Montazeri Shahtori, Narges2016-11-182016-11-182016-12-01http://hdl.handle.net/2097/34540Recent experience of Ebola outbreak of 2014 highlighted the importance of immediate response to impede Ebola transmission at its very early stage. To this aim, efficient and effective allocation of limited resources is crucial. Among standard interventions is the practice of following up with physical contacts of individuals diagnosed with Ebola virus disease -- known as contact tracing. In an effort to objectively understand the effect of possible contact tracing protocols, we explicitly develop a model of Ebola transmission incorporating contact tracing. Our modeling framework has several features to suit early–stage Ebola transmission: 1) the network model is patient–centric because when number of infected cases are small only the myopic networks of infected individuals matter and the rest of possible social contacts are irrelevant, 2) the Ebola disease model is individual–based and stochastic because at the early stages of spread, random fluctuations are significant and must be captured appropriately, 3) the contact tracing model is parameterizable to analyze the impact of critical aspects of contact tracing protocols. Notably, we propose an activity driven network approach to contact tracing, and develop a Monte-Carlo method to compute the basic reproductive number of the disease spread in different scenarios. Exhaustive simulation experiments suggest that while contact tracing is important in stopping the Ebola spread, it does not need to be done too urgently. This result is due to rather long incubation period of Ebola disease infection. However, immediate hospitalization of infected cases is crucial and requires the most attention and resource allocation. Moreover, to investigate the impact of mitigation strategies in the 2014 Ebola outbreak, we consider reported data in Guinea, one the three West Africa countries that had experienced the Ebola virus disease outbreak. We formulate a multivariate sequential Monte Carlo filter that utilizes mechanistic models for Ebola virus propagation to simultaneously estimate the disease progression states and the model parameters according to reported incidence data streams. This method has the advantage of performing the inference online as the new data becomes available and estimating the evolution of the basic reproductive ratio R₀(t) throughout the Ebola outbreak. Our analysis identifies a peak in the basic reproductive ratio close to the time of Ebola cases reports in Europe and the USA.en-USInfectious diseases spreadEbola virus diseaseMathematical modeling of infectious diseaseState estimationMonte Carlo methodsSequential Monte Carlo methodReproductive ratioBasic reproductive numberTemporal networkHeterogeneous networkContact tracingSensitivitySpecificityThesis