Abstract
Understanding transmission pathways of infectious diseases plays a crucial role in enabling effective surveillance and outbreak response. Recent advancements in genomic sequencing technology have led to an enormous data volume that can provide valuable insights into the spread of infectious diseases. GrapeTree (Zhou et al., 2018) is a fully interactive tree visualization program for investigating phylogenetic trees plus associated metadata that facilitates the analyses of large numbers of allelic profiles and supports interactive visualizations of large trees, allowing the manipulation of both tree layout and metadata. However, the current capabilities are limited in terms of conducting spatio-temporal analyses due to the lack of the integrated Geographic Information System (GIS) as well as a data visualization system across time. This study aims to address this limitation by developing a web application that integrates GrapeTree with GIS and a temporal visualization system, thereby enhancing its potential.
We leveraged the potential of GrapeTree enabling spatio-temporal analysis of disease transmission. The web application allows users to upload genomic data and metadata, including spatial and temporal data, visualized in the form of a minimum spanning tree. The tree can be manipulated to highlight different aspects, such as transmission pathways or genomic diversity. Effective management of geographic coordinates and temporal data of each sample allows to display them reflecting the selection in the tree on the map and vice versa, and reproducing a timelapse visualization both in the map and in the tree.
The developed web application offers an intuitive and user-friendly interface for the visualization and comprehension of infectious disease transmission pathways. Integrating GrapeTree with GIS and temporal data visualization functionalities, enables the joint analysis of genomic, spatial and temporal data, yielding a more holistic understanding of disease transmission. In particular, timelapse functionalities allow us to visualize and highlight the spread of an outbreak.
The integration of GrapeTree with GIS in this web application constitutes a valuable tool for the surveillance and operational early warning systems of infectious diseases, offering insights into potential outbreak sources and transmission pathways. The application is a fundamental integration in GenPat (https://genpat.izs.it), and in Cohesive Information System (Di Pasquale et al., 2022) (https://cohesive.izs.it) as an interactive dashboard implementing data results from bioinformatic analyses and currently it is used for displaying analyses carried out through Reportree (Mixão et al., 2023). The tool is fully Open Source and available at https://github.com/genpat-it/grapetree-gis. It is also feasible to utilize it directly from the browser without requiring any installation.
References
Zhou, Z., Alikhan, N., Sergeant, M. J., Luhmann, N., Vaz, C. V., Francisco, A. P., Carriço, J. A., & Achtman, M. (2018). GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Research, 28(9), 1395–1404. https://doi.org/10.1101/gr.232397.117
Di Pasquale, A., Radomski, N., Maassen, K., Cammà, C. (2022). One Health Structure in Europe for Omics-Based Surveillance. ASM Microbe 2022.
Mixão, V., Pinto, M., Sobral, D., Di Pasquale, A., Gomes, J. P., & Borges, V. (2023). ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Medicine, 15(1). https://doi.org/10.1186/s13073-023-01196-1