Evolutionary analysis of USVI Zika epidemic

Genetic characterization of the Zika virus epidemic in the US Virgin Islands

Allison Black1,2, Barney Potter1, Leora Feldstein1, M. Elizabeth Halloran1, Jorge L. Munoz-Jordan, Gilberto A. Santiago, Nathan D. Grubaugh4, Kristian G. Andersen4, Brett R. Ellis5, Esther M. Ellis5, Trevor Bedford1

1Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

2Department of Epidemiology, University of Washington, Seattle, WA, USA.

3Centers for Disease Control and Prevention, Dengue Branch, San Juan, Puerto Rico.

4Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, USA,

5United States Virgin Islands Department of Health, Christiansted, USVI.

Abstract

Using this repo to reproduce analyses in the paper.

First things first you can clone this repo by running the following command in your terminal.

git clone https://github.com/blab/zika-usvi.git

The analyses and scripts available in this repo require conda environments as well as nextstrain. Instructions for how to install conda and nextstrain components can be found here.

If you follow the above install instructions you will have made a nextstrain conda environment. To run the scripts I wrote for this project you'll need to make another conda environment: the zika-usvi-env environment in the envs directory linked here. If you are in this top level directory then you can make this environment by running the following command in your terminal:

conda env create -f envs/zika-usvi-env.yaml

Then, whenever you want to do something you'll need to activate the environment. To do so, run the following command in your terminal:

conda activate zika-usvi-env

You can find a ton of information about the data we generated, and the process of collating the contextual sequence data, in the data directory README.

While the paper's analyses are done in BEAST, there is also a Nextstrain build for this dataset as well. If you want to explore that build it's available at nextstrain.org/community/blab/zika-usvi.

Alternatively, you could also run the build locally. The pipeline is fully specified in the Snakefile, however please note that you'll need to have the nextstrain tools installed for the build to work.