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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.

SUBMITTER: Park DJ

PROVIDER: S-EPMC4503805 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

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

Cell 20150601 7

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 evide ...[more]

PMID: 26091036

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Project description:BackgroundSexual transmission of Ebola virus disease (EVD) 6 months after onset of symptoms has been recently documented, and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms. As countries affected by the 2013-2015 epidemic in West Africa, by far the largest to date, are declared free of Ebola virus disease (EVD), it remains unclear what threat is posed by rare sexual transmission events that could arise from survivors.Methodology/principal findingsWe devised a compartmental mathematical model that includes sexual transmission from convalescent survivors: a SEICR (susceptible-exposed-infectious-convalescent-recovered) transmission model. We fitted the model to weekly incidence of EVD cases from the 2014-2015 epidemic in Sierra Leone. Sensitivity analyses and Monte Carlo simulations showed that a 0.1% per sex act transmission probability and a 3-month convalescent period (the two key unknown parameters of sexual transmission) create very few additional cases, but would extend the epidemic by 83 days [95% CI: 68-98 days] (p < 0.0001) on average. Strikingly, a 6-month convalescent period extended the average epidemic by 540 days (95% CI: 508-572 days), doubling the current length, despite an insignificant rise in the number of new cases generated.Conclusions/significanceOur results show that reductions in the per sex act transmission probability via abstinence and condom use should reduce the number of sporadic sexual transmission events, but will not significantly reduce the epidemic size and may only minimally shorten the length of time the public health community must maintain response preparedness. While the number of infectious survivors is expected to greatly decline over the coming months, our results show that transmission events may still be expected for quite some time as each event results in a new potential cluster of non-sexual transmission. Precise measurement of the convalescent period is thus important for planning ongoing surveillance efforts.

Dataset Information

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Publications

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

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