Fig. 1.
Schematic of our forecasting process. First the line-list, if present, was used to 1) estimate the serial interval distribution, and 2) gain insight into the drivers of transmission and give us better situational awareness. Then we used the incidence of confirmed cases provided in the case-count and the serial interval distribution (either from the literature or from the line-list) to estimate the instantaneous reproduction number Rt. The estimation relied on the renewal equation and assumed transmissibility to be constant during a chosen time-window (either 2, 3 or 4 weeks). Then based on the ‘field report’ provided, assessment of the line-list (when present), and general trends in past incidence, an Rt estimate was chosen (by choosing a time-window) to be used to predict 4 weeks of future incidence. The same renewal equation was used for forecasting relying on posterior distribution of the estimated Rt.