Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic
Authors: Dudas Gytis , Carvalho Luiz Max , Bedford Trevor , Tatem Andrew J. , Baele Guy , Faria Nuno , Park Daniel J. , Ladner Jason , Arias Armando , Asogun Danny , Bielejec Filip , Caddy Sarah , Cotten Matt , Dambrozio Jonathan , Dellicour Simon , Di Caro Antonino , Diclaro Joseph W. , Duraffour Sophie , Elmore Mike , Fakoli Lawrence , Gilbert Merle , Gevao Sahr M. , Gire Stephen , Gladden-Young Adrianne , Gnirke Andreas , Goba Augustine , Grant Donald S. , Haagmans Bart , Hiscox Julian A. , Jah Umaru , Kargbo Brima , Kugelman Jeffrey , Liu Di , Lu Jia , Malboeuf Christine M. , Mate Suzanne , Matthews David A. , Matranga Christian B. , Meredith Luke , Qu James , Quick Joshua , Pas Susan D. , Phan My VT , Poliakis Georgios , Reusken Chantal , Sanchez-Lockhart Mariano , Schaffner Stephen F. , Schieffelin John S. , Sealfon Rachel S. , Simon-Loriere Etienne , Smits Saskia L. , Stoecker Kilian , Thorne Lucy , Tobin Ekaete A. , 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 , Bolay Fatorma , Carroll Miles , Dahn Bernice , Diallo Boubacar , Formenty Pierre , Fraser Christophe , Gao George F. , Garry Robert F. , Goodfellow Ian , Günther Stephan , Happi Christian , Holmes Edward C , Kargbo Brima , Kellam Paul , Koopmans Marion P.G. , Loman Nicholas J. , Magassouba N’Faly , Naidoo Dhamari , Nichol Stuart T. , Nyenswah Tolbert , Palacios Gustavo , Pybus Oliver G , Sabeti Pardis , Sall Amadou , Sakoba Keïta , Ströeher Ute , Wurie Isatta , Suchard Marc A , Lemey Philippe , Rambaut Andrew 
Published: September 2016

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.