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 Esteban; 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; 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 Wolfel; 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 Stroher; Isatta Wurie; Marc A. Suchard; Philippe Lemey; Andrew Rambaut

doi:10.1038/nature22040

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 Esteban, 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 Wolfel, 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 Stroher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, Andrew Rambaut

Research output: Contribution to journal › Journal article › Research › peer-review

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
Journal	Nature
Volume	544
Issue number	7650
Pages (from-to)	309-315
ISSN	0028-0836
DOIs	https://doi.org/10.1038/nature22040
Publication status	Published - 2017

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Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., Park, D. J., Ladner, J. T., Arias Esteban, A., Asogun, D., Bielejec, F., Caddy, S. L., Cotten, M., D'Ambrozio, J., Dellicour, S., Di Caro, A., Diclaro, J. W., Duraffour, S., Elmore, M. J., ... 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

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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.",

author = "Gytis Dudas and Carvalho, {Luiz Max} and Trevor Bedford and Tatem, {Andrew J.} and Guy Baele and Faria, {Nuno R.} and Park, {Daniel J.} and Ladner, {Jason T.} and {Arias Esteban}, Armando and Danny Asogun and Filip Bielejec and Caddy, {Sarah L.} and Matthew Cotten and Jonathan D'Ambrozio and Simon Dellicour and {Di Caro}, Antonino and Diclaro, {Joseph W.} and Sophie Duraffour and Elmore, {Michael J.} and Fakoli, {Lawrence S.} and Ousmane Faye and Gilbert, {Merle L.} and Gevao, {Sahr M.} and Stephen Gire and Adrianne Gladden-Young and Andreas Gnirke and Augustine Goba and Grant, {Donald S.} and Haagmans, {Bart L.} and Hiscox, {Julian A.} and Umaru Jah and Kugelman, {Jeffrey R.} and Di Liu and Jia Lu and Malboeuf, {Christine M.} and Suzanne Mate and Matthews, {David A.} and Matranga, {Christian B.} and Meredith, {Luke W.} and James Qu and Joshua Quick and Pas, {Suzan D.} and Phan, {My V. T.} and Georgios Pollakis and Reusken, {Chantal B.} and Mariano Sanchez-Lockhart and Schaffner, {Stephen F.} and Schieffelin, {John S.} and Sealfon, {Rachel S.} and Etienne Simon-Loriere and Smits, {Saskia L.} and Kilian Stoecker and Lucy Thorne and Tobin, {Ekaete Alice} and Vandi, {Mohamed A.} and {J. Watson}, Simon and Kendra West and Shannon Whitmer and Wiley, {Michael R.} and Winnicki, {Sarah M.} and Shirlee Wohl and Roman Wolfel and Yozwiak, {Nathan L.} and Andersen, {Kristian G.} and Blyden, {Sylvia O.} and Fatorma Bolay and Carroll, {Miles W.} and Bernice Dahn and Boubacar Diallo and Pierre Formenty and Christophe Fraser and Gao, {George F.} and Garry, {Robert F.} and Ian Goodfellow and Stephan G{\"u}nther and Happi, {Christian T.} and Holmes, {Edward C.} and Brima Kargbo and Sakoba Ke{\"i}ta and Paul Kellam and Koopmans, {Marion P. G.} and Kuhn, {Jens H.} and Loman, {Nicholas J.} and N'Faly Magassouba and Dhamari Naidoo and Nichol, {Stuart T.} and Tolbert Nyenswah and Gustavo Palacios and Pybus, {Oliver G.} and Sabeti, {Pardis C.} and Amadou Sall and Ute Stroher and Isatta Wurie and Suchard, {Marc A.} and Philippe Lemey and Andrew Rambaut",

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Dudas, G, Carvalho, LM, Bedford, T, Tatem, AJ, Baele, G, Faria, NR, Park, DJ, Ladner, JT, Arias Esteban, 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, J. Watson, S, West, K, Whitmer, S, Wiley, MR, Winnicki, SM, Wohl, S, Wolfel, 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, Stroher, 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

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 Esteban, 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 - J. Watson, Simon

AU - West, Kendra

AU - Whitmer, Shannon

AU - Wiley, Michael R.

AU - Winnicki, Sarah M.

AU - Wohl, Shirlee

AU - Wolfel, 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 - Stroher, Ute

AU - Wurie, Isatta

AU - Suchard, Marc A.

AU - Lemey, Philippe

AU - Rambaut, Andrew

PY - 2017

Y1 - 2017

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.

U2 - 10.1038/nature22040

DO - 10.1038/nature22040

M3 - Journal article

C2 - 28405027

SN - 0028-0836

VL - 544

SP - 309

EP - 315

JO - Nature

JF - Nature

IS - 7650

ER -

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Abstract

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