PT  - JOURNAL ARTICLE
AU  - Van Kinh Nguyen
AU  - Rafael Mikolajczyk
AU  - Esteban A. Hernandez-Vargas
TI  - High-Resolution Epidemic Simulation Using Within-Host Infection and Contact Data
AID  - 10.1101/133421
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 133421
4099  - http://biorxiv.org/content/early/2018/01/12/133421.short
4100  - http://biorxiv.org/content/early/2018/01/12/133421.full
AB  - Background Transmission in epidemics of infectious diseases is characterized by a high level of subject-specific elements. These include heterogeneous infection conditions, time-dependent transmission potential, and age-dependent contact structure. These insights are often lost in epidemic models using population data. Here we submit an approach that can capture these details, paving the way for studying epidemics in a more mechanistic and realistic way.Methods Using experimental data, we formulated mathematical models of a pathogen infection dynamics from which we can simulate its transmission potential mechanistically. The models were then embedded in our implement of an age-specific contact network structure that allows to express all elements relevant to the transmission process. This approach is illustrated here with an example of Ebola virus (EBOV).Results The results showed that within-host infection dynamics can capture EBOV’s transmission parameters as good as approaches using population data. Population age-structure, contact distribution and patterns can also be captured with our network generating algorithm. This framework opens vast opportunities for the investigations of each element involved in the epidemic process. Here, estimating EBOV’s reproduction number revealed a heterogeneous pattern among age-groups, prompting questions on current estimates which are not adjusted for this factor. Assessments of mass vaccination strategies showed that a time window from five months before to one week after the start of an epidemic appeared to be effective. Noticeably, compared to a non-intervention scenario, a low vaccination coverage of 33% could reduce number of cases by ten to hundred times as well as lessen the case-fatality rate.Conclusions This is the first effort coupling directly within-host infection model into an age-structured epidemic network model, adding more realistic elements in simulating epidemic processes. Experimental data at the within-host infection are shown able to capture upfront key parameters of a pathogen; the applications of this approach will give us more time to prepare for potential epidemics. Population of interest in epidemic assessments could be modeled with an age-specific contact network without exhaustive amount of data. Further assessments and adaptations for different pathogens and scenarios are underway to explore multilevel aspects in infectious diseases epidemics.EBOVEbola virusNHPsNonhuman primatesVSVVesicular stomatitis virusR0Basic Reproduction NumberReEffective Reproduction NumberAUCArea Under the CurveWHOWorld Health Organization