README.md

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition

Jover Lee^1,6, James Hadfield^1,6, Allison Black², Thomas R. Sibley¹, Richard A. Neher^3,4, Trevor Bedford^1,5, John Huddleston¹

¹Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA ²Chan Zuckerberg Initiative, CA, San Francisco, CA, USA ³Biozentrum, Universität Basel, Switzerland ⁴Swiss Institute of Bioinformatics, Switzerland ⁵Howard Hughes Medical Institute, Seattle, WA, USA ⁶These authors contributed equally to this work and share first authorship

Seasonal influenza vaccines must be updated regularly to account for mutations that allow influenza viruses to escape our existing immunity. A successful vaccine should represent the genetic diversity of recently circulating viruses and induce antibodies that effectively prevent infection by those recent viruses. Thus, linking the genetic composition of circulating viruses and the serological experimental results measuring antibody efficacy is crucial to the vaccine design decision. Historically, genetic and serological data have been presented separately in the form of static visualizations of phylogenetic trees and tabular serological results to identify vaccine candidates. To simplify this decision-making process, we have created an interactive tool for visualizing serological data that has been integrated into Nextstrain’s real-time phylogenetic visualization framework, Auspice. We show how the combined interactive visualizations may be used by decision-makers to explore the relationships between complex data sets for both prospective vaccine virus selection and retrospectively exploring the performance of vaccine viruses.

Explore the data on Nextstrain

Explore the measurements panel and its corresponding data on Nextstrain.

Run the Nextstrain analysis

Follow the data curation guide, to prepare the data required to run this workflow. Install Miniconda and then install Mamba into your base conda environment as shown below.

conda install mamba -n base -c conda-forge

Create a new conda environment with Snakemake installed.

mamba create -n snakemake -c conda-forge -c bioconda snakemake

Activate the conda environment with Snakemake.

conda activate snakemake

Run the workflow in "dry-run" mode to see all the steps and ensure that the files you need from the data curation guide exist.

snakemake -n -p

Run the workflow.

snakemake -p --cores all --use-conda --conda-frontend mamba

Open a file explorer window for the auspice/ directory, select all of the files in the directory, and drag those files on to https://auspice.us/. Explore the measurements panel, tree, and more.

Build manuscript

cd manuscript
./build.sh