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bioRxiv · 10.1101/2020.07.22.216275

MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response

Campbell, E. M.·Boyles, A. A.·Shankar, A.·Kim, J.·Knyazev, S.·Switzer, W. M.
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Abstract

MotivationOutbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. ResultsWe developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Using publicly available HIV sequences and other data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. Availability and ImplementationMicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully-operational without an internet connection. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. The source code is available at https://github.com/cdcgov/microbetrace. Contactells@cdc.gov

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Campbell, E. M., Boyles, A. A., Shankar, A., Kim, J., Knyazev, S., Switzer, W. M.. 2020-07-24. MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response. https://doi.org/10.1101/2020.07.22.216275

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