RT Journal Article SR Electronic T1 Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic JF bioRxiv FD Cold Spring Harbor Laboratory SP 071779 DO 10.1101/071779 A1 Gytis Dudas A1 Luiz Max Carvalho A1 Trevor Bedford A1 Andrew J. Tatem A1 Guy Baele A1 Nuno Faria A1 Daniel J. Park A1 Jason Ladner A1 Armando Arias A1 Danny Asogun A1 Filip Bielejec A1 Sarah Caddy A1 Matt Cotten A1 Jonathan Dambrozio A1 Simon Dellicour A1 Antonino Di Caro A1 Joseph W. Diclaro II A1 Sophie Duraffour A1 Mike Elmore A1 Lawrence Fakoli A1 Merle Gilbert A1 Sahr M Gevao A1 Stephen Gire A1 Adrianne Gladden-Young A1 Andreas Gnirke A1 Augustine Goba A1 Donald S. Grant A1 Bart Haagmans A1 Julian A. Hiscox A1 Umaru Jah A1 Brima Kargbo A1 Jeffrey Kugelman A1 Di Liu A1 Jia Lu A1 Christine M. Malboeuf A1 Suzanne Mate A1 David A. Matthews A1 Christian B. Matranga A1 Luke Meredith A1 James Qu A1 Joshua Quick A1 Susan D. Pas A1 My VT Phan A1 Georgios Poliakis A1 Chantal Reusken A1 Mariano Sanchez-Lockhart A1 Stephen F. Schaffner A1 John S. Schieffelin A1 Rachel S. Sealfon A1 Etienne Simon-Loriere A1 Saskia L. Smits A1 Kilian Stoecker A1 Lucy Thorne A1 Ekaete A. Tobin A1 Mohamed A. Vandi A1 Simon J. Watson A1 Kendra West A1 Shannon Whitmer A1 Michael R. Wiley A1 Sarah M. Winnicki A1 Shirlee Wohl A1 Roman Wölfel A1 Nathan L. Yozwiak A1 Kristian G. Andersen A1 Sylvia Blyden A1 Fatorma Bolay A1 Miles Carroll A1 Boubacar Diallo A1 Pierre Formenty A1 Christophe Fraser A1 George F. Gao A1 Robert F. Garry A1 Ian Goodfellow A1 Stephan Günther A1 Christian Happi A1 Edward C Holmes A1 Brima Kargbo A1 Paul Kellam A1 Marion P. G. Koopmans A1 Nicholas J. Loman A1 N’Faly Magassouba A1 Dhamari Naidoo A1 Stuart T. Nichol A1 Tolbert Nyenswah A1 Gustavo Palacios A1 Oliver G Pybus A1 Pardis Sabeti A1 Amadou Sall A1 Ute Ströher A1 Isatta Wury A1 Marc A Suchard A1 Philippe Lemey A1 Andrew Rambaut YR 2016 UL http://biorxiv.org/content/early/2016/09/02/071779.1.abstract AB 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.