Virus genomes reveal factors that spread and sustained the Ebola epidemic View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-04-12

AUTHORS

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, Andrew Rambaut

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. More... »

PAGES

309-315

Journal

TITLE

Nature

ISSUE

7650

VOLUME

544

Author Affiliations

  • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 98109, Seattle, Washington, USA
  • Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, EH9 3FL, Edinburgh, UK
  • Flowminder Foundation, Stockholm, Sweden
  • Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, 3000, Leuven, Belgium
  • Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
  • Broad Institute of Harvard and MIT, 02142, Cambridge, Massachusetts, USA
  • Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, 21702, Frederick, Maryland, USA
  • National Veterinary Institute, Technical University of Denmark, 27, 1870, Bülowsvej, Frederiksberg C, Denmark
  • The European Mobile Laboratory Consortium, 20359, Hamburg, Germany
  • Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, CB2 2QQ, Cambridge, UK
  • Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300, CA Rotterdam, the Netherlands
  • National Institute for Infectious Diseases ‘L. Spallanzani’—IRCCS, Via Portuense 292, 00149, Rome, Italy
  • Naval Medical Research Unit 3, 3A Imtidad Ramses Street, 11517, Cairo, Egypt
  • Bernhard Nocht Institute for Tropical Medicine, 20359, Hamburg, Germany
  • National Infections Service, Public Health England, Porton Down, SP4 0JG, Salisbury, Wilts, UK
  • Liberian Institute for Biomedical Research, Charlesville, Liberia
  • Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, 220, BP, DakarSénégal
  • University of Sierra Leone, Freetown, Sierra Leone
  • Department of Organismic and Evolutionary Biology, Center for Systems Biology, Harvard University, 02138, Cambridge, Massachusetts, USA
  • Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
  • NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, L69 3GL, Liverpool, UK
  • University of Makeni, Makeni, Sierra Leone
  • Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
  • University of Bristol, BS8 1TD, Bristol, UK
  • Institute of Microbiology and Infection, University of Birmingham, B15 2TT, Birmingham, UK
  • Institute of Infection and Global Health, University of Liverpool, L69 2BE, Liverpool, UK
  • University of Nebraska Medical Center, 68198, Omaha, Nebraska, USA
  • Department of Pediatrics, Section of Infectious Diseases, 70112, New Orleans, Louisiana, USA
  • Lewis-Sigler Institute for Integrative Genomics, Princeton University, 08544, Princeton, New Jersey, USA
  • Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, 75015, Paris, France
  • Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937, Munich, Germany
  • Virus Genomics, Wellcome Trust Sanger Institute, CB10 1SA, Hinxton, Cambridge, UK
  • Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, 30333, Atlanta, Georgia, USA
  • Scripps Translational Science Institute, 92037, La Jolla, California, USA
  • Ministry of Social Welfare, Gender and Children’s Affairs, New Englandville, Freetown, Sierra Leone
  • University of Southampton, South General Hospital, SO16 6YD, Southampton, UK
  • Minstry of Health Liberia, Monrovia, Liberia
  • World Health Organization, Conakry, Guinea
  • World Health Organization, Geneva, Switzerland
  • Nuffield Department of Medicine, Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7FZ, Oxford, UK
  • Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China
  • Department of Microbiology and Immunology, 70112, New Orleans, Louisiana, USA
  • African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
  • 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, 2006, Sydney, New South Wales, Australia
  • Ministry of Health Guinea, Conakry, Guinea
  • Division of Infectious Diseases, Faculty of Medicine, Imperial College London, W2 1PG, London, UK
  • Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, 21702, Frederick, Maryland, USA
  • Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea
  • Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, 90095, Los Angeles, California, USA
  • Fogarty International Center, National Institutes of Health, 20892, Bethesda, Maryland, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature22040

    DOI

    http://dx.doi.org/10.1038/nature22040

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1084754035

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28405027


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