Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

被引：95

作者：

Arias, Armando

Watson, Simon J. ^{[17
]}

Asogun, Danny

Tobin, Ekaete Alice

Lu, Jia ^{[10
,24
]}

Phan, My V. T. ^{[12
,15
]}

Jah, Umaru ^{[9
,13
]}

Wadoum, Raoul Emeric Guetiya ^{[2
,3
,11
,13
,20
,21
]}

Meredith, Luke ^{[4
,19
]}

Thorne, Lucy ^{[2
,19
]}

Caddy, Sarah ^{[4
,10
]}

Tarawalie, Alimamy ^{[12
,15
,18
]}

Langat, Pinky ^{[12
]}

Dudas, Gytis ^{[3
,10
,12
,13
]}

Faria, Nuno R.

Dellicour, Simon ^{[4
,10
,15
,19
]}

Kamara, Abdul ^{[14
,19
,23
]}

Kargbo, Brima ^{[7
,9
,12
,17
,18
,24
]}

Kamara, Brima Osaio ^{[22
,24
]}

Gevao, Sahr ^{[2
,3
,7
,14
,18
,23
,24
]}

Cooper, Daniel ^{[10
,21
]}

Newport, Matthew ^{[11
,16
,17
,20
]}

Horby, Peter ^{[22
]}

Dunning, Jake ^{[15
]}

Sahr, Foday

Brooks, Tim

Simpson, Andrew J. H.

Groppelli, Elisabetta

Liu, Guoying

Mulakken, Nisha ^{[3
]}

Rhodes, Kate ^{[3
,4
]}

Akpablie, James ^{[2
]}

Yoti, Zabulon

Lamunu, Margaret ^{[2
,3
,5
,7
]}

Vitto, Esther

Otim, Patrick ^{[8
]}

Owilli, Collins

Boateng, Isaac ^{[2
,5
]}

Okoror, Lawrence

Omomoh, Emmanuel ^{[6
]}

Oyakhilome, Jennifer

Omiunu, Racheal ^{[6
,7
]}

Yemisis, Ighodalo ^{[2
,5
]}

Adomeh, Donatus ^{[8
]}

Ehikhiametalor, Solomon ^{[3
]}

Akhilomen, Patience ^{[4
]}

Aire, Chris

Kurth, Andreas

Cook, Nicola

Baumann, Jan

机构：

[1] Univ Cambridge, Div Virol, Dept Pathol, Cambridge, MA USA

[2] Wellcome Trust Sanger Inst, Hinxton, England

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

[4] Bernhard Nocht Inst Trop Med, European Mobile Lab Consortium, Hamburg, Germany

[5] Univ Makeni, Makeni, Sierra Leone

[6] Inst Evolutionary Biol, Ashworth Labs, Edinburgh, Midlothian, Scotland

[7] Univ Oxford, Dept Zool, Oxford, England

[8] Sierra Leone Minist Hlth, Freetown, Sierra Leone

[9] Int Med Corps, Los Angeles, CA USA

[10] Univ Oxford, Ctr Trop Med & Global Hlth Nuffield, ERGO, Dept Med, Oxford, England

[11] Republ Sierra Leone Armed Forces, Freetown, Sierra Leone

[12] Publ Hlth England, Rare & Imported Pathogens Lab, Porton Down, England

[13] Thermo Fisher Sci, San Francisco, CA USA

[14] WHO Ebola Response Team, Geneva, Switzerland

[15] Fed Univ, Oye Ekit, Nigeria

[16] Robert Koch Inst, Berlin, Germany

[17] Publ Hlth England, Porton Down, England

[18] Bernhard Nocht Inst Trop Med, Hamburg, Germany

[19] Bundeswehr Inst Microbiol, Munich, Germany

[20] Natl Inst Infect Dis L Spallanzani, Rome, Italy

[21] Sierra Leone & Div Global Hlth Protect, Georgia Ctr Global Hlth Centers Dis Control & Pre, CDC Country Off, Atlanta, GA USA

[22] NIH, Fogarty Int Ctr, Bethesda, MD USA

[23] Ctr Immunol, Ashworth Labs, Infect & Evolut, Edinburgh, Midlothian, Scotland

[24] UCL, Divis Infect & Immun, London, England

来源：

VIRUS EVOLUTION | 2016年 / 2卷 / 01期

基金：

英国惠康基金;

关键词：

Ebola virus; evolution; transmission; outbreak sequencing; PHYLOGENETIC ANALYSIS; SEXUAL TRANSMISSION; DYNAMICS; SURVEILLANCE; EVOLUTION; LIBERIA;

D O I：

10.1093/ve/vew016

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

引用

页数：10

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