Key data for outbreak evaluation: building on the Ebola experience

Cori, Anne; Donnelly, Christl A.; Dorigatti, Ilaria; Ferguson, Neil M.; Fraser, Christophe; Garske, Tini; Jombart, Thibaut; Nedjati-Gilani, Gemma; Nouvellet, Pierre; Riley, Steven; Van Kerkhove, Maria D.; Mills, Harriet L.; Blake, Isobel M.

Disease natural history fundamentally affects outbreak dynamics. The generation time distribution (i.e. distribution of time between infection of an index case and infection of its secondary cases) determines-with the reproduction number-the growth rate of an epidemic [67] . Most commonly, the generation time distribution is estimated from data on the serial interval distribution of an infection-the delay between symptom onset in a case and symptom onset in his/her infector. Other delays between events in the natural history of infection (e.g. exposure, onset of symptoms, hospitalization and recovery or death) also affect disease transmission or have implications for control [43, 67] . Delays from symptom onset to recovery (or death) will determine the required duration of health-care and case isolation. The incubation period (the delay between infection and symptom onset of a case) and the extent to which infectiousness precedes symptom onset will determine the feasibility and effectiveness of contact tracing or prophylaxis [43] . Estimating these delay distributions requires detailed data on individual cases and their exposure, e.g. through transmission pairs identified in household studies [43] .