EVD case data

We used data on weekly incident cases of EVD in each subnational unit (here called 'district') of Guinea (préfécture), Liberia (county) and Sierra Leone (district), which are available at the Ebola data and statistics website of the World Health Organization (WHO) [32]. These weekly case counts were aggregated from the patient database and are considered to be more reliable for the early phase of the epidemic than the situation reports issued by the Ministries of Health of the affected countries [33]. We calculated the total incident cases for each week as the sum of confirmed and probable incident cases. To take account of recurrent outbreaks we defined epidemic waves within each district. A wave was considered terminated after a period of 42 days with no new cases, corresponding to twice the maximum incubation period [34]. New cases arising after this period were considered as a new wave. To ensure a minimum number of data points in each district for the fitting process, we restricted our analysis to the first wave with three or more non-zero data points. Districts with fewer than three non-zero data points per wave were excluded. We restricted the time variable to the first eight weeks since onset of a wave in each district, corresponding to approximately four serial intervals [34]. This time period was considered long enough to have a sufficient number of time points and reduce initial stochasticity, but short enough to capture only the initial exponential phase and exclude the effects of control measures or natural attenuation of the epidemic. The comparison of the dates of epidemic onset and the opening dates of Ebola Treatment Units (ETUs, see [35,36]) showed that only 9% of all districts had a functioning ETU in the first eight weeks since onset of the selected wave.