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Open AccessArticle

Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone

1
Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa
2
Center for Genome Sciences, United States Army Medical Research Institute for Infectious Diseases, Fort Detrick, MD 21702, USA
3
The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86001, USA
4
Department of Environmental, Agricultural & Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
5
Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham 2131, South Africa
6
Ministry of Health and Sanitation, Freetown 47235, Sierra Leone
7
Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2050, South Africa
*
Author to whom correspondence should be addressed.
Co-first authors.
Co-last authors.
Viruses 2019, 11(1), 71; https://doi.org/10.3390/v11010071
Received: 27 December 2018 / Revised: 11 January 2019 / Accepted: 14 January 2019 / Published: 16 January 2019
(This article belongs to the Special Issue Medical Advances in Viral Hemorrhagic Fever Research)
We generated genome sequences from 218 cases of Ebola virus disease (EVD) in Sierra Leone (SLE) during 2014–2015 to complement available datasets, particularly by including cases from a period of low sequence coverage during peak transmission of Ebola virus (EBOV) in the highly-affected Western Area division of SLE. The combined dataset was utilized to produce phylogenetic and phylodynamic inferences, to study sink–source dynamics and virus dispersal from highly-populated transmission hotspots. We identified four districts in SLE where EBOV was introduced and transmission occurred without onward exportation to other districts. We also identified six districts that substantially contributed to the dispersal of the virus and prolonged the EVD outbreak: five of these served as major hubs, with lots of movement in and out, and one acted primarily as a source, exporting the virus to other areas of the country. Positive correlations between case numbers, inter-district transition events, and district population sizes reaffirm that population size was a driver of EBOV transmission dynamics in SLE. The data presented here confirm the role of urban hubs in virus dispersal and of a delayed laboratory response in the expansion and perpetuation of the EVD outbreak in SLE. View Full-Text
Keywords: Ebola virus; filovirus; Filoviridae; phylodynamics; Ebola virus disease; Sierra Leone; West Africa Ebola virus; filovirus; Filoviridae; phylodynamics; Ebola virus disease; Sierra Leone; West Africa
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Jansen van Vuren, P.; Ladner, J.T.; Grobbelaar, A.A.; Wiley, M.R.; Lovett, S.; Allam, M.; Ismail, A.; le Roux, C.; Weyer, J.; Moolla, N.; Storm, N.; Kgaladi, J.; Sanchez-Lockhart, M.; Conteh, O.; Palacios, G.; Paweska, J.T. Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone. Viruses 2019, 11, 71.

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