Virus genomes reveal factors that spread and sustained the Ebola epidemic

被引：269

作者：

Dudas, Gytis ^{[1
,2
]}

Carvalho, Luiz Max ^{[1
]}

Bedford, Trevor ^{[2
]}

Tatem, Andrew J. ^{[3
,4
]}

Baele, Guy ^{[5
]}

Faria, Nuno R. ^{[6
]}

Park, Daniel J. ^{[7
]}

Ladner, Jason T. ^{[8
]}

Arias, Armando ^{[9
,10
]}

Asogun, Danny ^{[11
,12
]}

Bielejec, Filip ^{[5
]}

Caddy, Sarah L. ^{[9
]}

Cotten, Matthew ^{[13
,14
]}

D'Ambrozio, Jonathan ^{[8
]}

Dellicour, Simon ^{[5
]}

Di Caro, Antonino ^{[12
,15
]}

Diclaro, Joseph W. ^{[16
]}

Duraffour, Sophie ^{[12
,17
]}

Elmore, Michael J. ^{[18
]}

Fakoli, Lawrence S. ^{[19
]}

Faye, Ousmane ^{[20
]}

Gilbert, Merle L. ^{[8
]}

Gevao, Sahr M. ^{[21
]}

Gire, Stephen ^{[7
,22
]}

Gladden-Young, Adrianne ^{[7
]}

Gnirke, Andreas ^{[7
]}

Goba, Augustine ^{[23
,24
]}

Grant, Donald S. ^{[23
,24
]}

Haagmans, Bart L. ^{[14
]}

Hiscox, Julian A. ^{[25
,26
]}

Jah, Umaru ^{[27
]}

Kugelman, Jeffrey R. ^{[8
]}

Liu, Di ^{[28
]}

Lu, Jia ^{[9
]}

Malboeuf, Christine M. ^{[7
]}

Mate, Suzanne ^{[8
]}

Matthews, David A. ^{[29
]}

Matranga, Christian B. ^{[7
]}

Meredith, Luke W. ^{[9
,27
]}

Qu, James ^{[7
]}

Quick, Joshua ^{[30
]}

Pas, Suzan D. ^{[14
]}

Phan, My V. T. ^{[13
,14
]}

Pollakis, Georgios ^{[25
]}

Reusken, Chantal B. ^{[14
]}

Sanchez-Lockhart, Mariano ^{[8
,31
]}

Schaffner, Stephen F. ^{[7
]}

Schieffelin, John S. ^{[32
]}

Sealfon, Rachel S. ^{[7
,33
,34
]}

Simon-Loriere, Etienne ^{[35
,36
]}

机构：

[1] Univ Edinburgh, Inst Evolutionary Biol, Kings Bldg, Edinburgh EH9 3FL, Midlothian, Scotland

[2] Fred Hutchinson Canc Res Ctr, Vaccine & Infect Dis Div, Seattle, WA 98109 USA

[3] Univ Southampton, Dept Geog & Environm, WorldPop, Southampton SO17 1BJ, Hants, England

[4] Flowminder Fdn, Stockholm, Sweden

[5] Univ Leuven, KU Leuven, Rega Inst, Dept Microbiol & Immunol, B-3000 Leuven, Belgium

[6] Univ Oxford, Dept Zool, South Parks Rd, Oxford OX1 3PS, England

[7] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

[8] US Army, Med Res Inst Infect Dis, Ctr Genome Sci, Frederick, MD 21702 USA

[9] Univ Cambridge, Addenbrookes Hosp, Dept Pathol, Cambridge CB2 2QQ, England

[10] Tech Univ Denmark, Natl Vet Inst, Bulowsvej 27, DK-1870 Frederiksberg C, Denmark

[11] Irrua Specialist Teaching Hosp, Inst Lassa Fever Res & Control, Irrua, Nigeria

[12] European Mobile Lab Consortium, D-20359 Hamburg, Germany

[13] Wellcome Trust Sanger Inst, Virus Genom, Cambridge CB10 1SA, England

[14] Erasmus Univ, Dept Virosci, Med Ctr, POB 2040, NL-300 CA Rotterdam, Netherlands

[15] Natl Inst Infect Dis L Spallanzani IRCCS, Via Portuense 292, I-00149 Rome, Italy

[16] Naval Med Res Unit 3, 3A Lmtidad Ramses St, Cairo 11517, Egypt

[17] Bernhard Nocht Inst Trop Med, D-20359 Hamburg, Germany

[18] Publ Hlth England, Natl Infect Serv, Salisbury SP4 0JG, Wilts, England

[19] Liberian Inst Biomed Res, Charlesville, Liberia

[20] Inst Pasteur, Arbovirus & Viral Hemorrhag Fever Unit, 36 Ave Pasteur,BP 220, Dakar, Senegal

[21] Univ Sierra Leone, Freetown, Sierra Leone

[22] Harvard Univ, Dept Organism & Evolutionary Biol, Ctr Syst Biol, Cambridge, MA 02138 USA

[23] Kenema Govt Hosp, Viral Hemorrhag Fever Program, 1 Combema Rd, Kenema, Sierra Leone

[24] Minist Hlth & Sanitat, 4th Floor Youyi Bldg, Freetown, Sierra Leone

[25] Univ Liverpool, Inst Infect & Global Hlth, Liverpool L69 2BE, Merseyside, England

[26] Univ Liverpool, NIHR Hlth Protect Res Unit Emerging & Zoonot Infe, Liverpool L69 3GL, Merseyside, England

[27] Univ Makeni, Makeni, Sierra Leone

[28] Chinese Acad Sci, Inst Microbiol, Beijing 100101, Peoples R China

[29] Univ Bristol, Bristol BS8 1TD, Avon, England

[30] Univ Birmingham, Inst Microbiol & Infect, Birmingham B15 2TT, W Midlands, England

[31] Univ Nebraska Med Ctr, Omaha, NE 68198 USA

[32] Infect Dis Sect, Dept Pediat, New Orleans, LA 70112 USA

[33] Flatiron Inst, Ctr Computat Biol, New York, NY 10010 USA

[34] Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA

[35] Inst Pasteur, Funct Genet Infect Dis Unit, 28 Rue Docteur Roux, F-75724 Paris 15, France

[36] CNRS URA3012, Genet Fonct Malad Infect, F-75015 Paris, France

[37] Bundeswehr Inst Microbiol, Neuherbergstr 11, D-80937 Munich, Germany

[38] Ctr Dis Control & Prevent, Viral Special Pathogens Branch, 1600 Clifton Rd NE, Atlanta, GA 30333 USA

[39] Scripps Res Inst, Dept Immunol & Microbial Sci, La Jolla, CA 92037 USA

[40] Scripps Translat Sci Inst, La Jolla, CA 92037 USA

[41] Minist Social Welf Gender & Childrens Affairs, New Englandville, Freetown, Sierra Leone

[42] Univ Southampton, South Gen Hosp, Southampton SO16 6YD, Hants, England

[43] Minstry Hlth Liberia, Monrovia, Liberia

[44] WHO, Conakry, Guinea

[45] WHO, Geneva, Switzerland

[46] Univ Oxford, Oxford Big Data Inst, Nuffield Dept Med, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford OX3 7FZ, England

[47] Chinese Ctr Dis Control & Prevent China CDC, Beijing 102206, Peoples R China

[48] Dept Microbiol & Immunol, New Orleans, LA 70112 USA

[49] Redeemers Univ, Dept Biol Sci, Ede, Osun State, Nigeria

[50] Redeemers Univ, ACEGID, Ede, Osun State, Nigeria

来源：

NATURE | 2017年 / 544卷 / 7650期

基金：

美国国家科学基金会; 中国国家自然科学基金; 美国国家卫生研究院; 英国医学研究理事会; 英国惠康基金; 英国生物技术与生命科学研究理事会;

关键词：

REAL-TIME; DISEASE; EVOLUTION; DYNAMICS; OUTBREAK; TRANSMISSION; MEASLES; GUINEA; HYPERMUTATION; SURVEILLANCE;

D O I：

10.1038/nature22040

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The 2013-2016 West African epidemic caused by the Ebola virus was of unprecedented magnitude, duration and impact. Here we reconstruct the dispersal, proliferation and decline of Ebola virus throughout the region by analysing 1,610 Ebola virus genomes, which represent over 5% of the known cases. We test the association of geography, climate and demography with viral movement among administrative regions, inferring a classic 'gravity' model, with intense dispersal between larger and closer populations. Despite attenuation of international dispersal after border closures, cross-border transmission had already sown the seeds for an international epidemic, rendering these measures ineffective at curbing the epidemic. We address why the epidemic did not spread into neighbouring countries, showing that these countries were susceptible to substantial outbreaks but at lower risk of introductions. Finally, we reveal that this large epidemic was a heterogeneous and spatially dissociated collection of transmission clusters of varying size, duration and connectivity. These insights will help to inform interventions in future epidemics.

引用

页码：309 / +

页数：19

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