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. 2019 Jan 16;11(1):71.
doi: 10.3390/v11010071.

Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone

Petrus Jansen van Vuren  1 , Jason T Ladner  2   3 , Antoinette A Grobbelaar  4 , Michael R Wiley  5   6 , Sean Lovett  7 , Mushal Allam  8 , Arshad Ismail  9 , Chantel le Roux  10 , Jacqueline Weyer  11 , Naazneen Moolla  12 , Nadia Storm  13 , Joe Kgaladi  14 , Mariano Sanchez-Lockhart  15 , Ousman Conteh  16 , Gustavo Palacios  17 , Janusz T Paweska  18   19
Affiliations

Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone

Petrus Jansen van Vuren et al. Viruses. .

Abstract

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.

Keywords: Ebola virus; Ebola virus disease; Filoviridae; Sierra Leone; West Africa; filovirus; phylodynamics.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Sink/source dynamics of Ebola virus disease (EVD) in Sierra Leone based on 5 BEAST runs and >30,000 sampled trees. (A) Import/export events per district (means with error bars indicating 95 highest posterior density (HPD); mean of 225 total between district moves per tree, 95 HPD: 212–238); (B) heat map showing mean import events per district; (C) heat map showing mean import events over time per district; (D) heat map showing mean export events per district; and (E) heat map showing mean export events over time per district.
Figure 2
Figure 2
Phylogeographic BEAST reconstruction of transmission of Ebola virus in Sierra Leone. Colors of the lines correspond to the destination of the transmission event, while upward curving lines indicate eastward transmission and downward curving lines indicate westward transmission. The numbers represent the scale relative to the size of the lines.
Figure 3
Figure 3
Phylogeny based on BEAST analysis of 1062 sequences from Sierra Leone (SLE). Lineages SL3.1.1, SL3.1.2, and SL3.2.1–3.2.5 are highlighted, as indicated in the legend. A time scale below the tree shows the time from the root of the tree, in years, and corresponding calendar dates.
Figure 4
Figure 4
Distribution of lineages in Western Area Urban (WAU) over time (259 sequences).
See this image and copyright information in PMC

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