Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature
Authors
Gytis Dudas
Luiz Carvalho
Trevor Bedford
Andrew Tatem
Guy Baele
Nuno Faria
Daniel Park
Jason Ladner
Armando Arias
Danny Asogun
Filip Bielejec
Sarah Caddy
Matthew Cotten
Jonathan D'Ambrozio
Simon Dellicour
Antonino Di Caro
Joseph Diclaro
Sophie Duraffour
Michael Elmore
Lawrence Fakoli
Ousmane Faye
Merle Gilbert
Sahr Gevao
Stephen Gire
Adrianne Gladden-Young
Andreas Gnirke
Augustine Goba
Donald Grant
Bart Haagmans
Julian Hiscox
Umaru Jah
Jeffrey Kugelman
Di Liu
Jia Lu
Christine Malboeuf
Suzanne Mate
David Matthews
Christian Matranga
Luke Meredith
James Qu
Joshua Quick
Suzan Pas
My Phan
Georgios Pollakis
Chantal Reusken
Mariano Sanchez-Lockhart
Stephen Schaffner
John Schieffelin
Rachel Sealfon
Etienne Simon-Loriere
Saskia Smits
Kilian Stoecker
Lucy Thorne
Ekaete Tobin
Mohamed Vandi
Simon Watson
Kendra West
Shannon Whitmer
Michael Wiley
Sarah Winnicki
Shirlee Wohl
Roman Wölfel
Nathan Yozwiak
Kristian Andersen
Sylvia Blyden
Fatorma Bolay
Miles Carroll
Bernice Dahn
Boubacar Diallo
Pierre Formenty
Christophe Fraser
George Gao
Robert Garry
Ian Goodfellow
Stephan Günther
Christian Happi
Edward Holmes
Brima Kargbo
Sakoba Keita
Paul Kellam
Marion Koopmans
Jens Kuhn
Nicholas Loman
N'Faly Magassouba
Dhamari Naidoo
Stuart Nichol
Tolbert Nyenswah
Gustavo Palacios
Oliver Pybus
Pardis Sabeti
Amadou Sall
Ute Ströher
Isatta Wurie
Marc Suchard
Philippe Lemey
Andrew Rambaut
Keywords
Humans
Phylogeny
Ebolavirus
Hemorrhagic Fever, Ebola
Genome, Viral
Disease Outbreaks
Linear Models
Geography
Climate
Molecular Epidemiology
Internationality
Travel
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.
Year of Publication
2017
Journal
Nature
Volume
544
Issue
7650
Pages
309-315
Date Published
2017 04 20
ISSN
1476-4687
DOI
10.1038/nature22040
PubMed ID
28405027
PubMed Central ID
PMC5712493
Links
Grant list
HHSN272200700016I / AO / NIAID NIH HHS / United States
U01 AI082119 / AI / NIAID NIH HHS / United States
R01 AI114855 / AI / NIAID NIH HHS / United States
R01 AI081982 / AI / NIAID NIH HHS / United States
106866/Z/15/Z / Wellcome Trust / United Kingdom
R01 AI107034 / AI / NIAID NIH HHS / United States
UL1 TR001114 / TR / NCATS NIH HHS / United States
AI082805 / NH / NIH HHS / United States
R01 AI117011 / AI / NIAID NIH HHS / United States
R01 HG006139 / HG / NHGRI NIH HHS / United States
R13 AI104216 / AI / NIAID NIH HHS / United States
U01 HG007480 / HG / NHGRI NIH HHS / United States
AI104621 / NH / NIH HHS / United States
AI104216 / NH / NIH HHS / United States
R44 AI115754 / AI / NIAID NIH HHS / United States
UL1 RR025774 / RR / NCRR NIH HHS / United States
AI115754 / NH / NIH HHS / United States
R35 GM119774 / GM / NIGMS NIH HHS / United States
5R01AI/114855-03 / National Institute of Allergy and Infectious Disease / International
R44 AI088843 / AI / NIAID NIH HHS / United States
AI088843 / NH / NIH HHS / United States
Wellcome Trust / United Kingdom
R01 AI104621 / AI / NIAID NIH HHS / United States
260864 / European Research Council / International
AI082119 / NH / NIH HHS / United States
R43 AI088843 / AI / NIAID NIH HHS / United States
1U01HG007480-01 / NH / NIH HHS / United States
U19 AI110818 / AI / NIAID NIH HHS / United States
AI081982 / NH / NIH HHS / United States
HHSN272201400048C / AI / NIAID NIH HHS / United States

Recent Broad Publications