Phycova — a tool for exploring covariates of pathogen spread

Genetic analyses of fast-evolving pathogens are frequently undertaken to test the impact of covariates on their dispersal. In particular, a popular approach consists of parameterizing a discrete phylogeographic model as a generalized linear model to identify and analyse the predictors of the dispersal rates of viral lineages among discrete locations. However, such a full probabilistic inference is often computationally demanding and time-consuming. In the face of the increasing amount of viral genomes sequenced in epidemic outbreaks, there is a need for a fast exploration of covariates that might be relevant to consider in formal analyses. We here present PhyCovA (short for ‘Phylogeographic Covariate Analysis’), a web-based application allowing users to rapidly explore the association between candidate covariates and the number of phylogenetically informed transition events among locations. Specifically, PhyCovA takes as input a phylogenetic tree with discrete state annotations at the internal nodes, or reconstructs those states if not available, to subsequently conduct univariate and multivariate linear regression analyses, as well as an exploratory variable selection analysis. In addition, the application can also be used to generate and explore various visualizations related to the regression analyses or to the phylogenetic tree annotated by the ancestral state reconstruction. PhyCovA is freely accessible at https://evolcompvir-kuleuven.shinyapps.io/PhyCovA/ and also distributed in a dockerized form obtainable from https://hub.docker.com/repository/docker/timblokker/phycova. The source code and tutorial are available from the GitHub repository https://github.com/TimBlokker/PhyCovA.