Add lineages from https://dengue-lineages.org/

[j23414]

Context

Link to slack thread for context.

• Paper: Verity Hill et al, 2024
• Website: https://dengue-lineages.org/
• Nextclade dataset: https://github.com/nextstrain/nextclade_data/tree/master/data/community/v-gen-lab/dengue
• Along with PR with plenty of comments and Nextclade review at: Add dengue lineages dataset nextclade_data#223 merged on August 30, 2024
• Nextclade dataset source code: https://github.com/V-GEN-Lab/dengue-lineages-workflow
• Place to suggest new lineage designations: https://github.com/DENV-lineages/denv-lineage-designation

Description

Since we added the frequency panel (which can depict frequency of clades among other things) on January 4, 2025, I circled back to looking at dengue sub-serotype lineages.

A new dengue community dataset based on Verity Hill et al, 2024 was added to Nextclade community dataset after substantial PR review from the Nextclade team on August 30, 2024. This community dataset seems suitable for sub-serotype lineage calling and includes individual datasets for denv1, denv2, denv3 and denv4 and "lineage nomenclature seems to be part of a collaborative effort involving various research groups from different countries".

I propose swapping out our denv1 to denv4 level datasets to the Verity Hill lineage system dataset. This has the added benefit of solving the following issues:

• Fine tune the "Dengue virus DENVx genotypes" dataset #69
• Improve serotype assignment in Dengue virus DENVx genotypes datasets #70
• Switch DENV2 genotypes to numeric to be consistent with DENV1, 3, and 4 #32

Examples

Possible solution

Copied from slack thread:

We should probabily add this [Hill dataset] as a coloring to nextstrain.org/dengue in the same fashion as https://nextstrain.org/measles / https://github.com/nextstrain/measles/blob/main/ingest/rules/nextclade.smk.

[j23414]

A remaining question is if we want to create two levels (metadata fields) of coloring for "major" and "minor" lineage? Perhaps named "Major lineage" and "Minor lineage"?

from #32 (comment)

dengue classification further from serotype and genotype by splitting genotypes into major and minor lineages.