@article {Dudas071779, author = {Gytis Dudas and Luiz Max Carvalho and Trevor Bedford and Andrew J. Tatem and Guy Baele and Nuno Faria and Daniel J. Park and Jason Ladner and Armando Arias and Danny Asogun and Filip Bielejec and Sarah Caddy and Matt Cotten and Jonathan Dambrozio and Simon Dellicour and Antonino Di Caro and Joseph W. Diclaro II and Sophie Duraffour and Mike Elmore and Lawrence Fakoli and Merle Gilbert and Sahr M Gevao and Stephen Gire and Adrianne Gladden-Young and Andreas Gnirke and Augustine Goba and Donald S. Grant and Bart Haagmans and Julian A. Hiscox and Umaru Jah and Brima Kargbo and Jeffrey Kugelman and Di Liu and Jia Lu and Christine M. Malboeuf and Suzanne Mate and David A. Matthews and Christian B. Matranga and Luke Meredith and James Qu and Joshua Quick and Susan D. Pas and My VT Phan and Georgios Poliakis and Chantal Reusken and Mariano Sanchez-Lockhart and Stephen F. Schaffner and John S. Schieffelin and Rachel S. Sealfon and Etienne Simon-Loriere and Saskia L. Smits and Kilian Stoecker and Lucy Thorne and Ekaete A. Tobin and Mohamed A. Vandi and Simon J. Watson and Kendra West and Shannon Whitmer and Michael R. Wiley and Sarah M. Winnicki and Shirlee Wohl and Roman W{\"o}lfel and Nathan L. Yozwiak and Kristian G. Andersen and Sylvia Blyden and Fatorma Bolay and Miles Carroll and Bernice Dahn and Boubacar Diallo and Pierre Formenty and Christophe Fraser and George F. Gao and Robert F. Garry and Ian Goodfellow and Stephan G{\"u}nther and Christian Happi and Edward C Holmes and Brima Kargbo and Sakoba Ke{\"\i}ta and Paul Kellam and Marion P. G. Koopmans and Nicholas J. Loman and N{\textquoteright}Faly Magassouba and Dhamari Naidoo and Stuart T. Nichol and Tolbert Nyenswah and Gustavo Palacios and Oliver G Pybus and Pardis Sabeti and Amadou Sall and Ute Str{\"o}her and Isatta Wurie and Marc A Suchard and Philippe Lemey and Andrew Rambaut}, title = {Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic}, elocation-id = {071779}, year = {2016}, doi = {10.1101/071779}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 {\textquoteleft}gravity{\textquoteright} 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.}, URL = {https://www.biorxiv.org/content/early/2016/09/07/071779}, eprint = {https://www.biorxiv.org/content/early/2016/09/07/071779.full.pdf}, journal = {bioRxiv} }