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.

The relevant modes (e.g. airborne, foodborne) and pathways (e.g. animal-human, human-human) of transmission may be identified using information on exposure reported by cases. Cases can report contact both with sick individuals (their potential source of infection) and healthy individuals they have contacted since becoming ill (who may need to be traced and monitored as potential new cases). These data will be more informative if the majority of infections are symptomatic (and hence easily identifiable), if individuals are mostly infectious after the onset of symptoms [43] and if the time window over which exposures and contacts are monitored is as long as the upper bound of the incubation period distribution. If exposure information is collected with enough demographic information to allow record linkage, these backward and forward contacts can be identified in the case line-list, defining transmission pairs. Depending on the mutation rate of the pathogen, genetic data can also be used to identify or confirm these epidemiological links [56, 85] . The increasing availability of full genome pathogen sequences offers exciting prospects in that respect. Some genetic sequence information was available during the Ebola epidemic, but most sequences could not be linked to case records, limiting the use of sequence data in this context. On the other hand, individuals who were named as potential sources of infection could often be identified in the case linelist, although this process was hindered by non-unique names and limited demographic information collected on the potential sources [10] . These exposure data were used to characterize variation in transmission over the course of infection [10] , and to estimate the serial interval and the incubation period [3] . The upper bound of the incubation period distribution was estimated to be 21 days [3] , which supported monitoring contacts for up to three weeks.