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

Armando Arias; Simon J. Watson; Danny Asogun; Ekaete Alice Tobin; Jia Lu; My V. T. Phan; Umaru Jah; Raoul Emeric Guetiya Wadoum; Luke Meredith; Lucy Thorne; Sarah Caddy; Alimamy Tarawalie; Pinky Langat; Gytis Dudas; Nuno R. Faria; Simon Dellicour; Abdul Kamara; Brima Kargbo; Brima Osaio Kamara; Sahr Gevao; Daniel Cooper; Matthew Newport; Peter Horby; Jake Dunning; Foday Sahr; Tim Brooks; Andrew J.H. Simpson; Elisabetta Groppelli; Guoying Liu; Nisha Mulakken; Kate Rhodes; James Akpablie; Zabulon Yoti; Margaret Lamunu; Esther Vitto; Patrick Otim; Collins Owilli; Isaac Boateng; Lawrence Okoror; Emmanuel Omomoh; Jennifer Oyakhilome; Racheal Omiunu; Ighodalo Yemisis; Donatus Adomeh; Solomon Ehikhiametalor; Patience Akhilomen; Chris Aire; Andreas Kurth; Nicola Cook; Jan  Baumann; Martin Gabriel; Roman Wölfel; Antonino Di Caro; Miles W. Carroll; Stephan Günther; John Redd; Dhamari Naidoo; Oliver G. Pybus; Andrew Rambaut; Paul Kellam; Ian Goodfellow; Matthew Cotten

doi:10.1093/ve/vew016

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

Armando Arias, Simon J. Watson, Danny Asogun, Ekaete Alice Tobin, Jia Lu, My V. T. Phan, Umaru Jah, Raoul Emeric Guetiya Wadoum, Luke Meredith, Lucy Thorne, Sarah Caddy, Alimamy Tarawalie, Pinky Langat, Gytis Dudas, Nuno R. Faria, Simon Dellicour, Abdul Kamara, Brima Kargbo, Brima Osaio Kamara, Sahr GevaoDaniel Cooper, Matthew Newport, Peter Horby, Jake Dunning, Foday Sahr, Tim Brooks, Andrew J.H. Simpson, Elisabetta Groppelli, Guoying Liu, Nisha Mulakken, Kate Rhodes, James Akpablie, Zabulon Yoti, Margaret Lamunu, Esther Vitto, Patrick Otim, Collins Owilli, Isaac Boateng, Lawrence Okoror, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Ighodalo Yemisis, Donatus Adomeh, Solomon Ehikhiametalor, Patience Akhilomen, Chris Aire, Andreas Kurth, Nicola Cook, Jan Baumann, Martin Gabriel, Roman Wölfel, Antonino Di Caro, Miles W. Carroll, Stephan Günther, John Redd, Dhamari Naidoo, Oliver G. Pybus, Andrew Rambaut, Paul Kellam, Ian Goodfellow, Matthew Cotten

Research output: Contribution to journal › Journal article › Research › peer-review

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Abstract

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.

Original language	English
Article number	vew016
Journal	Virus Evolution
Volume	2
Issue number	1
ISSN	2057-1577
DOIs	https://doi.org/10.1093/ve/vew016
Publication status	Published - 2016
Externally published	Yes

Bibliographical note

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

Keywords

Ebola virus
Evolution
Transmission
Outbreak sequencing

Access to Document

10.1093/ve/vew016

Arias et al 2016Final published version, 1 MB

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Arias, A., Watson, S. J., Asogun, D., Tobin, E. A., Lu, J., Phan, M. V. T., Jah, U., Wadoum, R. E. G., Meredith, L., Thorne, L., Caddy, S., Tarawalie, A., Langat, P., Dudas, G., Faria, N. R., Dellicour, S., Kamara, A., Kargbo, B., Kamara, B. O., ... Cotten, M. (2016). Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evolution, 2(1), [vew016]. https://doi.org/10.1093/ve/vew016

Arias, Armando ; Watson, Simon J. ; Asogun, Danny ; Tobin, Ekaete Alice ; Lu, Jia ; Phan, My V. T. ; Jah, Umaru ; Wadoum, Raoul Emeric Guetiya ; Meredith, Luke ; Thorne, Lucy ; Caddy, Sarah ; Tarawalie, Alimamy ; Langat, Pinky ; Dudas, Gytis ; Faria, Nuno R. ; Dellicour, Simon ; Kamara, Abdul ; Kargbo, Brima ; Kamara, Brima Osaio ; Gevao, Sahr ; Cooper, Daniel ; Newport, Matthew ; Horby, Peter ; Dunning, Jake ; Sahr, Foday ; Brooks, Tim ; Simpson, Andrew J.H. ; Groppelli, Elisabetta ; Liu, Guoying ; Mulakken, Nisha ; Rhodes, Kate ; Akpablie, James ; Yoti, Zabulon ; Lamunu, Margaret ; Vitto, Esther ; Otim, Patrick ; Owilli, Collins ; Boateng, Isaac ; Okoror, Lawrence ; Omomoh, Emmanuel ; Oyakhilome, Jennifer ; Omiunu, Racheal ; Yemisis, Ighodalo ; Adomeh, Donatus ; Ehikhiametalor, Solomon ; Akhilomen, Patience ; Aire, Chris ; Kurth, Andreas ; Cook, Nicola ; Baumann, Jan ; Gabriel, Martin ; Wölfel, Roman ; Di Caro, Antonino ; Carroll, Miles W. ; Günther, Stephan ; Redd, John ; Naidoo, Dhamari ; Pybus, Oliver G. ; Rambaut, Andrew ; Kellam, Paul ; Goodfellow, Ian ; Cotten, Matthew. / Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. In: Virus Evolution. 2016 ; Vol. 2, No. 1.

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

abstract = "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.",

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author = "Armando Arias and Watson, {Simon J.} and Danny Asogun and Tobin, {Ekaete Alice} and Jia Lu and Phan, {My V. T.} and Umaru Jah and Wadoum, {Raoul Emeric Guetiya} and Luke Meredith and Lucy Thorne and Sarah Caddy and Alimamy Tarawalie and Pinky Langat and Gytis Dudas and Faria, {Nuno R.} and Simon Dellicour and Abdul Kamara and Brima Kargbo and Kamara, {Brima Osaio} and Sahr Gevao and Daniel Cooper and Matthew Newport and Peter Horby and Jake Dunning and Foday Sahr and Tim Brooks and Simpson, {Andrew J.H.} and Elisabetta Groppelli and Guoying Liu and Nisha Mulakken and Kate Rhodes and James Akpablie and Zabulon Yoti and Margaret Lamunu and Esther Vitto and Patrick Otim and Collins Owilli and Isaac Boateng and Lawrence Okoror and Emmanuel Omomoh and Jennifer Oyakhilome and Racheal Omiunu and Ighodalo Yemisis and Donatus Adomeh and Solomon Ehikhiametalor and Patience Akhilomen and Chris Aire and Andreas Kurth and Nicola Cook and Jan Baumann and Martin Gabriel and Roman W{\"o}lfel and {Di Caro}, Antonino and Carroll, {Miles W.} and Stephan G{\"u}nther and John Redd and Dhamari Naidoo and Pybus, {Oliver G.} and Andrew Rambaut and Paul Kellam and Ian Goodfellow and Matthew Cotten",

note = "This is an Open Access article distributed under the terms of the Creative Commons Attribution License",

year = "2016",

doi = "10.1093/ve/vew016",

language = "English",

volume = "2",

journal = "Virus Evolution",

issn = "2057-1577",

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Arias, A, Watson, SJ, Asogun, D, Tobin, EA, Lu, J, Phan, MVT, Jah, U, Wadoum, REG, Meredith, L, Thorne, L, Caddy, S, Tarawalie, A, Langat, P, Dudas, G, Faria, NR, Dellicour, S, Kamara, A, Kargbo, B, Kamara, BO, Gevao, S, Cooper, D, Newport, M, Horby, P, Dunning, J, Sahr, F, Brooks, T, Simpson, AJH, Groppelli, E, Liu, G, Mulakken, N, Rhodes, K, Akpablie, J, Yoti, Z, Lamunu, M, Vitto, E, Otim, P, Owilli, C, Boateng, I, Okoror, L, Omomoh, E, Oyakhilome, J, Omiunu, R, Yemisis, I, Adomeh, D, Ehikhiametalor, S, Akhilomen, P, Aire, C, Kurth, A, Cook, N, Baumann, J, Gabriel, M, Wölfel, R, Di Caro, A, Carroll, MW, Günther, S, Redd, J, Naidoo, D, Pybus, OG, Rambaut, A, Kellam, P, Goodfellow, I & Cotten, M 2016, 'Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases', Virus Evolution, vol. 2, no. 1, vew016. https://doi.org/10.1093/ve/vew016

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. / Arias, Armando; Watson, Simon J.; Asogun, Danny; Tobin, Ekaete Alice; Lu, Jia; Phan, My V. T.; Jah, Umaru; Wadoum, Raoul Emeric Guetiya; Meredith, Luke; Thorne, Lucy; Caddy, Sarah; Tarawalie, Alimamy; Langat, Pinky; Dudas, Gytis; Faria, Nuno R.; Dellicour, Simon; Kamara, Abdul; Kargbo, Brima; Kamara, Brima Osaio; Gevao, Sahr; Cooper, Daniel; Newport, Matthew; Horby, Peter; Dunning, Jake; Sahr, Foday; Brooks, Tim; Simpson, Andrew J.H.; Groppelli, Elisabetta; Liu, Guoying; Mulakken, Nisha; Rhodes, Kate; Akpablie, James; Yoti, Zabulon; Lamunu, Margaret; Vitto, Esther; Otim, Patrick; Owilli, Collins; Boateng, Isaac; Okoror, Lawrence; Omomoh, Emmanuel; Oyakhilome, Jennifer; Omiunu, Racheal; Yemisis, Ighodalo; Adomeh, Donatus; Ehikhiametalor, Solomon; Akhilomen, Patience; Aire, Chris; Kurth, Andreas; Cook, Nicola; Baumann, Jan ; Gabriel, Martin; Wölfel, Roman; Di Caro, Antonino; Carroll, Miles W.; Günther, Stephan; Redd, John; Naidoo, Dhamari; Pybus, Oliver G.; Rambaut, Andrew; Kellam, Paul; Goodfellow, Ian; Cotten, Matthew.

In: Virus Evolution, Vol. 2, No. 1, vew016, 2016.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

AU - Arias, Armando

AU - Watson, Simon J.

AU - Asogun, Danny

AU - Tobin, Ekaete Alice

AU - Lu, Jia

AU - Phan, My V. T.

AU - Jah, Umaru

AU - Wadoum, Raoul Emeric Guetiya

AU - Meredith, Luke

AU - Thorne, Lucy

AU - Caddy, Sarah

AU - Tarawalie, Alimamy

AU - Langat, Pinky

AU - Dudas, Gytis

AU - Faria, Nuno R.

AU - Dellicour, Simon

AU - Kamara, Abdul

AU - Kargbo, Brima

AU - Kamara, Brima Osaio

AU - Gevao, Sahr

AU - Cooper, Daniel

AU - Newport, Matthew

AU - Horby, Peter

AU - Dunning, Jake

AU - Sahr, Foday

AU - Brooks, Tim

AU - Simpson, Andrew J.H.

AU - Groppelli, Elisabetta

AU - Liu, Guoying

AU - Mulakken, Nisha

AU - Rhodes, Kate

AU - Akpablie, James

AU - Yoti, Zabulon

AU - Lamunu, Margaret

AU - Vitto, Esther

AU - Otim, Patrick

AU - Owilli, Collins

AU - Boateng, Isaac

AU - Okoror, Lawrence

AU - Omomoh, Emmanuel

AU - Oyakhilome, Jennifer

AU - Omiunu, Racheal

AU - Yemisis, Ighodalo

AU - Adomeh, Donatus

AU - Ehikhiametalor, Solomon

AU - Akhilomen, Patience

AU - Aire, Chris

AU - Kurth, Andreas

AU - Cook, Nicola

AU - Baumann, Jan

AU - Gabriel, Martin

AU - Wölfel, Roman

AU - Di Caro, Antonino

AU - Carroll, Miles W.

AU - Günther, Stephan

AU - Redd, John

AU - Naidoo, Dhamari

AU - Pybus, Oliver G.

AU - Rambaut, Andrew

AU - Kellam, Paul

AU - Goodfellow, Ian

AU - Cotten, Matthew

N1 - This is an Open Access article distributed under the terms of the Creative Commons Attribution License

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

KW - Ebola virus

KW - Evolution

KW - Transmission

KW - Outbreak sequencing

U2 - 10.1093/ve/vew016

DO - 10.1093/ve/vew016

M3 - Journal article

C2 - 28694998

VL - 2

JO - Virus Evolution

JF - Virus Evolution

SN - 2057-1577

IS - 1

M1 - vew016

ER -