Real-time projections of epidemic transmission and estimation of vaccination impact during an Ebola virus disease outbreak in Northeastern Democratic Republic of Congo

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

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/461285 doi: bioRxiv preprint estimated from dates available from situation reports [3] . 190 To generate forecasts from each data set, 320 to 330 outbreaks were collected that 191 passed the step of filtering on approximate agreement with DRC case counts. The 192 simulated outbreaks that were retained after filtering were continued until they 193 generated no further cases. Rare outlying simulated outbreaks that exceeded 300,000 194 cases were capped at the first value reached above that number, to limit unnecessary 195 computation. We used this ensemble to derive a distribution of final outbreak sizes, and 196 of cumulative counts at specific forecasting dates. Projection distributions were 197 constructed using kernel density estimation with leave-one-out cross-validation to 198 determine bandwidth, using a log-normal kernel for final sizes, due to the extended tail 199 of the values, and a normal kernel for all other estimates. We calculated median values 200 and 95% prediction intervals using the 2.5th and 97.5th percentiles of simulated 201 outbreak size.