Virus genomes reveal factors that spread and sustained the Ebola epidemic

Research output: Contribution to journalArticle

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
  • 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
  • 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

Colleges, School and Institutes

External organisations

  • 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.
  • WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
  • Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
  • Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
  • Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
  • Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
  • University of Cambridge
  • Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria.
  • Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
  • The European Mobile Laboratory Consortium, 20359 Hamburg, Germany.
  • Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo 11517, Egypt.
  • National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK.
  • Liberian Institute for Biomedical Research, Charlesville, Liberia.
  • Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, 36 Avenue Pasteur, BP 220, Dakar, Sénégal.
  • University of Sierra Leone, Freetown, Sierra Leone.
  • Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone.
  • Department of Viroscience, Erasmus University Medical Centre, PO Box 2040, 300 CA Rotterdam, the Netherlands.
  • University of Liverpool
  • Department of Public Health, University of Makeni, Sierra Leone.
  • Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
  • BRISTOL UNIVERSITY
  • Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. n.j.loman@bham.ac.uk.
  • Department of Pediatrics, Section of Infectious Diseases, New Orleans, Louisiana 70112, USA.
  • Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
  • Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, Georgia 30333, USA.
  • The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, California 92037, USA.
  • Ministry of Social Welfare, Gender and Children's Affairs, New Englandville, Freetown, Sierra Leone.
  • Minstry of Health Liberia, Monrovia, Liberia.
  • World Health Organization, Conakry, Guinea.
  • World Health Organization, Geneva, Switzerland; and.
  • Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK.
  • Department of Microbiology and Immunology, New Orleans, Louisiana 70112, USA.
  • Department of Biological Sciences, 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, Sydney, New South Wales 2006, Australia.
  • Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone.
  • Ministry of Health, Conakry, Guinea.
  • 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.
  • Université Gamal Abdel Nasser de Conakry, Laboratoire des Fièvres Hémorragiques en Guinée, Conakry, Guinea.
  • Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, California 90095, 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.

Details

Original languageEnglish
Pages (from-to)309-315
Number of pages7
JournalNature
Volume544
Issue number7650
Early online date12 Apr 2017
Publication statusPublished - 20 Apr 2017

Keywords

  • Statistical methods, Viral infection, Phylogenetics , Epidemiology