Designate clade 24C (KP.3)

[corneliusroemer]

With this PR, we are designating 1 new Nextstrain clade:

• 24C = KP.3 (=JN.1.11.1.3, =BA.2.86.1.1.11.1.3)

24C = KP.3 (=JN.1.11.1.3, =BA.2.86.1.1.11.1.3)

24C = KP.3 (=JN.1.11.1.3, =BA.2.86.1.1.11.1.3) is a sublineage of 24B = JN.1.11.1 = BA.2.86.1.1.11.1 with extra spike receptor binding domain mutation Q493E.

It descends from JN.1.11.1, a globally very successful JN.1 sublineage with extra spike receptor binding domain substitution S:F456L and S2 substitution S:V1104L.

The first 24C sequences to become available were all shared by the US airport traveler surveillance program underlining its value. The first sample was shared on the 25nd of February, the 4th on the 8th of March. On the 12th of March, Spain and Canada were the next countries to upload 1 sequence each.

The earliest known collection date for a 24C sequence is 2024-01-30 in England, though that sequence only became publicly available in mid May.

24C likely first became widespread in South or South East Asia based on a combination of evidence:

• US traveler surveillance sequences indicate early sequences were from India
• The parent 24B is known to have spread first in India
• There are sequences from early March from the Indian state of Maharashtra, around 3% of all sequences collected in March 2024
• 6 of the around 100 sequences from Thailand collected in March are 24C

Among countries with continued active surveillance, 24C has become dominant by end of May in Japan and Portugal, it is close to dominance also in Australia. In many countries it makes up at least 15% by the end of May.

24C satisfies clade criteria 4: "A clade shows consistent >0.05 per day growth in frequency where it’s circulating and has reached >5% regional frequency" (criterion 4).

Below is a 2m global tree showing 24C (KP.3) in the darkest red at the top:

Share of all sequences being 24C in the countries that shared the largest number of 24C samples to date on a log scale:

Relative growth advantage compared to all JN.1* is around 50% per week (or 6% per day):

Relative growth advantage compared to all JN.1.11.1* is around 20% per week. The advantage decreases toward the end of the period due to other fit JN.1.11.1 descendants (having S:R346T and some also S:S31- instead of KP.3's S:Q493E - the large number of independent occurrences this genotype precludes clade designation of a lineage with the 346T + 31- genotype as no single lineage has reached a large global share):

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)
• ncov-ingest file update: https://github.com/nextstrain/ncov-ingest/blob/master/defaults/clade-legacy-mapping.yml
• Explain in PR why we are elevating
• Check trial builds:
  • https://nextstrain.org/staging/ncov/gisaid/trial/clades-2024-06/global/1m
  • https://nextstrain.org/staging/ncov/gisaid/21L/trial/clades-2024-06/global/1m
  • https://nextstrain.org/staging/ncov/open/trial/clades-2024-06/global/1m
• 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 great to me @corneliusroemer. I think we can go ahead and merge this?