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Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Science (New York, N.Y.) (2014-09-13)
Stephen K Gire, Augustine Goba, Kristian G Andersen, Rachel S G Sealfon, Daniel J Park, Lansana Kanneh, Simbirie Jalloh, Mambu Momoh, Mohamed Fullah, Gytis Dudas, Shirlee Wohl, Lina M Moses, Nathan L Yozwiak, Sarah Winnicki, Christian B Matranga, Christine M Malboeuf, James Qu, Adrianne D Gladden, Stephen F Schaffner, Xiao Yang, Pan-Pan Jiang, Mahan Nekoui, Andres Colubri, Moinya Ruth Coomber, Mbalu Fonnie, Alex Moigboi, Michael Gbakie, Fatima K Kamara, Veronica Tucker, Edwin Konuwa, Sidiki Saffa, Josephine Sellu, Abdul Azziz Jalloh, Alice Kovoma, James Koninga, Ibrahim Mustapha, Kandeh Kargbo, Momoh Foday, Mohamed Yillah, Franklyn Kanneh, Willie Robert, James L B Massally, Sinéad B Chapman, James Bochicchio, Cheryl Murphy, Chad Nusbaum, Sarah Young, Bruce W Birren, Donald S Grant, John S Scheiffelin, Eric S Lander, Christian Happi, Sahr M Gevao, Andreas Gnirke, Andrew Rambaut, Robert F Garry, S Humarr Khan, Pardis C Sabeti

In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.