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Nature. 2017 Apr 20;544(7650):309-315. doi: 10.1038/nature22040. Epub 2017 Apr 12.

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Author information

1
Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.
2
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
3
WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
4
Flowminder Foundation, Stockholm, Sweden.
5
Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
6
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
7
Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
8
Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
9
Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
10
National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
11
Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.
12
The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.
13
Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
14
Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
15
National Institute for Infectious Diseases 'L. Spallanzani'-IRCCS, Via Portuense 292, 00149 Rome, Italy.
16
Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo 11517, Egypt.
17
Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany.
18
National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK.
19
Liberian Institute for Biomedical Research, Charlesville, Liberia.
20
Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal.
21
University of Sierra Leone, Freetown, Sierra Leone.
22
Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
23
Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.
24
Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
25
Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK.
26
NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L69 3GL, UK.
27
University of Makeni, Makeni, Sierra Leone.
28
Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
29
University of Bristol, Bristol BS8 1TD, UK.
30
Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
31
University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
32
Department of Pediatrics, Section of Infectious Diseases, New Orleans, Louisiana 70112, USA.
33
Center for Computational Biology, Flatiron Institute, New York, New York 10010, USA.
34
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
35
Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
36
Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, Paris 75015, France.
37
Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany.
38
Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30333, USA.
39
The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, California 92037, USA.
40
Scripps Translational Science Institute, La Jolla, California 92037, USA.
41
Ministry of Social Welfare, Gender and Children's Affairs, New Englandville, Freetown, Sierra Leone.
42
University of Southampton, South General Hospital, Southampton SO16 6YD, UK.
43
Minstry of Health Liberia, Monrovia, Liberia.
44
World Health Organization, Conakry, Guinea.
45
World Health Organization, Geneva, Switzerland.
46
Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
47
Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
48
Department of Microbiology and Immunology, New Orleans, Louisiana 70112, USA.
49
Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria.
50
African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
51
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, Sydney, New South Wales 2006, Australia.
52
Ministry of Health Guinea, Conakry, Guinea.
53
Division of Infectious Diseases, Faculty of Medicine, Imperial College London, London W2 1PG, UK.
54
Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, Maryland 21702, USA.
55
Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea.
56
Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California 90095, USA.
57
Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA.
58
Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA.
59
Centre for Immunology, Infection and Evolution, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.
60
Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA.

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.

PMID:
28405027
PMCID:
PMC5712493
DOI:
10.1038/nature22040
[Indexed for MEDLINE]
Free PMC Article

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