Virus genomes reveal factors that spread and sustained the Ebola epidemic

Dudas G, Max Carvalho L, Bedford T, Tatem AJ, Baele G, Faria N, Park DJ, Ladner J, Arias A, Asogun D, Bielejec F, Caddy S, Cotten M, Dambrozio J, Dellicour S, Di Caro A, Diclaro JW II, Duraffour S, Elmore M, Fakoli L, Gilbert M, Sahr M Gevao, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans B, Hiscox JA, Jah U, Kargbo B, Kugelman J, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith L, Qu J, Quick J, Pas SD, Phan MVT, Poliakis G, Reusken C, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Roman Wölfel, Yozwiak NL, Andersen KG, Blyden S, Bolay F, Carroll M, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi C, Holmes EC, Kargbo B, Kellam P, Koopmans MPG, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti P, Sall A, Ströeher U, Wury I, Suchard MA, Lemey P, Rambaut A 2017. Nature 544: 309-315.

Abstract

The 2013–2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.