TY - JOUR T1 - Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic JF - bioRxiv DO - 10.1101/071779 SP - 071779 AU - Gytis Dudas AU - Luiz Max Carvalho AU - Trevor Bedford AU - Andrew J. Tatem AU - Guy Baele AU - Nuno Faria AU - Daniel J. Park AU - Jason Ladner AU - Armando Arias AU - Danny Asogun AU - Filip Bielejec AU - Sarah Caddy AU - Matt Cotten AU - Jonathan Dambrozio AU - Simon Dellicour AU - Antonino Di Caro AU - Joseph W. Diclaro II AU - Sophie Duraffour AU - Mike Elmore AU - Lawrence Fakoli AU - Merle Gilbert AU - Sahr M Gevao AU - Stephen Gire AU - Adrianne Gladden-Young AU - Andreas Gnirke AU - Augustine Goba AU - Donald S. Grant AU - Bart Haagmans AU - Julian A. Hiscox AU - Umaru Jah AU - Brima Kargbo AU - Jeffrey Kugelman AU - Di Liu AU - Jia Lu AU - Christine M. Malboeuf AU - Suzanne Mate AU - David A. Matthews AU - Christian B. Matranga AU - Luke Meredith AU - James Qu AU - Joshua Quick AU - Susan D. Pas AU - My VT Phan AU - Georgios Poliakis AU - Chantal Reusken AU - Mariano Sanchez-Lockhart AU - Stephen F. Schaffner AU - John S. Schieffelin AU - Rachel S. Sealfon AU - Etienne Simon-Loriere AU - Saskia L. Smits AU - Kilian Stoecker AU - Lucy Thorne AU - Ekaete A. Tobin AU - Mohamed A. Vandi AU - Simon J. Watson AU - Kendra West AU - Shannon Whitmer AU - Michael R. Wiley AU - Sarah M. Winnicki AU - Shirlee Wohl AU - Roman Wölfel AU - Nathan L. Yozwiak AU - Kristian G. Andersen AU - Sylvia Blyden AU - Fatorma Bolay AU - Miles Carroll AU - Boubacar Diallo AU - Pierre Formenty AU - Christophe Fraser AU - George F. Gao AU - Robert F. Garry AU - Ian Goodfellow AU - Stephan Günther AU - Christian Happi AU - Edward C Holmes AU - Brima Kargbo AU - Paul Kellam AU - Marion P. G. Koopmans AU - Nicholas J. Loman AU - N’Faly Magassouba AU - Dhamari Naidoo AU - Stuart T. Nichol AU - Tolbert Nyenswah AU - Gustavo Palacios AU - Oliver G Pybus AU - Pardis Sabeti AU - Amadou Sall AU - Ute Ströher AU - Isatta Wury AU - Marc A Suchard AU - Philippe Lemey AU - Andrew Rambaut Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/09/02/071779.1.abstract N2 - 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 a 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. 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. ER -