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Phycova - a tool for exploring covariates of pathogen spread.
Tim Blokker1, Guy Baele, Philippe Lemey1
1Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium.
Virus Evolution
|March 17, 2022
Summary
PhyCovA is a new web application that rapidly explores associations between pathogen dispersal and environmental factors. This tool aids in identifying key drivers of viral lineage spread, accelerating epidemiological analyses.
Area of Science:
- Epidemiology
- Computational Biology
- Genomics
Background:
- Genetic analyses of pathogens are crucial for understanding dispersal patterns.
- Current phylogeographic models can be computationally intensive, limiting rapid analysis of large genomic datasets.
- Fast exploration of potential dispersal predictors is needed for epidemic outbreaks.
Purpose of the Study:
- To introduce PhyCovA, a web-based application for fast phylogeographic covariate analysis.
- To enable rapid exploration of associations between covariates and viral lineage dispersal rates.
- To provide a user-friendly tool for identifying predictors of pathogen spread.
Main Methods:
- PhyCovA utilizes phylogenetic trees with discrete state annotations.
- It performs univariate and multivariate linear regression analyses.
- The application includes exploratory variable selection and ancestral state reconstruction.
Main Results:
- PhyCovA allows rapid exploration of associations between candidate covariates and dispersal events.
- It facilitates identification of predictors influencing viral lineage transitions.
- The tool supports various visualizations for regression and phylogenetic analyses.
Conclusions:
- PhyCovA offers a computationally efficient approach to phylogeographic covariate analysis.
- The application accelerates the identification of factors driving pathogen dispersal.
- It is a valuable resource for epidemiological research and outbreak investigations.
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