Designate clade 24J (LP.8.1)

[corneliusroemer]

With this PR, we are designating clade 24J (lineage LP.8.1).

Clade 24J, lineage LP.8.1

Clade 24J, lineage LP.8.1, descends from KP.1.1.3 (JN.1.11.1.1.1.3), a JN.1 + 456L + 1086R + 346T + 31- (whose S1 is identical to KP.2.3) with extra Spike mutations F186L, R190S, H445R, Q493E. 493E is well-known to be beneficial from KP.3, R190S has been beneficial across much of the current JN.1 descendants and 445R is at a key site that has had beneficial substitutions in the past.

The first sequence was shared by the US inbound airport surveillance program in a traveller from the Philippines in early September. 24J appears to be most common in (South) East Asia around the Philippines, making up more than 10% of recent sequences from Asia, showing steady growth above 5% per day (in particular the sub-lineage LP.8.1.1 with extra S:K679R).

It satisfies clade designation criterion 4 "A clade shows consistent >0.05 per day growth in frequency where it's circulating and has reached >5% regional frequency" in sequences collected in mid-November to mid-December in Asia.

Share of LP.8.1 sequences collected around the world:

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=LP.8.1*&

Position in global phylogeny (LP.8.1 is red):

Pre-merge checklist

• ncov file updates:
  • defaults/clades.tsv
  • defaults/clade_emergence_dates.tsv
  • defaults/clade_hierarchy.tsv
  • defaults/clades_display_names.yml
  • defaults/color_ordering.tsv
  • defaults/emerging_lineages.tsv (if needed)
• Explain in PR why we are elevating
• Check trial builds:
  • https://github.com/nextstrain/ncov/actions/runs/12424843126
  • https://github.com/nextstrain/ncov/actions/runs/12424844892
• PR approval

Post merge checklist

• Add new variant (with new name) to Nextclade dataset color_ordering.tsv
• Update clade diagram figure
• Trigger full runs on GISAID & Genbank once Nextclade updated
• Tweet about new variant

[trvrb]

This looks good. Thanks so much for keeping up with things @corneliusroemer!

A couple trial build outputs:

• Frequency in Asia in the last 2 months: https://nextstrain.org/staging/ncov/gisaid/trial/clades-2024-12/asia/2m?f_region=Asia
• Global distribution of 24J in the last 2 months: https://nextstrain.org/staging/ncov/gisaid/trial/clades-2024-12/global/2m?f_clade_membership=24J%20%28LP.8.1%29

It looks like Brazil actually the majority of recent 24J sequences.

Here's frequency in South America:

• https://nextstrain.org/staging/ncov/gisaid/trial/clades-2024-12/south-america/2m?f_region=South%20America

It looks like it's currently ~44% in South America and ~7% in Asia. Definitely agree that this should be a clade. Please merge whenever you'd like Cornelius.

[xz-keg]

NB.1 seems to be reaching the 5%/5% criteria in Asia, too.(needs check as the growth seems around borderline, don't know in how it performs in population-based version)

It reaches 90% in multiple Chinese provinces now.