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bioRxiv · 10.1101/2022.04.19.488067

Phylogeny and Metadata Network Database for Epidemiologic Surveillance

Stott, G. L.·Lyu, L.·Veytsel, G.·Kuo, J.·Lewis, R.·Brown, A.·Fujimoto, K.·Bahl, J.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWThe ongoing SARS-CoV-2 pandemic has highlighted the difficulty in integrating disparate data sources for epidemiologic surveillance. To address this challenge, we have created a graph database to integrate phylogenetic trees, associated metadata, and community surveillance data for phylodynamic inference. As an example use case, we divided 22,713 SARS-CoV-2 samples into 5 groups, generated maximum likelihood trees, and inferred a potential transmission network from a forest of minimum spanning trees built on patristic distances between samples. We then used Cytoscape to visualize the resultant graphs.

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Stott, G. L., Lyu, L., Veytsel, G., Kuo, J., Lewis, R., Brown, A., Fujimoto, K., Bahl, J.. 2022-04-19. Phylogeny and Metadata Network Database for Epidemiologic Surveillance. https://doi.org/10.1101/2022.04.19.488067

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