Virus genomes reveal factors that spread and sustained the Ebola epidemic

Gytis Dudas; Luiz Max Carvalho; Trevor Bedford; Andrew J. Tatem; Guy Baele; Nuno Rodrigues 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 II; Sophie Duraffour; Michael J Elmore; Lawrence S Fakoli; Ousmane Faye; Merle L. Gilbert; Sahr M. Gevao; Stephen K. 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; Saska L. Smits; Kilian Stoecker; Lucy Thorne; Ekaete Alice Tobin; Mohamed A. Vandi; Simon J. Watson; Kendra West; Shannon L.M. Whitmer; Michael R. Wiley; Sarah M. Winnicki; Shirlee Wohl; Roman Wölfel; Nathan L. Yozwiak; Kristian G. Andersen; Sylvia O. Blyden; Fatorma K. Bolay; Miles W Carroll; Bernice Dahn; Boubacar Diallo; Pierre Formenty; Christophe Fraser; George F. Gao; Robert F Garry; Ian Goodfellow; Stephan Günther; Christian Happi; Edward C. Holmes; Brima Kargbo; Sakoba Keïta; Paul Kellam; Marion P G Koopmans; Jens H. Kuhn; Nicholas Loman; N’Faly Magassouba; Dhamari Naidoo; Stuart T. Nichol; Tolbert Nyenswah; Gustavo F. Palacios; Oliver G. Pybus; Paradis C Sabeti; Amadou A. Sall; Ute Ströher; 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 Rodrigues 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 II, Sophie Duraffour, Michael J Elmore, Lawrence S FakoliOusmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen K. 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, Saska L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon L.M. Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma K. Bolay, Miles W Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F Garry, Ian Goodfellow, Stephan Günther, Christian Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion P G Koopmans, Jens H. Kuhn, Nicholas Loman, N’Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo F. Palacios, Oliver G. Pybus, Paradis C Sabeti, Amadou A. Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, Andrew Rambaut

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region. 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 set the seeds for an international epidemic, rendering these measures ineffective in curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing they were susceptible to significant outbreaks but at lower risk of introductions. Finally, we reveal this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform interventions in future epidemics.

Original language	English
Pages (from-to)	309–315
Number of pages	7
Journal	Nature
Volume	544
DOIs	https://doi.org/10.1038/nature22040
Publication status	Published - 12 Apr 2017

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10.1038/nature22040

Virus genomes reveal factors that spread and sustained the Ebola epidemicAccepted author manuscript, 19.6 MB

COMPARE: COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe
Woolhouse, M.
EU government bodies
1/12/14 → 30/11/19
Project: Research
PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach
Rambaut, A.
EU government bodies
1/11/11 → 30/04/17
Project: Research
VIRAL PHYLOGEOGRAPHY: Evolutionary reconstruction of viral spread in time and space
Rambaut, A.
EU government bodies
1/10/10 → 30/09/15
Project: Research

Virus genomes reveal factors that spread and sustained the Ebola epidemic
Dudas, G. (Creator), Lemey, P. (Creator) & Rambaut, A. (Creator), Edinburgh DataShare, 15 Feb 2017
DOI: 10.7488/ds/1711
Dataset

Andrew Rambaut
- a.rambauted.acuk
- School of Biological Sciences - Personal Chair in Molecular Evolution
Person: Academic: Research Active

Cite this

Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., Park, D. J., Ladner, JT., Arias, A., Asogun, D., Bielejec, F., Caddy, S. L., Cotten, M., D'Ambrozio, J., Dellicour, S., Di Caro, A., Diclaro II, J. W., Duraffour, S., Elmore, M. J., ... Rambaut, A. (2017). Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 544 , 309–315. https://doi.org/10.1038/nature22040

@article{4fea81066e0247e095be9ec746a71bca,

title = "Virus genomes reveal factors that spread and sustained the Ebola epidemic",

abstract = "The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic {\textquoteleft}gravity{\textquoteright} model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already set the seeds for an international epidemic, rendering these measures ineffective in curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing they were susceptible to significant outbreaks but at lower risk of introductions. Finally, we reveal this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help 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 Rodrigues} and Park, {Daniel J.} and Jason T. Ladner and Armando Arias 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 II}, {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 Gire, {Stephen K.} 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 Jeffrey R. Kugelman 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 John S. Schieffelin and Sealfon, {Rachel S.} and Etienne Simon-Loriere and Smits, {Saska L.} and Kilian Stoecker and Lucy Thorne and Tobin, {Ekaete Alice} and Mohamed A. Vandi and Watson, {Simon J.} and Kendra West and Shannon L.M. Whitmer and Wiley, {Michael R.} and Sarah M. Winnicki and Shirlee Wohl and Roman W{\"o}lfel and Yozwiak, {Nathan L.} and Andersen, {Kristian G.} and Blyden, {Sylvia O.} and Bolay, {Fatorma K.} 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 Christian Happi and Holmes, {Edward C.} and Brima Kargbo and Sakoba Ke{\"i}ta and Paul Kellam and Koopmans, {Marion P G} and Jens H. Kuhn and Nicholas Loman and N{\textquoteright}Faly Magassouba and Dhamari Naidoo and Stuart T. Nichol and Tolbert Nyenswah and Gustavo F. Palacios and Pybus, {Oliver G.} and Sabeti, {Paradis C} and Sall, {Amadou A.} and Ute Str{\"o}her and Isatta Wurie and Suchard, {Marc A.} and Philippe Lemey and Andrew Rambaut",

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day = "12",

doi = "10.1038/nature22040",

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pages = "309–315",

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}

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 II, JW, Duraffour, S, Elmore, MJ, Fakoli, LS, Faye, O, Gilbert, ML, Gevao, SM, Gire, SK, 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, SLM, Wiley, MR, Winnicki, SM, Wohl, S, Wölfel, R, Yozwiak, NL, Andersen, KG, Blyden, SO, Bolay, FK, Carroll, MW, Dahn, B, Diallo, B, Formenty, P, Fraser, C, Gao, GF, Garry, RF, Goodfellow, I, Günther, S, Happi, C, Holmes, EC, Kargbo, B, Keïta, S, Kellam, P, Koopmans, MPG, Kuhn, JH, Loman, N, Magassouba, NF, Naidoo, D, Nichol, ST, Nyenswah, T, Palacios, GF, Pybus, OG, Sabeti, PC, Sall, AA, 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 , 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 Rodrigues

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 II, 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 K.

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, Saska 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 L.M.

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 K.

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

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

AU - Magassouba, N’Faly

AU - Naidoo, Dhamari

AU - Nichol, Stuart T.

AU - Nyenswah, Tolbert

AU - Palacios, Gustavo F.

AU - Pybus, Oliver G.

AU - Sabeti, Paradis C

AU - Sall, Amadou A.

AU - Ströher, Ute

AU - Wurie, Isatta

AU - Suchard, Marc A.

AU - Lemey, Philippe

AU - Rambaut, Andrew

PY - 2017/4/12

Y1 - 2017/4/12

N2 - The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region. 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 set the seeds for an international epidemic, rendering these measures ineffective in curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing they were susceptible to significant outbreaks but at lower risk of introductions. Finally, we reveal this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform interventions in future epidemics.

AB - The 2013–2016 epidemic of Ebola virus disease was of unprecedented magnitude, duration and impact. Analysing 1610 Ebola virus genomes, representing over 5% of known cases, we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region. 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 set the seeds for an international epidemic, rendering these measures ineffective in curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing they were susceptible to significant outbreaks but at lower risk of introductions. Finally, we reveal this large epidemic to be a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help inform interventions in future epidemics.

U2 - 10.1038/nature22040

DO - 10.1038/nature22040

M3 - Article

SN - 0028-0836

VL - 544

SP - 309

EP - 315

JO - Nature

JF - Nature

ER -

Virus genomes reveal factors that spread and sustained the Ebola epidemic

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Projects

COMPARE: COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe

PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach

VIRAL PHYLOGEOGRAPHY: Evolutionary reconstruction of viral spread in time and space

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Virus genomes reveal factors that spread and sustained the Ebola epidemic

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Andrew Rambaut

Cite this