Virus genomes reveal factors that spread and sustained the Ebola epidemic

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. FakoliOusmane 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, Joshua Quick, 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, Nicholas J. Loman, 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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Pages (from-to)309-315
Number of pages7
JournalNature
Volume544
Issue number7650
DOIs
StatePublished - Apr 20 2017
Externally publishedYes

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Ebolavirus
Genome
Viruses
Geography
Gravitation
Climate
Disease Outbreaks
Seeds
Demography
Population

ASJC Scopus subject areas

  • General

Cite this

Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., ... Rambaut, A. (2017). Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 544(7650), 309-315. https://doi.org/10.1038/nature22040

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 journalArticle

Dudas, G, Carvalho, LM, Bedford, T, Tatem, AJ, Baele, G, Faria, NR, Park, DJ, Ladner, JT, Arias, A, Asogun, D, Bielejec, F, Caddy, SL, Cotten, M, D'Ambrozio, J, Dellicour, S, Di Caro, A, Diclaro, JW, Duraffour, S, Elmore, MJ, Fakoli, LS, Faye, O, Gilbert, ML, Gevao, SM, Gire, S, Gladden-Young, A, Gnirke, A, Goba, A, Grant, DS, Haagmans, BL, Hiscox, JA, Jah, U, Kugelman, JR, Liu, D, Lu, J, Malboeuf, CM, Mate, S, Matthews, DA, Matranga, CB, Meredith, LW, Qu, J, Quick, J, Pas, SD, Phan, MVT, Pollakis, G, Reusken, CB, Sanchez-Lockhart, M, Schaffner, SF, Schieffelin, JS, Sealfon, RS, Simon-Loriere, E, Smits, SL, Stoecker, K, Thorne, L, Tobin, EA, Vandi, MA, Watson, SJ, West, K, Whitmer, S, Wiley, MR, Winnicki, SM, Wohl, S, Wölfel, R, Yozwiak, NL, Andersen, KG, Blyden, SO, Bolay, F, Carroll, MW, Dahn, B, Diallo, B, Formenty, P, Fraser, C, Gao, GF, Garry, RF, Goodfellow, I, Günther, S, Happi, CT, Holmes, EC, Kargbo, B, Keïta, S, Kellam, P, Koopmans, MPG, Kuhn, JH, Loman, NJ, Magassouba, NF, Naidoo, D, Nichol, ST, Nyenswah, T, Palacios, G, Pybus, OG, Sabeti, PC, Sall, A, Ströher, U, Wurie, I, Suchard, MA, Lemey, P & Rambaut, A 2017, 'Virus genomes reveal factors that spread and sustained the Ebola epidemic', Nature, vol. 544, no. 7650, pp. 309-315. https://doi.org/10.1038/nature22040
Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR et al. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature. 2017 Apr 20;544(7650):309-315. https://doi.org/10.1038/nature22040
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. / Virus genomes reveal factors that spread and sustained the Ebola epidemic. In: Nature. 2017 ; Vol. 544, No. 7650. pp. 309-315.
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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

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