title: Quantifying the epidemic spread of Ebola virus (EBOV) in Sierra Leone using phylodynamics.
abstract: Measuring epidemic parameters early in an outbreak is essential to inform control efforts. Using the viral genome sequence and collection date from 78 infections in the 2014 Ebola virus outbreak in Sierra Leone, we estimate key epidemiological parameters such as infectious period duration (approximately 71 hours) and date of the first case in Sierra Leone (approximately April 25th). We also estimate the effective reproduction number, Re, (approximately 1.26), which is the number of secondary infections effectively caused by an infected individual and accounts for public health control measures. This study illustrates that phylodynamics methods, applied during the initial phase of an outbreak on fewer and more easily attainable data, can yield similar estimates to count-based epidemiological studies.
authors.affiliation: a Laboratoire MIVEGEC (UMR CNRS 5290, IRD 224, UM1, UM2) ; Montpellier Cedex 5, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Alizon
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lion
authors.forename: Carmen Lía
authors.initials: CL
authors.lastname: Murall
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Abbate
mesh_terms: D060085:Coinfection; D004196:Disease Outbreaks; D029043:Ebolavirus / Q000235:genetics*; D058872:Epidemics; D016679:Genome, Viral; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology*; D006801:Humans; D010802:Phylogeny; D012807:Sierra Leone / Q000453:epidemiology
keywords: Bayesian inference; Ebola virus (EBOV); R0; epidemiology; phylogenetics