Phylodynamic Analysis of Ebola Virus Disease Transmission in Sierra Leone

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.

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

“…12 Molecular epidemiological investigation has a historical and scientific application in global infection diseases. In several relevant and recent pandemic events, as severe acute respiratory syndrome, [17][18][19][20] avian influenza A subtype H5N1 virus, [21][22][23] H1N1 influenza A virus, [24][25][26][27][28] Zaire Ebola virus, [29][30][31][32] and lastly Zika virus (ZIKV), phylodynamic analysis has been fruitful applied. [33][34][35][36] All these epidemic events have been resolved, first applying the principles of classical epidemiology, quarantine, and isolation, and then using phylodynamic principles representing drivers to the solution of the origin and the diffusion of the epidemics.…”