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, R_e, (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.

Keywords:

• Bayesian inference
• Ebola virus (EBOV)
• epidemiology
• phylogenetics
• R₀

Addendum

During the reviewing process of this article, another study was published that also used phylodynamics methods to estimate several epidemiological parameters.²⁰ Stadler et al.'s results might seem different from ours but this is because they only included 72 of the 78 patients we included in our study. By ignoring these 6 patients that cluster on the top of the phylogeny (see Fig. S1 in the Online materials), they are likely to have less introduction events in their dataset, which should improve their estimate of the date of the origin of the outbreak in Sierra-Leone. At the same time, focusing on the largest cluster of the phylogeny might overestimate disease spread.

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

The authors thank Gire et al. (2014) for publishing EBOV genome sequences and collection dates in the timely and open manner that facilitated this research.

Funding

SA is funded by an ATIP-Avenir from CNRS and INSERM. SL, C-LM and JLA were funded by the ANR grant 10-PDOC- 017–01 ‘SPATEVOLEPID’.

Supplemental Material

Supplemental data for this article can be accessed on the publisher's website.