kikawa-seqneut-2025-VCM

Nextstrain analysis of Kikawa et al. neutralization assay experiments for 2025 Southern Hemisphere VCM

Configure the workflow

The workflow uses sequences that the Bloom lab used in their neutralization experiments which do not have any metadata stored with them. This workflow uses minimal metadata for each sequence which requires a mapping of Bloom lab strain names to Nextstrain strain names to link sequences and metadata. This map must be manually curated, but the workflow can generate an initial map to work from.

Build the initial map for each lineage like so.

nextstrain build --docker . \
    data/h1n1pdm/strains-kikawa-2025-SH-VCM.tsv \
    data/h3n2/strains-kikawa-2025-SH-VCM.tsv

Then, copy those files to the corresponding lineage directory in the config/ directory. Manually update the files, as needed to create the map between Nextstrain, Bloom lab, and GISAID strain names.

Run the workflow

Run the workflow with the default Nextstrain Docker image.

nextstrain build --docker .

View the trees

View the trees locally with Auspice.

nextstrain view --docker auspice

Or view the H1N1pdm HA tree or the H3N2 HA tree in the "blab" Nextstrain Group.

Acknowledgments

We gratefully acknowledge the authors and originating and submitting laboratories of the sequences from the GISAID EpiFlu Database (Shu and McCauley 2017) on which this research is based. This repository contains a list of sequence accessions and contributing laboratories per subtype.