Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

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

doi:10.1016/j.cell.2015.06.007

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

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

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1516-1526
Number of pages	11
Journal	Cell
Volume	161
Issue number	7
DOIs	https://doi.org/10.1016/j.cell.2015.06.007
Publication status	Published - 18 Jun 2015

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10.1016/j.cell.2015.06.007Licence: Creative Commons: Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND)

SabetiEtalC2015EbolaVirusEpidemiologyTransmissionAndEvolutionFinal published version, 1.2 MBLicence: Creative Commons: Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND)

PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach
Rambaut, A. (Principal Investigator)
EU government bodies
1/11/11 → 30/04/17
Project: Research
VIRAL PHYLOGEOGRAPHY: Evolutionary reconstruction of viral spread in time and space
Rambaut, A. (Principal Investigator)
EU government bodies
1/10/10 → 30/09/15
Project: Research

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)
Rambaut, A. (Member)
Sept 2009 → Aug 2015
Activity: Membership types › Membership of external research organisation

Cite this

Park, DJ., Dudas, G., Wohl, S., Goba, A., Whitmer, SL. M., Andersen, KG., Sealfon, RS., Ladner, JT., Kugelman, JR., Matranga, CB., Winnicki, SM., Qu, J., Gire, SK., Gladden-Young, A., Jalloh, S., Nosamiefan, D., Yozwiak, NL., Moses, LM., Jiang, P.-P., ... Sabeti, PC. (2015). Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone. Cell, 161(7), 1516-1526. https://doi.org/10.1016/j.cell.2015.06.007

@article{6c9bc9aaafee40dd931b82395680e31f,

title = "Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone",

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.",

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

year = "2015",

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doi = "10.1016/j.cell.2015.06.007",

language = "English",

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pages = "1516--1526",

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Park, DJ, Dudas, G, Wohl, S, Goba, A, Whitmer, SLM, Andersen, KG, Sealfon, RS, Ladner, JT, Kugelman, JR, Matranga, CB, Winnicki, SM, Qu, J, Gire, SK, Gladden-Young, A, Jalloh, S, Nosamiefan, D, Yozwiak, NL, Moses, LM, Jiang, P-P, Lin, AE, Schaffner, SF, Bird, B, Towner, J, Mamoh, M, Gbakie, M, Kanneh, L, Kargbo, D, Massally, JLB, Kamara, FK, Konuwa, E, Sellu, J, Jalloh, AA, Mustapha, I, Foday, M, Yillah, M, Erickson, BR, Sealy, T, Blau, D, Paddock, C, Brault, A, Amman, B, Basile, J, Bearden, S, Belser, J, Bergeron, E, Campbell, S, Chakrabarti, A, Dodd, K, Flint, M, Gibbons, A, Goodman, C, Klena, J, McMullan, L, Morgan, L, Russell, B, Salzer, J, Sanchez, A, Wang, D, Jungreis, I, Tomkins-Tinch, C, Kislyuk, A, Lin, MF, Chapman, S, MacInnis, B, Matthews, A, Bochicchio, J, Hensley, LE, Kuhn, JH, Nusbaum, C, Schieffelin, JS, Birren, BW, Forget, M, Nichol, ST, Palacios, GF, Ndiaye, D, Happi, C, Gevao, SM, Vandi, MA, Kargbo, B, Holmes, EC, Bedford, T, Gnirke, A, Ströher, U, Rambaut, A, Garry, RF & Sabeti, PC 2015, 'Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone', Cell, vol. 161, no. 7, pp. 1516-1526. https://doi.org/10.1016/j.cell.2015.06.007

TY - JOUR

T1 - Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

AU - Park, Daniel J.

AU - Dudas, Gytis

AU - Wohl, Shirlee

AU - Goba, Augustine

AU - Whitmer, Shannon L.M.

AU - Andersen, Kristian G.

AU - Sealfon, Rachel S.

AU - Ladner, Jason T.

AU - Kugelman, Jeffrey R.

AU - Matranga, Christian B.

AU - Winnicki, Sarah M.

AU - Qu, James

AU - Gire, Stephen K.

AU - Gladden-Young, Adrianne

AU - Jalloh, Simbirie

AU - Nosamiefan, Dolo

AU - Yozwiak, Nathan L.

AU - Moses, Lina M.

AU - Jiang, Pan-Pan

AU - Lin, Aaron E.

AU - Schaffner, Stephen F.

AU - Bird, Brian

AU - Towner, Jonathan

AU - Mamoh, Mambu

AU - Gbakie, Michael

AU - Kanneh, Lansana

AU - Kargbo, David

AU - Massally, James L.B.

AU - Kamara, Fatima K.

AU - Konuwa, Edwin

AU - Sellu, Josephine

AU - Jalloh, Abdul A.

AU - Mustapha, Ibrahim

AU - Foday, Momoh

AU - Yillah, Mohamed

AU - Erickson, Bobbie R.

AU - Sealy, Tara

AU - Blau, Dianna

AU - Paddock, Christopher

AU - Brault, Aaron

AU - Amman, Brian

AU - Basile, Jane

AU - Bearden, Scott

AU - Belser, Jessica

AU - Bergeron, Eric

AU - Campbell, Shelley

AU - Chakrabarti, Ayan

AU - Dodd, Kimberly

AU - Flint, Mike

AU - Gibbons, Aridth

AU - Goodman, Christin

AU - Klena, John

AU - McMullan, Laura

AU - Morgan, Laura

AU - Russell, Brandy

AU - Salzer, Johanna

AU - Sanchez, Angela

AU - Wang, David

AU - Jungreis, Irwin

AU - Tomkins-Tinch, Christopher

AU - Kislyuk, Andrey

AU - Lin, Michael F.

AU - Chapman, Sinead

AU - MacInnis, Bronwyn

AU - Matthews, Ashley

AU - Bochicchio, James

AU - Hensley, Lisa E.

AU - Kuhn, Jens H.

AU - Nusbaum, Chad

AU - Schieffelin, John S.

AU - Birren, Bruce W.

AU - Forget, Marc

AU - Nichol, Stuart T.

AU - Palacios, Gustavo F.

AU - Ndiaye, Daouda

AU - Happi, Christian

AU - Gevao, Sahr M.

AU - Vandi, Mohamed A.

AU - Kargbo, Brima

AU - Holmes, Edward C.

AU - Bedford, Trevor

AU - Gnirke, Andreas

AU - Ströher, Ute

AU - Rambaut, Andrew

AU - Garry, Robert F.

AU - Sabeti, Pardis C.

PY - 2015/6/18

Y1 - 2015/6/18

N2 - 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.

AB - 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.

U2 - 10.1016/j.cell.2015.06.007

DO - 10.1016/j.cell.2015.06.007

M3 - Article

SN - 0092-8674

VL - 161

SP - 1516

EP - 1526

JO - Cell

JF - Cell

IS - 7

ER -

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone

Abstract

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Projects

PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach

VIRAL PHYLOGEOGRAPHY: Evolutionary reconstruction of viral spread in time and space

Activities

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)

Cite this