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MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response

Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, William M. Switzer
doi: https://doi.org/10.1101/2020.07.22.216275
Ellsworth M. Campbell
1Centers for Disease Control and Prevention, Atlanta, GA 30329
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  • For correspondence: ells@cdc.gov
Anthony Boyles
2Northrup Grumman, Atlanta, GA 30345
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Anupama Shankar
1Centers for Disease Control and Prevention, Atlanta, GA 30329
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Jay Kim
2Northrup Grumman, Atlanta, GA 30345
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Sergey Knyazev
1Centers for Disease Control and Prevention, Atlanta, GA 30329
3Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830
4Department of Computer Science, Georgia State University, Atlanta, GA, 30303
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William M. Switzer
1Centers for Disease Control and Prevention, Atlanta, GA 30329
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Abstract

Motivation Outbreak 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.

Results We 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 Implementation MicrobeTrace 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.

Contact ells{at}cdc.gov

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Conflicts of Interest and Source of Funding: None

  • http://github.com/cdcgov/microbetrace

  • https://microbetrace.cdc.gov

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Posted July 24, 2020.
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MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response
Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, William M. Switzer
bioRxiv 2020.07.22.216275; doi: https://doi.org/10.1101/2020.07.22.216275
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MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response
Ellsworth M. Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, Sergey Knyazev, William M. Switzer
bioRxiv 2020.07.22.216275; doi: https://doi.org/10.1101/2020.07.22.216275

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