title: Virus genomes reveal factors that spread and sustained the Ebola epidemic.
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.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.|Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Gytis
authors.initials: G
authors.lastname: Dudas
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.
authors.forename: Luiz Max
authors.initials: LM
authors.lastname: Carvalho
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
authors.affiliation: WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK.|Flowminder Foundation, Stockholm, Sweden.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Tatem
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Baele
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Nuno R
authors.initials: NR
authors.lastname: Faria
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Park
authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
authors.forename: Jason T
authors.initials: JT
authors.lastname: Ladner
authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.|National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
authors.forename: Armando
authors.initials: A
authors.lastname: Arias
authors.affiliation: Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.|The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.
authors.forename: Danny
authors.initials: D
authors.lastname: Asogun
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
authors.forename: Filip
authors.initials: F
authors.lastname: Bielejec
authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
authors.forename: Sarah L
authors.initials: SL
authors.lastname: Caddy
authors.affiliation: Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.|Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: Matthew
authors.initials: M
authors.lastname: Cotten
authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: D'Ambrozio
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
authors.forename: Simon
authors.initials: S
authors.lastname: Dellicour
authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|National Institute for Infectious Diseases 'L. Spallanzani'-IRCCS, Via Portuense 292, 00149 Rome, Italy.
authors.forename: Antonino
authors.initials: A
authors.lastname: Di Caro
authors.affiliation: Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo 11517, Egypt.
authors.forename: Joseph W
authors.initials: JW
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authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany.
authors.forename: Sophie
authors.initials: S
authors.lastname: Duraffour
authors.affiliation: National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK.
authors.forename: Michael J
authors.initials: MJ
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authors.affiliation: Liberian Institute for Biomedical Research, Charlesville, Liberia.
authors.forename: Lawrence S
authors.initials: LS
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authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal.
authors.forename: Ousmane
authors.initials: O
authors.lastname: Faye
authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
authors.forename: Merle L
authors.initials: ML
authors.lastname: Gilbert
authors.affiliation: University of Sierra Leone, Freetown, Sierra Leone.
authors.forename: Sahr M
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Stephen
authors.initials: S
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.initials: A
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.|Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
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authors.affiliation: Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.|Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
authors.forename: Donald S
authors.initials: DS
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authors.affiliation: Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
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authors.initials: BL
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authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK.|NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L69 3GL, UK.
authors.forename: Julian A
authors.initials: JA
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authors.affiliation: University of Makeni, Makeni, Sierra Leone.
authors.forename: Umaru
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authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
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authors.affiliation: Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Di
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authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.initials: CM
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authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
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authors.affiliation: University of Bristol, Bristol BS8 1TD, UK.
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authors.initials: DA
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors.forename: Christian B
authors.initials: CB
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authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.|University of Makeni, Makeni, Sierra Leone.
authors.forename: Luke W
authors.initials: LW
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Joshua
authors.initials: J
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authors.affiliation: Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: Suzan D
authors.initials: SD
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authors.affiliation: Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.|Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: My V T
authors.initials: MVT
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authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, UK.
authors.forename: Georgios
authors.initials: G
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authors.affiliation: Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: Chantal B
authors.initials: CB
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authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.|University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
authors.forename: Mariano
authors.initials: M
authors.lastname: Sanchez-Lockhart
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.initials: SF
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authors.affiliation: Department of Pediatrics, Section of Infectious Diseases, New Orleans, Louisiana 70112, USA.
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authors.initials: JS
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Center for Computational Biology, Flatiron Institute, New York, New York 10010, USA.|Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA.
authors.forename: Rachel S
authors.initials: RS
authors.lastname: Sealfon
authors.affiliation: Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.|Génétique Fonctionelle des Maladies Infectieuses, CNRS URA3012, Paris 75015, France.
authors.forename: Etienne
authors.initials: E
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authors.affiliation: Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: Saskia L
authors.initials: SL
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authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany.
authors.forename: Kilian
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authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.
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authors.initials: EA
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authors.affiliation: Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.|Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
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authors.affiliation: Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
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authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.|University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany.
authors.forename: Roman
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authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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authors.initials: NL
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authors.affiliation: The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, California 92037, USA.|Scripps Translational Science Institute, La Jolla, California 92037, USA.
authors.forename: Kristian G
authors.initials: KG
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authors.initials: SO
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authors.affiliation: Liberian Institute for Biomedical Research, Charlesville, Liberia.
authors.forename: Fatorma
authors.initials: F
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authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK.|NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool L69 3GL, UK.|University of Southampton, South General Hospital, Southampton SO16 6YD, UK.
authors.forename: Miles W
authors.initials: MW
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authors.affiliation: Minstry of Health Liberia, Monrovia, Liberia.
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authors.initials: B
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authors.affiliation: World Health Organization, Conakry, Guinea.
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authors.initials: B
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authors.affiliation: World Health Organization, Geneva, Switzerland.
authors.forename: Pierre
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authors.affiliation: Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
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authors.initials: C
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authors.affiliation: Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.|Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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authors.initials: GF
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authors.affiliation: Department of Microbiology and Immunology, New Orleans, Louisiana 70112, USA.
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authors.initials: RF
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authors.affiliation: Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK.|University of Makeni, Makeni, Sierra Leone.
authors.forename: Ian
authors.initials: I
authors.lastname: Goodfellow
authors.affiliation: The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.|Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany.
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authors.initials: S
authors.lastname: Günther
authors.affiliation: Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria.|African Center of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria.
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authors.initials: CT
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authors.affiliation: 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.
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authors.affiliation: Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
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authors.affiliation: Ministry of Health Guinea, Conakry, Guinea.
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authors.initials: S
authors.lastname: Keïta
authors.affiliation: Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.|Division of Infectious Diseases, Faculty of Medicine, Imperial College London, London W2 1PG, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Kellam
authors.affiliation: Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
authors.forename: Marion P G
authors.initials: MPG
authors.lastname: Koopmans
authors.affiliation: 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.
authors.forename: Jens H
authors.initials: JH
authors.lastname: Kuhn
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Loman
authors.affiliation: Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea.
authors.forename: N'Faly
authors.initials: N
authors.lastname: Magassouba
authors.affiliation: World Health Organization, Geneva, Switzerland.
authors.forename: Dhamari
authors.initials: D
authors.lastname: Naidoo
authors.affiliation: Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30333, USA.
authors.forename: Stuart T
authors.initials: ST
authors.lastname: Nichol
authors.affiliation: Minstry of Health Liberia, Monrovia, Liberia.
authors.forename: Tolbert
authors.initials: T
authors.lastname: Nyenswah
authors.affiliation: Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Palacios
authors.affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Pardis C
authors.initials: PC
authors.lastname: Sabeti
authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal.
authors.forename: Amadou
authors.initials: A
authors.lastname: Sall
authors.affiliation: Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30333, USA.
authors.forename: Ute
authors.initials: U
authors.lastname: Ströher
authors.affiliation: University of Sierra Leone, Freetown, Sierra Leone.
authors.forename: Isatta
authors.initials: I
authors.lastname: Wurie
authors.affiliation: Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California 90095, USA.|Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA.|Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, California 90095, USA.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, 3000 Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.|Centre for Immunology, Infection and Evolution, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.|Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
mesh_terms: D002980:Climate; D004196:Disease Outbreaks / Q000706:statistics & numerical data; D029043:Ebolavirus / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology*; D016679:Genome, Viral / Q000235:genetics*; D005843:Geography; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D006801:Humans; D038622:Internationality; D016014:Linear Models; D017720:Molecular Epidemiology; D010802:Phylogeny; D014195:Travel / Q000331:legislation & jurisprudence / Q000706:statistics & numerical data