New Results
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno Faria, Daniel J. Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro II, Sophie Duraffour, Mike Elmore, Lawrence Fakoli, Merle Gilbert, Sahr M Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart Haagmans, Julian A. Hiscox, Umaru Jah, Brima Kargbo, Jeffrey Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke Meredith, James Qu, Joshua Quick, Susan D. Pas, My VT Phan, Georgios Poliakis, Chantal Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete A. 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 Blyden, Fatorma Bolay, Miles Carroll, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward C Holmes, Brima Kargbo, Paul Kellam, Marion P. G. Koopmans, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G Pybus, Pardis Sabeti, Amadou Sall, Ute Ströher, Isatta Wury, Marc A Suchard, Philippe Lemey, Andrew Rambaut
doi: https://doi.org/10.1101/071779
Gytis Dudas
1Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Luiz Max Carvalho
1Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
Trevor Bedford
2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Andrew J. Tatem
3WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK
4Flowminder Foundation, Stockholm, Sweden
Guy Baele
5Department of Microbiology and Immunology, Rega Institute, KU Leuven University of Leuven, Leuven, Belgium
Nuno Faria
6Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Daniel J. Park
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Jason Ladner
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
Armando Arias
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
10Section for Virology, National Veterinary Institute, Technical University of Denmark, Blowsvej 27, 1870, Frederiksberg C, Denmark
Danny Asogun
11Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Filip Bielejec
5Department of Microbiology and Immunology, Rega Institute, KU Leuven University of Leuven, Leuven, Belgium
Sarah Caddy
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
Matt Cotten
13Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Jonathan Dambrozio
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
Simon Dellicour
5Department of Microbiology and Immunology, Rega Institute, KU Leuven University of Leuven, Leuven, Belgium
Antonino Di Caro
14National Institute for Infectious Diseases “L. Spallanzani” - IRCCS, Via Portuense 292, 00149 Rome, Italy
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Joseph W. Diclaro II
15Naval Medical Research Unit 3, 3A Imtidad Ramses Street, Cairo, 11517, Egypt
Sophie Duraffour
16Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Mike Elmore
17National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
Lawrence Fakoli
18Liberian Institute for Biomedical Research, Charlesville, Liberia.
Merle Gilbert
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
Sahr M Gevao
19University of Sierra Leone, Freetown, Sierra Leone
Stephen Gire
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
20Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Adrianne Gladden-Young
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Andreas Gnirke
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Augustine Goba
21Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Donald S. Grant
21Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Bart Haagmans
23Department of Viroscience, Erasmus University Medical Centre, P.O. Box 20140, 300 CA Rotterdam, the Netherlands
Julian A. Hiscox
24Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, United Kingdom
25NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, UK.
Umaru Jah
26University of Makeni, Makeni, Sierra Leone
Brima Kargbo
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Jeffrey Kugelman
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
Di Liu
27Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
Jia Lu
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
Christine M. Malboeuf
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Suzanne Mate
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
David A. Matthews
28University of Bristol, BS8 1TD, United Kingdom
Christian B. Matranga
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Luke Meredith
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
26University of Makeni, Makeni, Sierra Leone
James Qu
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Joshua Quick
29Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
Susan D. Pas
23Department of Viroscience, Erasmus University Medical Centre, P.O. Box 20140, 300 CA Rotterdam, the Netherlands
My VT Phan
13Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Georgios Poliakis
24Institute of Infection and Global Health, University of Liverpool, Liverpool L69 2BE, United Kingdom
Chantal Reusken
23Department of Viroscience, Erasmus University Medical Centre, P.O. Box 20140, 300 CA Rotterdam, the Netherlands
Mariano Sanchez-Lockhart
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
30University of Nebraska Medical Center, Omaha, NE, USA
Stephen F. Schaffner
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
John S. Schieffelin
31Department of Pediatrics, Section of Infectious Diseases, New Orleans, LA 70112, USA
Rachel S. Sealfon
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Etienne Simon-Loriere
32Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
33CNRS URA3012, Paris 75015, France
Saskia L. Smits
23Department of Viroscience, Erasmus University Medical Centre, P.O. Box 20140, 300 CA Rotterdam, the Netherlands
Kilian Stoecker
34Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Lucy Thorne
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
Ekaete A. Tobin
11Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Mohamed A. Vandi
21Viral Hemorrhagic Fever Program, Kenema Government Hospital, 1 Combema Road, Kenema, Sierra Leone
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Simon J. Watson
13Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
Kendra West
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Shannon Whitmer
35Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
Michael R. Wiley
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
30University of Nebraska Medical Center, Omaha, NE, USA
Sarah M. Winnicki
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
20Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Shirlee Wohl
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
20Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Roman Wölfel
34Bundeswehr Institute of Microbiology, Neuherbergstrasse 11, 80937 Munich, Germany
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Nathan L. Yozwiak
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
20Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Kristian G. Andersen
36The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA.
37Scripps Translational Science Institute, La Jolla, CA 92037, USA
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
Sylvia Blyden
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Fatorma Bolay
18Liberian Institute for Biomedical Research, Charlesville, Liberia.
Miles Carroll
17National Infections Service, Public Health England, Porton Down, Salisbury, Wilts SP4 0JG, UK
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Boubacar Diallo
39World Health Organization, Conakry, Guinea
Pierre Formenty
40WHO Ebola Response Team
Christophe Fraser
41Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analyses and Modelling, School of Public Health, Imperial College London, UK
George F. Gao
27Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
42Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
Robert F. Garry
43Department of Microbiology & Immunology, New Orleans, LA 70112, USA
Ian Goodfellow
9Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 2QQ, UK
26University of Makeni, Makeni, Sierra Leone
Stephan Günther
16Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
12The European Mobile Laboratory Consortium, 20359 Hamburg, Germany
Christian Happi
44Redeemer’s University, Ede, Osun State, Nigeria
Edward C Holmes
45Marie 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, NSW 2006, Australia
Brima Kargbo
22Ministry of Health and Sanitation, 4th Floor Youyi Building, Freetown, Sierra Leone
Paul Kellam
13Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
47Division of Infectious Diseases, Imperial College Faculty of Medicine, London W2 1PG, UK
Marion P. G. Koopmans
23Department of Viroscience, Erasmus University Medical Centre, P.O. Box 20140, 300 CA Rotterdam, the Netherlands
Nicholas J. Loman
29Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
N’Faly Magassouba
48Universit Gamal Abdel Nasser de Conakry, Laboratoire des Fivres Hmorragiques en Guine, Conakry, Guinea
Dhamari Naidoo
40WHO Ebola Response Team
Stuart T. Nichol
35Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
Tolbert Nyenswah
38Minstry of Health Liberia, Monrovia, Liberia
Gustavo Palacios
8Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702, USA
Oliver G Pybus
6Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
Pardis Sabeti
7Broad Institute of Harvard and MIT, Cambridge, MA 02138, USA
20Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
Amadou Sall
32Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
Ute Ströher
35Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia, USA
Isatta Wury
46Ministry of Health Guinea, Conakry, Guinea
Marc A Suchard
49Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
50Department of Biomathematics David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
51Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
Philippe Lemey
5Department of Microbiology and Immunology, Rega Institute, KU Leuven University of Leuven, Leuven, Belgium
Andrew Rambaut
1Institute of Evolutionary Biology, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
52Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
53Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
Article usage
Posted September 02, 2016.
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno Faria, Daniel J. Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro II, Sophie Duraffour, Mike Elmore, Lawrence Fakoli, Merle Gilbert, Sahr M Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart Haagmans, Julian A. Hiscox, Umaru Jah, Brima Kargbo, Jeffrey Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke Meredith, James Qu, Joshua Quick, Susan D. Pas, My VT Phan, Georgios Poliakis, Chantal Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete A. 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 Blyden, Fatorma Bolay, Miles Carroll, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward C Holmes, Brima Kargbo, Paul Kellam, Marion P. G. Koopmans, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G Pybus, Pardis Sabeti, Amadou Sall, Ute Ströher, Isatta Wury, Marc A Suchard, Philippe Lemey, Andrew Rambaut
bioRxiv 071779; doi: https://doi.org/10.1101/071779
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno Faria, Daniel J. Park, Jason Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah Caddy, Matt Cotten, Jonathan Dambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro II, Sophie Duraffour, Mike Elmore, Lawrence Fakoli, Merle Gilbert, Sahr M Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart Haagmans, Julian A. Hiscox, Umaru Jah, Brima Kargbo, Jeffrey Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke Meredith, James Qu, Joshua Quick, Susan D. Pas, My VT Phan, Georgios Poliakis, Chantal Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete A. 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 Blyden, Fatorma Bolay, Miles Carroll, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward C Holmes, Brima Kargbo, Paul Kellam, Marion P. G. Koopmans, Nicholas J. Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo Palacios, Oliver G Pybus, Pardis Sabeti, Amadou Sall, Ute Ströher, Isatta Wury, Marc A Suchard, Philippe Lemey, Andrew Rambaut
bioRxiv 071779; doi: https://doi.org/10.1101/071779
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