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

Research output: Contribution to journalArticle

130 Citations (Scopus)

Abstract

Summary 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 languageEnglish (US)
Pages (from-to)1516-1526
Number of pages11
JournalCell
Volume161
Issue number7
DOIs
StatePublished - Jun 20 2015
Externally publishedYes

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Sierra Leone
Ebolavirus
Epidemiology
Viruses
Ebola Hemorrhagic Fever
Genome
Mucins
Genes
Disease Outbreaks
Sequence Analysis
Glycoproteins

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Park, D. J., Dudas, G., Wohl, S., Goba, A., Whitmer, S. L. M., Andersen, K. G., ... Sabeti, P. C. (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

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

In: Cell, Vol. 161, No. 7, 20.06.2015, p. 1516-1526.

Research output: Contribution to journalArticle

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, PP, 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
Park DJ, Dudas G, Wohl S, Goba A, Whitmer SLM, Andersen KG et al. Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell. 2015 Jun 20;161(7):1516-1526. https://doi.org/10.1016/j.cell.2015.06.007
Park, Daniel J. ; Dudas, Gytis ; Wohl, Shirlee ; Goba, Augustine ; Whitmer, Shannon L.M. ; Andersen, Kristian G. ; Sealfon, Rachel S. ; Ladner, Jason T. ; Kugelman, Jeffrey R. ; Matranga, Christian B. ; Winnicki, Sarah M. ; Qu, James ; Gire, Stephen K. ; Gladden-Young, Adrianne ; Jalloh, Simbirie ; Nosamiefan, Dolo ; Yozwiak, Nathan L. ; Moses, Lina M. ; Jiang, Pan Pan ; Lin, Aaron E. ; Schaffner, Stephen F. ; Bird, Brian ; Towner, Jonathan ; Mamoh, Mambu ; Gbakie, Michael ; Kanneh, Lansana ; Kargbo, David ; Massally, James L.B. ; Kamara, Fatima K. ; Konuwa, Edwin ; Sellu, Josephine ; Jalloh, Abdul A. ; Mustapha, Ibrahim ; Foday, Momoh ; Yillah, Mohamed ; Erickson, Bobbie R. ; Sealy, Tara ; Blau, Dianna ; Paddock, Christopher ; Brault, Aaron ; Amman, Brian ; Basile, Jane ; Bearden, Scott ; Belser, Jessica ; Bergeron, Eric ; Campbell, Shelley ; Chakrabarti, Ayan ; Dodd, Kimberly ; Flint, Mike ; Gibbons, Aridth ; Goodman, Christin ; Klena, John ; McMullan, Laura ; Morgan, Laura ; Russell, Brandy ; Salzer, Johanna ; Sanchez, Angela ; Wang, David ; Jungreis, Irwin ; Tomkins-Tinch, Christopher ; Kislyuk, Andrey ; Lin, Michael F. ; Chapman, Sinead ; Macinnis, Bronwyn ; Matthews, Ashley ; Bochicchio, James ; Hensley, Lisa E. ; Kuhn, Jens H. ; Nusbaum, Chad ; Schieffelin, John S. ; Birren, Bruce W. ; Forget, Marc ; Nichol, Stuart T. ; Palacios, Gustavo F. ; Ndiaye, Daouda ; Happi, Christian ; Gevao, Sahr M. ; Vandi, Mohamed A. ; Kargbo, Brima ; Holmes, Edward C. ; Bedford, Trevor ; Gnirke, Andreas ; Ströher, Ute ; Rambaut, Andrew ; Garry, Robert F. ; Sabeti, Pardis C. / Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. In: Cell. 2015 ; Vol. 161, No. 7. pp. 1516-1526.
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abstract = "Summary 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.",
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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

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AU - Erickson, Bobbie R.

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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.

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AB - Summary 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.

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