address
address: OUDE MARKT 13
city: LEUVEN
postcode: 3000
website: www.kuleuven.be

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 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.

# participants  country  role  EC contrib. [€] 
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
List of publications.
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, Nídia 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, Miša Korva, Tatjana Avšič Županc, 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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