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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

By 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, 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 Matthews, Christian B. Matranga, Luke Meredith, James Qu, Joshua Quick, Susan D. Pas, My 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 G 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, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F Garry, Ian G. Goodfellow, Stephan Günther, Christian Happi, Edward C Holmes, 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, Keïta Sakoba, Ute Ströeher, Isatta Wurie, Marc A Suchard, Philippe Lemey, Andrew Rambaut

Posted 02 Sep 2016
bioRxiv DOI: 10.1101/071779 (published DOI: 10.1038/nature22040)

The 2013-2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude, duration and impact. Extensive collaborative sequencing projects have produced a large collection of over 1600 Ebola virus genomes, representing over 5% of known cases, unmatched for any single human epidemic. In this comprehensive analysis of this entire dataset, we reconstruct in detail the history of migration, proliferation and decline of Ebola virus throughout the region. We test the association of geography, climate, administrative boundaries, demography and culture with viral movement among 56 administrative regions. Our results show that during the outbreak viral lineages moved according to a classic 'gravity' model, with more intense migration between larger and more proximate population centers. Notably, we find that despite a strong attenuation of international dispersal after border closures, localized cross-border transmission beforehand had already set the seeds for an international epidemic, rendering these measures relatively ineffective in curbing the epidemic. We use this empirical evidence to address why the epidemic did not spread into neighboring countries, showing that although these regions were susceptible to developing significant outbreaks, they were also at lower risk of viral introductions. Finally, viral genome sequence data uniquely reveals 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 approaches to intervention in such epidemics in the future.

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