Virus genomes reveal factors that spread and sustained the Ebola epidemic

Gytis Dudas (), Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D’Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion P. G. Koopmans, Jens H. Kuhn, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey () and Andrew Rambaut ()
Additional contact information
Gytis Dudas: Institute of Evolutionary Biology, University of Edinburgh
Luiz Max Carvalho: Institute of Evolutionary Biology, University of Edinburgh
Trevor Bedford: Fred Hutchinson Cancer Research Center
Andrew J. Tatem: WorldPop, University of Southampton
Guy Baele: Rega Institute, KU Leuven – University of Leuven
Nuno R. Faria: University of Oxford
Daniel J. Park: Broad Institute of Harvard and MIT
Jason T. Ladner: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Armando Arias: University of Cambridge, Addenbrooke’s Hospital
Danny Asogun: Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital
Filip Bielejec: Rega Institute, KU Leuven – University of Leuven
Sarah L. Caddy: University of Cambridge, Addenbrooke’s Hospital
Matthew Cotten: Virus Genomics, Wellcome Trust Sanger Institute
Jonathan D’Ambrozio: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Simon Dellicour: Rega Institute, KU Leuven – University of Leuven
Antonino Di Caro: The European Mobile Laboratory Consortium
Joseph W. Diclaro: Naval Medical Research Unit 3
Sophie Duraffour: The European Mobile Laboratory Consortium
Michael J. Elmore: National Infections Service, Public Health England
Lawrence S. Fakoli: Liberian Institute for Biomedical Research
Ousmane Faye: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit
Merle L. Gilbert: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Sahr M. Gevao: University of Sierra Leone
Stephen Gire: Broad Institute of Harvard and MIT
Adrianne Gladden-Young: Broad Institute of Harvard and MIT
Andreas Gnirke: Broad Institute of Harvard and MIT
Augustine Goba: Viral Hemorrhagic Fever Program, Kenema Government Hospital
Donald S. Grant: Viral Hemorrhagic Fever Program, Kenema Government Hospital
Bart L. Haagmans: Erasmus University Medical Centre
Julian A. Hiscox: Institute of Infection and Global Health, University of Liverpool
Umaru Jah: University of Makeni
Jeffrey R. Kugelman: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Di Liu: Institute of Microbiology, Chinese Academy of Sciences
Jia Lu: University of Cambridge, Addenbrooke’s Hospital
Christine M. Malboeuf: Broad Institute of Harvard and MIT
Suzanne Mate: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
David A. Matthews: University of Bristol
Christian B. Matranga: Broad Institute of Harvard and MIT
Luke W. Meredith: University of Cambridge, Addenbrooke’s Hospital
James Qu: Broad Institute of Harvard and MIT
Joshua Quick: Institute of Microbiology and Infection, University of Birmingham
Suzan D. Pas: Erasmus University Medical Centre
My V. T. Phan: Virus Genomics, Wellcome Trust Sanger Institute
Georgios Pollakis: Institute of Infection and Global Health, University of Liverpool
Chantal B. Reusken: Erasmus University Medical Centre
Mariano Sanchez-Lockhart: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Stephen F. Schaffner: Broad Institute of Harvard and MIT
John S. Schieffelin: Section of Infectious Diseases
Rachel S. Sealfon: Broad Institute of Harvard and MIT
Etienne Simon-Loriere: Institut Pasteur, Functional Genetics of Infectious Diseases Unit
Saskia L. Smits: Erasmus University Medical Centre
Kilian Stoecker: The European Mobile Laboratory Consortium
Lucy Thorne: University of Cambridge, Addenbrooke’s Hospital
Ekaete Alice Tobin: Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital
Mohamed A. Vandi: Viral Hemorrhagic Fever Program, Kenema Government Hospital
Simon J. Watson: Virus Genomics, Wellcome Trust Sanger Institute
Kendra West: Broad Institute of Harvard and MIT
Shannon Whitmer: Viral Special Pathogens Branch, Centers for Disease Control and Prevention
Michael R. Wiley: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Sarah M. Winnicki: Broad Institute of Harvard and MIT
Shirlee Wohl: Broad Institute of Harvard and MIT
Roman Wölfel: The European Mobile Laboratory Consortium
Nathan L. Yozwiak: Broad Institute of Harvard and MIT
Kristian G. Andersen: The Scripps Research Institute
Sylvia O. Blyden: Ministry of Social Welfare, Gender and Children’s Affairs
Fatorma Bolay: Liberian Institute for Biomedical Research
Miles W. Carroll: The European Mobile Laboratory Consortium
Bernice Dahn: Minstry of Health Liberia
Boubacar Diallo: World Health Organization
Pierre Formenty: World Health Organization
Christophe Fraser: Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford
George F. Gao: Institute of Microbiology, Chinese Academy of Sciences
Robert F. Garry: Department of Microbiology and Immunology
Ian Goodfellow: University of Cambridge, Addenbrooke’s Hospital
Stephan Günther: The European Mobile Laboratory Consortium
Christian T. Happi: Redeemer’s University
Edward C. Holmes: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney
Brima Kargbo: Ministry of Health and Sanitation
Sakoba Keïta: Ministry of Health Guinea
Paul Kellam: Virus Genomics, Wellcome Trust Sanger Institute
Marion P. G. Koopmans: Erasmus University Medical Centre
Jens H. Kuhn: Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza
Nicholas J. Loman: Institute of Microbiology and Infection, University of Birmingham
N’Faly Magassouba: Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée
Dhamari Naidoo: World Health Organization
Stuart T. Nichol: Viral Special Pathogens Branch, Centers for Disease Control and Prevention
Tolbert Nyenswah: Minstry of Health Liberia
Gustavo Palacios: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases
Oliver G. Pybus: University of Oxford
Pardis C. Sabeti: Broad Institute of Harvard and MIT
Amadou Sall: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit
Ute Ströher: Viral Special Pathogens Branch, Centers for Disease Control and Prevention
Isatta Wurie: University of Sierra Leone
Marc A. Suchard: UCLA Fielding School of Public Health, University of California
Philippe Lemey: Rega Institute, KU Leuven – University of Leuven
Andrew Rambaut: Institute of Evolutionary Biology, University of Edinburgh

Nature, 2017, vol. 544, issue 7650, 309-315

Abstract: Abstract The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic ‘gravity’ model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

Date: 2017
References: Add references at CitEc
Citations: View citations in EconPapers (5)

Downloads: (external link)
https://www.nature.com/articles/nature22040 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:544:y:2017:i:7650:d:10.1038_nature22040

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/nature22040

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().