Projections of epidemic transmission and estimation of vaccination impact during an ongoing Ebola virus disease outbreak in Northeastern Democratic Republic of Congo, as of Feb. 25, 2019

Worden, Lee; Wannier, Rae; Hoff, Nicole A.; Musene, Kamy; Selo, Bernice; Mossoko, Mathias; Okitolonda-Wemakoy, Emile; Muyembe Tamfum, Jean Jacques; Rutherford, George W.; Lietman, Thomas M.; Rimoin, Anne W.; Porco, Travis C.; Kelly, J. Daniel

This model generated randomly varying simulated outbreaks with a range of case counts per day. The outbreak was assumed to begin with a single case. The simulation was run multiple times, each instance producing a proposed epidemic trajectory, generated by the above branching process with the given parameters R initial , Ï„, and k. These proposed trajectories were then filtered, by discarding all proposed trajectories except those whose cumulative case counts matched known counts of the current 2018 EVD outbreak on known dates. In earlier, smaller data sets we filtered against all reported case counts, while in later, more complete data sets we used a thinned series of case counts for filtering, for computational tractability, by selecting five case counts evenly spaced in the data set plus the final case count (S1 Fig). The filtration required an exact match of the first target value, and at subsequent target dates accepted epidemics within a number of cases more or less than each recorded value. On the earlier data sets in which the beginning dates of the epidemic were unknown, the first target value was allowed to match on any day, and subsequent target dates were assigned relative to that day.