Probabilistic reconstruction of measles transmission clusters from routinely collected surveillance data
Alexis Robert, Adam J Kucharski, Paul A Gastañaduy, Prabasaj Paul, Sebastian Funk
doi: https://doi.org/10.1101/2020.02.13.20020891
Abstract
Pockets of susceptibility resulting from spatial or social heterogeneity in vaccine coverage can drive measles outbreaks, as cases imported into such pockets are likely to cause further transmission and lead to large transmission clusters. Characterising the dynamics of transmission is essential for identifying which individuals and regions might be most at risk. As data from detailed contact tracing investigations are not available in many settings, we combined age, location, genotype, and onset date of cases in order to probabilistically reconstruct the importation status and transmission clusters within a newly developed R package called o2geosocial. We compared our inferred cluster size distributions to 737 transmission clusters identified through detailed contact-tracing in the United States between 2001 and 2016. We were able to reconstruct the importation status of the cases and found good agreement between the inferred and reference clusters. The results were improved when the contact-tracing investigations were used to set the importation status before running the model. Spatial heterogeneity in vaccine coverage is difficult to measure directly. Our approach was able to highlight areas with potential for local transmission using a minimal number of variables and could be applied to assess the intensity of ongoing transmission in a region.
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