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Cell. 2015 Jun 18;161(7):1516-26. doi: 10.1016/j.cell.2015.06.007.

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Author information

1
Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA. Electronic address: dpark@broadinstitute.org.
2
Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK.
3
Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
4
Kenema Government Hospital, Kenema, Sierra Leone.
5
National Center for Emerging and Zoonotic Infectious Diseases and National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Mailstop-G14, Atlanta, GA 30333, USA.
6
Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA.
7
Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
8
US Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Fort Detrick, Frederick, MD 21702, USA.
9
Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
10
Tulane University, 1430 Tulane Avenue, SL-38, New Orleans, LA 70112, USA.
11
Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
12
DNAnexus, 1975 West El Camino Real, Suite 101, Mountain View, CA 94040, USA.
13
Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA.
14
Médecins Sans Frontières, Rue de l'Arbre Bénit 46, 1050 Bruxelles, Belgium.
15
Université Cheikh Anta Diop, BP 5005, Dakar, Sénégal.
16
Redeemers University Nigeria, KM 46 Lagos-Ibadan Expressway, Redemption City, Ogun State, Nigeria.
17
University of Sierra Leone, A.J. Momoh St, Tower Hill, Freetown, Sierra Leone.
18
Sierra Leone Ministry of Health and Sanitation, Youyi Building, Freetown, Sierra Leone.
19
University of Sydney, Johns Hopkins Drive, Camperdown NSW 2050, Australia.
20
Fred Hutchinson Cancer Research Center, 110 Fairview Avenue North, Seattle, WA 98109, USA.
21
Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3FL, UK; Centre for Immunology, Infection and Evolution, University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, UK; Fogarty International Center, National Institutes of Health, 31 Center Drive, MSC 2220 Bethesda, MD 20892, USA. Electronic address: a.rambaut@ed.ac.uk.
22
Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address: pardis@broadinstitute.org.

Abstract

The 2013-2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission and offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission.

PMID:
26091036
PMCID:
PMC4503805
DOI:
10.1016/j.cell.2015.06.007
[Indexed for MEDLINE]
Free PMC Article

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