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

Cell

Volumn 161, Issue 7, 2015, Pages 1516-1526

  Park, Daniel J ^a   Dudas, Gytis ^b   Wohl, Shirlee ^a,c   Goba, Augustine ^d   Whitmer, Shannon L M ^e   Andersen, Kristian G ^f   Sealfon, Rachel S ^a,g   Ladner, Jason T ^h   Kugelman, Jeffrey R ^h   Matranga, Christian B ^a   Winnicki, Sarah M ^a,c   Qu, James ^a   Gire, Stephen K ^a,c   Gladden Young, Adrianne ^a   Jalloh, Simbirie ^d   Nosamiefan, Dolo ^a   Yozwiak, Nathan L ^a,c   Moses, Lina M ⁱ   Jiang, Pan Pan ^a,c   Lin, Aaron E ^a,c   Schaffner, Stephen F ^a,c   Bird, Brian ^e   Towner, Jonathan ^e   Mamoh, Mambu ^d   Gbakie, Michael ^d   Kanneh, Lansana ^d   Kargbo, David ^d   Massally, James L B ^d   Kamara, Fatima K ^d   Konuwa, Edwin ^d   Sellu, Josephine ^d   Jalloh, Abdul A ^d   Mustapha, Ibrahim ^d   Foday, Momoh ^d   Yillah, Mohamed ^d   Erickson, Bobbie R ^e   Sealy, Tara ^e   Blau, Dianna ^e   Paddock, Christopher ^e   Brault, Aaron ^e   Amman, Brian ^e   Basile, Jane ^e   Bearden, Scott ^e   Belser, Jessica ^e   Bergeron, Eric ^e   Campbell, Shelley ^e   Chakrabarti, Ayan ^e   Dodd, Kimberly ^e   Flint, Mike ^e   Gibbons, Aridth ^e   Goodman, Christin ^e   Klena, John ^e   McMullan, Laura ^e   Morgan, Laura ^e   Russell, Brandy ^e   Salzer, Johanna ^e   Sanchez, Angela ^e   Wang, David ^e   Jungreis, Irwin ^g   Tomkins Tinch, Christopher ^a   Kislyuk, Andrey ^j   Lin, Michael F ^j   Chapman, Sinead ^a   Macinnis, Bronwyn ^a   Matthews, Ashley ^a,c   Bochicchio, James ^a   Hensley, Lisa E ^k   Kuhn, Jens H ^k   Nusbaum, Chad ^a   Schieffelin, John S ⁱ   Birren, Bruce W ^a   Forget, Marc ^l   Nichol, Stuart T ^e   Palacios, Gustavo F ^h   Ndiaye, Daouda ^m   Happi, Christian ⁿ   Gevao, Sahr M ^o   Vandi, Mohamed A ^p   Kargbo, Brima ^p   Holmes, Edward C ^q   Bedford, Trevor ^r   Gnirke, Andreas ^a   Ströher, Ute ^e   Rambaut, Andrew ^b,s   Garry, Robert F ⁱ   Sabeti, Pardis C ^a,c   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c HARVARD UNIVERSITY   (United States)

^d Kenema Government Hospital   (Sierra Leone)

^e NATIONAL CENTER FOR IMMUNIZATION AND RESPIRATORY DISEASES   (United States)

^f SCRIPPS RESEARCH INSTITUTE   (United States)

^g MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^h UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

ⁱ TULANE UNIVERSITY   (United States)

^j DNAnexus   (United States)

^k NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^l MÉDECINS SANS FRONTIÈRES   (Belgium)

^m UNIVERSITÉ CHEIKH ANTA DIOP   (Senegal)

ⁿ REDEEMER S UNIVERSITY   (Nigeria)

^o UNIVERSITY OF SIERRA LEONE   (Sierra Leone)

^p Ministry of Health and Sanitation   (Sierra Leone)

^q UNIVERSITY OF SYDNEY   (Australia)

^r Fred Hutchinson Cancer Research Center   (United States)

^s NATIONAL INSTITUTES OF HEALTH   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BALANCING SELECTION; BINDING SITE; DIVERSIFYING SELECTION; EBOLA HEMORRHAGIC FEVER; EBOLAVIRUS; EPIDEMIC; EVOLUTIONARY RATE; GENE LIBRARY; GENEALOGY; GENETIC VARIABILITY; GENOME ANALYSIS; HOST; HUMAN; HUMORAL IMMUNITY; IMMUNE EVASION; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PURIFYING SELECTION; SIERRA LEONE; SINGLE NUCLEOTIDE POLYMORPHISM; VIRUS GENOME; VIRUS MUTATION; VIRUS TRANSMISSION; CLASSIFICATION; EVOLUTION; GENETICS; HEMORRHAGIC FEVER, EBOLA; ISOLATION AND PURIFICATION; LABORATORY DIAGNOSIS; MUTATION; TRANSMISSION; VIROLOGY;

EBOLA VIRUS;

BIOLOGICAL EVOLUTION; DISEASE OUTBREAKS; EBOLAVIRUS; GENOME, VIRAL; HEMORRHAGIC FEVER, EBOLA; HUMANS; MUTATION; SIERRA LEONE; SPECIMEN HANDLING;

EID: 84934981152     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.06.007     Document Type: Article

References (31)

1. S. Alizon, S. Lion, C.L. Murall, and J.L. Abbate Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics Virulence 5 2014 825 827
2. S. Baize, D. Pannetier, L. Oestereich, T. Rieger, L. Koivogui, N. Magassouba, B. Soropogui, M.S. Sow, S. Keïta, and H. De Clerck Emergence of Zaire Ebola virus disease in Guinea N. Engl. J. Med. 371 2014 1418 1425
3. P. Becquart, T. Mahlakõiv, D. Nkoghe, and E.M. Leroy Identification of continuous human B-cell epitopes in the VP35, VP40, nucleoprotein and glycoprotein of Ebola virus PLoS ONE 9 2014 e96360
4. T. Bedford, S. Cobey, and M. Pascual Strength and tempo of selection revealed in viral gene genealogies BMC Evol. Biol. 11 2011 220
5. J.A. Carpenter, L.P. Keegan, L. Wilfert, M.A. O'Connell, and F.M. Jiggins Evidence for ADAR-induced hypermutation of the Drosophila sigma virus (Rhabdoviridae) BMC Genet. 10 2009 75
6. A.J. Drummond, M.A. Suchard, D. Xie, and A. Rambaut Bayesian phylogenetics with BEAUti and the BEAST 1.7 Mol. Biol. Evol. 29 2012 1969 1973
7. S. Duchene, E.C. Holmes, and S.Y. Ho Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates Proc. Biol. Sci. 281 2014 10.1098/rspb.2014.0732 Published online July 7, 2014
8. K.J. Emmett, A. Lee, and R. Rabadan High-resolution genomic surveillance of 2014 Ebolavirus using shared subclonal variants PLoS Curr. 2015 10.1371/currents.outbreaks.c7fd7946ba606c982668a96bcba43c90 Published online February 9, 2015
9. O.A. Folarin, A.N. Happi, and C.T. Happi Empowering African genomics for infectious disease control Genome Biol. 15 2014 515
10. J.-F. Gélinas, G. Clerzius, E. Shaw, and A. Gatignol Enhancement of replication of RNA viruses by ADAR1 via RNA editing and inhibition of RNA-activated protein kinase J. Virol. 85 2011 8460 8466
11. S.K. Gire, A. Goba, K.G. Andersen, R.S.G. Sealfon, D.J. Park, L. Kanneh, S. Jalloh, M. Momoh, M. Fullah, and G. Dudas Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak Science 345 2014 1369 1372
12. S.Y.W. Ho, M.J. Phillips, A. Cooper, and A.J. Drummond Time dependency of molecular rate estimates and systematic overestimation of recent divergence times Mol. Biol. Evol. 22 2005 1561 1568
13. T. Hoenen, D. Safronetz, A. Groseth, K.R. Wollenberg, O.A. Koita, B. Diarra, I.S. Fall, F.C. Haidara, F. Diallo, and M. Sanogo Virology. Mutation rate and genotype variation of Ebola virus from Mali case sequences Science 348 2015 117 119
14. J. Köster, and S. Rahmann Snakemake - a scalable bioinformatics workflow engine Bioinformatics 28 2012 2520 2522
15. J.R. Kugelman, M. Sanchez-Lockhart, K.G. Andersen, S. Gire, D.J. Park, R. Sealfon, A.E. Lin, S. Wohl, P.C. Sabeti, J.H. Kuhn, and G.F. Palacios Evaluation of the potential impact of Ebola virus genomic drift on the efficacy of sequence-based candidate therapeutics MBio 6 2015 e02227-e14
16. J.R. Kugelman, M.R. Wiley, S. Mate, J.T. Ladner, B. Beitzel, and L. Fakoli Monitoring of Ebola virus Makona evolution through establishment of advanced genomic capability in Liberia Emerg. Infect. Dis. 21 2015 10.3201/eid2107.150522
17. J.H. Kuhn, K.G. Andersen, S. Baize, Y. Bào, S. Bavari, N. Berthet, O. Blinkova, J.R. Brister, A.N. Clawson, and J. Fair Nomenclature- and database-compatible names for the two Ebola virus variants that emerged in Guinea and the Democratic Republic of the Congo in 2014 Viruses 6 2014 4760 4799
18. C.B. Matranga, K.G. Andersen, S. Winnicki, M. Busby, A.D. Gladden, R. Tewhey, M. Stremlau, A. Berlin, S.K. Gire, and E. England Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples Genome Biol. 15 2014 519
19. C.D. Murin, M.L. Fusco, Z.A. Bornholdt, X. Qiu, G.G. Olinger, L. Zeitlin, G.P. Kobinger, A.B. Ward, and E.O. Saphire Structures of protective antibodies reveal sites of vulnerability on Ebola virus Proc. Natl. Acad. Sci. USA 111 2014 17182 17187
20. D. Olal, A.I. Kuehne, S. Bale, P. Halfmann, T. Hashiguchi, M.L. Fusco, J.E. Lee, L.B. King, Y. Kawaoka, J.M. Dye Jr., and E.O. Saphire Structure of an antibody in complex with its mucin domain linear epitope that is protective against Ebola virus J. Virol. 86 2012 2809 2816
21. Park, D., Jungreis, I., Tomkins-Tinch, C., and Lin, M. (2015). viral-ngs: v1.0.0. http://dx.doi.org/10.5281/zenodo.17560.
22. B.E. Pickett, E.L. Sadat, Y. Zhang, J.M. Noronha, R.B. Squires, V. Hunt, M. Liu, S. Kumar, S. Zaremba, and Z. Gu ViPR: an open bioinformatics database and analysis resource for virology research Nucleic Acids Res. 40 2012 D593 D598
23. O.G. Pybus, A. Rambaut, R. Belshaw, R.P. Freckleton, A.J. Drummond, and E.C. Holmes Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution Mol. Biol. Evol. 24 2007 845 852
24. A. Sanchez, S.G. Trappier, U. Ströher, S.T. Nichol, M.D. Bowen, and H. Feldmann Variation in the glycoprotein and VP35 genes of Marburg virus strains Virology 240 1998 138 146
25. T. Stadler, D. Kühnert, D.A. Rasmussen, and L. du Plessis Insights into the early epidemic spread of Ebola in Sierra Leone provided by viral sequence data PLoS Curr. 2014 10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f Published online October 6, 2014
26. Y.-G. Tong, W.-F. Shi, Di Liu, J. Qian, L. Liang, X.-C. Bo, J. Liu, H.G. Ren, H. Fan, M. Ni China Mobile Laboratory Testing Team in Sierra Leone Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone Nature 2015 10.1038/nature14490 Published online May 13, 2015
27. E. Volz, and S. Pond Phylodynamic analysis of Ebola virus in the 2014 Sierra Leone Epidemic PLoS Curr. 2014 10.1371/currents.outbreaks.6f7025f1271821d4c815385b08f5f80e Published online October 24, 2014
28. J.O. Wertheim, and M. Worobey Relaxed selection and the evolution of RNA virus mucin-like pathogenicity factors J. Virol. 83 2009 4690 4694
29. World Health Organization. (2015). Ebola Situation Reports. http://apps.who.int/ebola/en/ebola-situation-reports.
30. N.L. Yozwiak, S.F. Schaffner, and P.C. Sabeti Data sharing: Make outbreak research open access Nature 518 2015 477 479
31. R.C. Zahn, I. Schelp, O. Utermöhlen, and D. von Laer A-to-G hypermutation in the genome of lymphocytic choriomeningitis virus J. Virol. 81 2007 457 464