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.
Original language | English (US) |
---|---|
Pages (from-to) | 309-315 |
Number of pages | 7 |
Journal | Nature |
Volume | 544 |
Issue number | 7650 |
DOIs | |
State | Published - Apr 20 2017 |
Externally published | Yes |
ASJC Scopus subject areas
- General
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Virus genomes reveal factors that spread and sustained the Ebola epidemic. / Dudas, Gytis; Carvalho, Luiz Max; Bedford, Trevor; Tatem, Andrew J.; Baele, Guy; Faria, Nuno R.; Park, Daniel J.; Ladner, Jason T.; Arias, Armando; Asogun, Danny; Bielejec, Filip; Caddy, Sarah L.; Cotten, Matthew; D'Ambrozio, Jonathan; Dellicour, Simon; Di Caro, Antonino; Diclaro, Joseph W.; Duraffour, Sophie; Elmore, Michael J.; Fakoli, Lawrence S.; Faye, Ousmane; Gilbert, Merle L.; Gevao, Sahr M.; Gire, Stephen; Gladden-Young, Adrianne; Gnirke, Andreas; Goba, Augustine; Grant, Donald S.; Haagmans, Bart L.; Hiscox, Julian A.; Jah, Umaru; Kugelman, Jeffrey R.; Liu, Di; Lu, Jia; Malboeuf, Christine M.; Mate, Suzanne; Matthews, David A.; Matranga, Christian B.; Meredith, Luke W.; Qu, James; Quick, Joshua; Pas, Suzan D.; Phan, My V.T.; Pollakis, Georgios; Reusken, Chantal B.; Sanchez-Lockhart, Mariano; Schaffner, Stephen F.; Schieffelin, John S.; Sealfon, Rachel S.; Simon-Loriere, Etienne; Smits, Saskia L.; Stoecker, Kilian; Thorne, Lucy; Tobin, Ekaete Alice; Vandi, Mohamed A.; Watson, Simon J.; West, Kendra; Whitmer, Shannon; Wiley, Michael R.; Winnicki, Sarah M.; Wohl, Shirlee; Wölfel, Roman; Yozwiak, Nathan L.; Andersen, Kristian G.; Blyden, Sylvia O.; Bolay, Fatorma; Carroll, Miles W.; Dahn, Bernice; Diallo, Boubacar; Formenty, Pierre; Fraser, Christophe; Gao, George F.; Garry, Robert F.; Goodfellow, Ian; Günther, Stephan; Happi, Christian T.; Holmes, Edward C.; Kargbo, Brima; Keïta, Sakoba; Kellam, Paul; Koopmans, Marion P.G.; Kuhn, Jens H.; Loman, Nicholas J.; Magassouba, N'Faly; Naidoo, Dhamari; Nichol, Stuart T.; Nyenswah, Tolbert; Palacios, Gustavo; Pybus, Oliver G.; Sabeti, Pardis C.; Sall, Amadou; Ströher, Ute; Wurie, Isatta; Suchard, Marc A.; Lemey, Philippe; Rambaut, Andrew.
In: Nature, Vol. 544, No. 7650, 20.04.2017, p. 309-315.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Virus genomes reveal factors that spread and sustained the Ebola epidemic
AU - Dudas, Gytis
AU - Carvalho, Luiz Max
AU - Bedford, Trevor
AU - Tatem, Andrew J.
AU - Baele, Guy
AU - Faria, Nuno R.
AU - Park, Daniel J.
AU - Ladner, Jason T.
AU - Arias, Armando
AU - Asogun, Danny
AU - Bielejec, Filip
AU - Caddy, Sarah L.
AU - Cotten, Matthew
AU - D'Ambrozio, Jonathan
AU - Dellicour, Simon
AU - Di Caro, Antonino
AU - Diclaro, Joseph W.
AU - Duraffour, Sophie
AU - Elmore, Michael J.
AU - Fakoli, Lawrence S.
AU - Faye, Ousmane
AU - Gilbert, Merle L.
AU - Gevao, Sahr M.
AU - Gire, Stephen
AU - Gladden-Young, Adrianne
AU - Gnirke, Andreas
AU - Goba, Augustine
AU - Grant, Donald S.
AU - Haagmans, Bart L.
AU - Hiscox, Julian A.
AU - Jah, Umaru
AU - Kugelman, Jeffrey R.
AU - Liu, Di
AU - Lu, Jia
AU - Malboeuf, Christine M.
AU - Mate, Suzanne
AU - Matthews, David A.
AU - Matranga, Christian B.
AU - Meredith, Luke W.
AU - Qu, James
AU - Quick, Joshua
AU - Pas, Suzan D.
AU - Phan, My V.T.
AU - Pollakis, Georgios
AU - Reusken, Chantal B.
AU - Sanchez-Lockhart, Mariano
AU - Schaffner, Stephen F.
AU - Schieffelin, John S.
AU - Sealfon, Rachel S.
AU - Simon-Loriere, Etienne
AU - Smits, Saskia L.
AU - Stoecker, Kilian
AU - Thorne, Lucy
AU - Tobin, Ekaete Alice
AU - Vandi, Mohamed A.
AU - Watson, Simon J.
AU - West, Kendra
AU - Whitmer, Shannon
AU - Wiley, Michael R.
AU - Winnicki, Sarah M.
AU - Wohl, Shirlee
AU - Wölfel, Roman
AU - Yozwiak, Nathan L.
AU - Andersen, Kristian G.
AU - Blyden, Sylvia O.
AU - Bolay, Fatorma
AU - Carroll, Miles W.
AU - Dahn, Bernice
AU - Diallo, Boubacar
AU - Formenty, Pierre
AU - Fraser, Christophe
AU - Gao, George F.
AU - Garry, Robert F.
AU - Goodfellow, Ian
AU - Günther, Stephan
AU - Happi, Christian T.
AU - Holmes, Edward C.
AU - Kargbo, Brima
AU - Keïta, Sakoba
AU - Kellam, Paul
AU - Koopmans, Marion P.G.
AU - Kuhn, Jens H.
AU - Loman, Nicholas J.
AU - Magassouba, N'Faly
AU - Naidoo, Dhamari
AU - Nichol, Stuart T.
AU - Nyenswah, Tolbert
AU - Palacios, Gustavo
AU - Pybus, Oliver G.
AU - Sabeti, Pardis C.
AU - Sall, Amadou
AU - Ströher, Ute
AU - Wurie, Isatta
AU - Suchard, Marc A.
AU - Lemey, Philippe
AU - Rambaut, Andrew
N1 - Funding Information: The authors acknowledge support from: European Union Seventh Framework 278433-PREDEMICS (P.L., A.R.) and ERC 260864 (P.L., A.R., M.A.S.) European Union Horizon 2020 643476-COMPARE (M.P.G.K., A.R.), 634650-VIROGENESIS (P.L., M.P.G.K.), 666100-EVIDENT and European Commission IFS/2011/272-372, EMLab (S.G.), National Institutes of Health R01 AI107034, R01 AI117011 and R01 HG006139 and National Science Foundation IIS 1251151 and DMS 1264153 (M.A.S.), NIH AI081982, AI082119, AI082805 AI088843, AI104216, AI104621, AI115754, HSN272200900049C, HHSN272201400048C (R.F.G.), NIH R35 GM119774-01 (T.B.) National Health & Medical Research Council (Australia) (E.C.H.). The Research Foundation - Flanders G0D5117N (G.B., P.L.), Work in Liberia was funded by the Defense Threat Reduction Agency, the Global Emerging Infections System and the Targeted Acquisition of Reference Materials Augmenting Capabilities (TARMAC) Initiative agencies from the US Department of Defense (G.Pa.), Bill and Melinda Gates Foundation OPP1106427, 1032350, OPP1134076, Wellcome Trust 106866/Z/15/Z, Clinton Health Access Initiative (A.J.T.), National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections (J.A.H.), Key Research and Development Program from the Ministry of Science and Technology of China 2016YFC1200800 (D.L.), National Natural Science Foundation of China 81590760 and 81321063 (G.F.G.), Mahan Post-doctoral fellowship Fred Hutchinson Cancer Research Center (G.D.), National Institute of Allergy and Infectious Disease U19AI110818, 5R01AI114855-03, United States Agency for International Development OAA-G-15-00001 and the Bill and Melinda Gates Foundation OPP1123407 (P.C.S.), NIH 1U01HG007480-01 and the World Bank ACE019 (C.T.H.), PEW Biomedical Scholarship, NIH UL1TR001114, and NIAID contract HHSN272201400048C (K.G.A.). J.H.K., an employee of Tunnell Government Services, Inc., is a subcontractor under Battelle Memorial Institute's prime contract with the NIAID (contract HHSN272200700016I). Colour-blind-friendly colour palettes were designed by C. Brewer, Pennsylvania State University (http://colorbrewer2.org). Matplotlib (http://matplotlib.org) was used extensively throughout this article for data visualisation. We acknowledge support from NVIDIA Corporation with the donation of parallel computing resources used for this research. Finally, we recognize the contributions made by our colleagues who died from Ebola virus disease whilst fighting the epidemic. Publisher Copyright: © 2017 Macmillan Publishers Limited, part of Springer Nature.
PY - 2017/4/20
Y1 - 2017/4/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85017439030&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85017439030&partnerID=8YFLogxK
U2 - 10.1038/nature22040
DO - 10.1038/nature22040
M3 - Article
C2 - 28405027
AN - SCOPUS:85017439030
VL - 544
SP - 309
EP - 315
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7650
ER -