title: Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.
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.
authors.affiliation: Center 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.
authors.forename: Stephen K
authors.initials: SK
authors.lastname: Gire
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone. andersen@broadinstitute.org augstgoba@yahoo.com psabeti@oeb.harvard.edu.
authors.forename: Augustine
authors.initials: A
authors.lastname: Goba
authors.affiliation: Center 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.
authors.forename: Kristian G
authors.initials: KG
authors.lastname: Andersen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Rachel S G
authors.initials: RS
authors.lastname: Sealfon
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Park
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Lansana
authors.initials: L
authors.lastname: Kanneh
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Simbirie
authors.initials: S
authors.lastname: Jalloh
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone.
authors.forename: Mambu
authors.initials: M
authors.lastname: Momoh
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone. Eastern Polytechnic College, Kenema, Sierra Leone.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Fullah
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
authors.forename: Gytis
authors.initials: G
authors.lastname: Dudas
authors.affiliation: Center 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.
authors.forename: Shirlee
authors.initials: S
authors.lastname: Wohl
authors.affiliation: Tulane University Medical Center, New Orleans, LA 70112, USA.
authors.forename: Lina M
authors.initials: LM
authors.lastname: Moses
authors.affiliation: Center 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.
authors.forename: Nathan L
authors.initials: NL
authors.lastname: Yozwiak
authors.affiliation: Center 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.
authors.forename: Sarah
authors.initials: S
authors.lastname: Winnicki
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Christian B
authors.initials: CB
authors.lastname: Matranga
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Malboeuf
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: James
authors.initials: J
authors.lastname: Qu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Adrianne D
authors.initials: AD
authors.lastname: Gladden
authors.affiliation: Center 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.
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Schaffner
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.affiliation: Center 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.
authors.forename: Pan-Pan
authors.initials: PP
authors.lastname: Jiang
authors.affiliation: Center 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.
authors.forename: Mahan
authors.initials: M
authors.lastname: Nekoui
authors.affiliation: Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Andres
authors.initials: A
authors.lastname: Colubri
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Moinya Ruth
authors.initials: MR
authors.lastname: Coomber
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Mbalu
authors.initials: M
authors.lastname: Fonnie
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Alex
authors.initials: A
authors.lastname: Moigboi
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Michael
authors.initials: M
authors.lastname: Gbakie
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Fatima K
authors.initials: FK
authors.lastname: Kamara
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Veronica
authors.initials: V
authors.lastname: Tucker
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Edwin
authors.initials: E
authors.lastname: Konuwa
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Sidiki
authors.initials: S
authors.lastname: Saffa
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Josephine
authors.initials: J
authors.lastname: Sellu
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Abdul Azziz
authors.initials: AA
authors.lastname: Jalloh
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Alice
authors.initials: A
authors.lastname: Kovoma
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: James
authors.initials: J
authors.lastname: Koninga
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Mustapha
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Kandeh
authors.initials: K
authors.lastname: Kargbo
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Momoh
authors.initials: M
authors.lastname: Foday
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Yillah
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Franklyn
authors.initials: F
authors.lastname: Kanneh
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Willie
authors.initials: W
authors.lastname: Robert
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: James L B
authors.initials: JL
authors.lastname: Massally
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Sinéad B
authors.initials: SB
authors.lastname: Chapman
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: James
authors.initials: J
authors.lastname: Bochicchio
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Murphy
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: Donald S
authors.initials: DS
authors.lastname: Grant
authors.affiliation: Tulane University Medical Center, New Orleans, LA 70112, USA.
authors.forename: John S
authors.initials: JS
authors.lastname: Scheiffelin
authors.affiliation: Broad 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.
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.affiliation: Redeemer's University, Ogun State, Nigeria.
authors.forename: Christian
authors.initials: C
authors.lastname: Happi
authors.affiliation: University of Sierra Leone, Freetown, Sierra Leone.
authors.forename: Sahr M
authors.initials: SM
authors.lastname: Gevao
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
authors.affiliation: Institute 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.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Tulane University Medical Center, New Orleans, LA 70112, USA.
authors.forename: Robert F
authors.initials: RF
authors.lastname: Garry
authors.affiliation: Kenema Government Hospital, Kenema, Sierra Leone.
authors.forename: S Humarr
authors.initials: SH
authors.lastname: Khan
authors.affiliation: Center 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.
authors.forename: Pardis C
authors.initials: PC
authors.lastname: Sabeti
mesh_terms: D001483:Base Sequence; D004196:Disease Outbreaks; D029043:Ebolavirus / Q000235:genetics* / Q000302:isolation & purification; D062665:Epidemiological Monitoring; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics; D023281:Genomics / Q000379:methods; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology / Q000635:transmission* / Q000821:virology*; D006801:Humans; D009154:Mutation; D017422:Sequence Analysis, DNA; D012807:Sierra Leone / Q000453:epidemiology