Test new builds (not full prior yet)

[corneliusroemer]

Description of proposed changes

Checklist

• Check if changes affect downstream workflows which depend on this dataset. For instance, Nextstrain ingest workflows may break if clade nomenclature changes. Consider fixing those workflows or making an issue at least.

https://master.clades.nextstrain.org/?dataset-server=gh:@sc2-clades-25-12@

[Copilot]

Pull request overview

This PR adds 299 newly designated Pango lineages for SARS-CoV-2, updating clade nomenclature data for the period between September 20 and December 4, 2025. The changes include extensive updates to mutation-to-clade mappings and corresponding changelog entries across multiple reference builds.

Key changes:

• Addition of new clade associations ("25C" through "25I") for thousands of mutation positions in the pathogen.json file
• Identical changelog entries added to three separate CHANGELOG.md files documenting the 299 new lineages
• Reordering of existing clade associations in the mutation mapping data

Reviewed changes

Copilot reviewed 16 out of 34 changed files in this pull request and generated no comments.

File	Description
data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/pathogen.json	Extensive updates adding new clade associations (25C-25I) to mutation positions, reordering existing entries, and adding new mutation positions
data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/CHANGELOG.md	Added "Unreleased" section documenting 299 new Pango lineages with designation dates
data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/CHANGELOG.md	Added "Unreleased" section documenting 299 new Pango lineages with designation dates
data/nextstrain/sars-cov-2/BA.2.86/CHANGELOG.md	Added "Unreleased" section documenting 299 new Pango lineages with designation dates

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