trile83/phyloview

Visualization of COVID-19 Phylogenetic Data

Data for PhyloView

Visualization of COVID-19 Phylogenetic Data
This is the first step to acquire COVID-19 phylogenetic data for the visualization. The data are available publicly on GISAID website with its visualization for Louisiana state. The time span of the data is between December 1st, 2019 to October 1st, 2021.
The provided Jupyter notebook contains the Python code to request the data directly from GISAID website, and output the data into a graph file format (.gv) that can be open in Gephi and then can be exported to .csv format. Publically accessible link to Global COVID-19 ArcGIS Dashboard

ArcGIS Insights Dashboard Example

Louisiana Dashboard

The first use case using locally available data of the state of Louisiana, USA.

Phylogenetic Network (COVID-19 Evolution through time)

Geographic Network (COVID-19 spread through geographic locations)

Global COVID-19 Dashboard using directly GISAID data

Full Visualization Dashboard with 10000 global data points

Geographic Network using the provided geographic data (aggregated to continental level)

Global COVID-19 Geographic Network after applying ACCTRAN algorithm on the global GISAID data

ACCTRAN algorithm allowed researchers to infer the data characteristics of intermediate nodes within a large graph network. We used ACCTRAN to extract information from parent and child nodes for geographic locations to create a detailed COVID-19 spread network.

Geographic Network