Science. 2014 Sep 12;345(6202):1369-72. doi: 10.1126/science.1259657. Epub 2014 Aug 28.

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

Gire SK¹, Goba A², Andersen KG³, Sealfon RS⁴, Park DJ⁵, Kanneh L⁶, Jalloh S⁶, Momoh M⁷, Fullah M⁷, Dudas G⁸, Wohl S⁹, Moses LM¹⁰, Yozwiak NL¹, Winnicki S¹, Matranga CB⁵, Malboeuf CM⁵, Qu J⁵, Gladden AD⁵, Schaffner SF¹, Yang X⁵, Jiang PP¹, Nekoui M¹, Colubri A¹¹, Coomber MR⁶, Fonnie M⁶, Moigboi A⁶, Gbakie M⁶, Kamara FK⁶, Tucker V⁶, Konuwa E⁶, Saffa S⁶, Sellu J⁶, Jalloh AA⁶, Kovoma A⁶, Koninga J⁶, Mustapha I⁶, Kargbo K⁶, Foday M⁶, Yillah M⁶, Kanneh F⁶, Robert W⁶, Massally JL⁶, Chapman SB⁵, Bochicchio J⁵, Murphy C⁵, Nusbaum C⁵, Young S⁵, Birren BW⁵, Grant DS⁶, Scheiffelin JS¹⁰, Lander ES¹², Happi C¹³, Gevao SM¹⁴, Gnirke A⁵, Rambaut A¹⁵, Garry RF¹⁰, Khan SH⁶, Sabeti PC³.

Author information

¹Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
²Kenema Government Hospital, Kenema, Sierra Leone. andersen@broadinstitute.org augstgoba@yahoo.com psabeti@oeb.harvard.edu.
³Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. andersen@broadinstitute.org augstgoba@yahoo.com psabeti@oeb.harvard.edu.
⁴Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁵Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁶Kenema Government Hospital, Kenema, Sierra Leone.
⁷Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone.
⁸Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
⁹Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
¹⁰Tulane University Medical Center, New Orleans, LA 70112, USA.
¹¹Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
¹²Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
¹³Redeemer's University, Ogun State, Nigeria.
¹⁴University of Sierra Leone, Freetown, Sierra Leone.
¹⁵Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA. Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, UK.

Abstract

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.