Designate clades 24A (JN.1) and 24B (JN.1.11.1)

[corneliusroemer]

With this PR, we are designating 2 new Nextstrain clades:

• 24A = JN.1 (= BA.2.86.1.1)
• 24B = JN.1.11.1 (=BA.2.86.1.1.11.1)

24A = JN.1 (= BA.2.86.1.1)

24A = JN.1 (= BA.2.86.1.1) is a sublineage of 23I = BA.2.86 with extra spike receptor binding domain mutation L455S.

It descends from BA.2.86.1, the BA.2.86 lineage that spread most successfully, globally, with extra AA substitution ORF1a:K1973R.

24A was first sequenced in Iceland (collection date 2023-08-29, submission date to GISAID 2023-09-20) and became dominant in Iceland by the end of October 2023. The first large country where 24A was dominant was France, by the end of November 2023. JN.1 reached dominance in the majority of countries with active surveillance by the end of 2024.

24A satisfies clade criteria 2, 3 and 4: "A clade reaches >20% regional frequency (criterion 3 for Europe), >30% global frequency (criterion 2) for 2 or more months" and "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 6m global tree showing 24A (JN.1) in red:

https://nextstrain.org/ncov/gisaid/global/6m?branchLabel=emerging_lineage&c=emerging_lineage f8a6">

24B = JN.1.11.1 (=BA.2.86.1.1.11.1) = KP

24B = JN.1.11.1 (=BA.2.86.1.1.11.1) is a sublineage of 24A = JN.1 with extra spike receptor binding domain substitutions S:F456L and S2 substitution S:V1104L. It also has synonymous nuc substitution G17334T and non-synonymous C7113T=ORF1a:T2283I, a mutation that has appeared multiple times during the pandemic, e.g. as defining in C.39, XDE and making up around 10% of EG.5.1.4.

JN.1.11.1 is aliased to KP, so all sublineages start with KP

The first 24B sequence was sequenced and released in India (Karnataka) in December 2023 (collection date 2023-12, submission date 2023-12-24) by the National Centre for Biological Sciences, TIFR - Rockefeller Foundation. India shared the first 4 known sequences and also sequenced many ancestral JN.1.11.

US traveller surveillance suggests JN.1.11.1 is common in Asia, particularly in India, but with imports from a variety of countries stretching from Turkey, via Qatar to Japan. Around 20% of recent US traveler sequences (collection date early March) were from JN.1.11.1. In Singapore, in sequences collected since March 1, 16 out of 67 JN.1* (20-25%) were JN.1.11.1.

Due to reducing global surveillance, and submission delays of up to 2 months, it is difficult to estimate the overall growth advantage of JN.1.11.1 (for instance, the most recent Indian sequence on GISAID was collected on Feb 5, more than 7 weeks ago).

S:R346T has appeared at least 2 times independently in JN.1.11.1 and seems to confer an additional growth advantage that contributes to the overall fast rise of JN.1.11.1

24B satisfies clade criterion 4: "A clade shows consistent >0.05 per day growth in frequency where it’s circulating and has reached >5% regional frequency" as it is clearly above 5% frequency in South Asia with a growth advantage significantly above 5% per day.

Below is a 1m global tree showing 24B (JN.1.11.1) in red:

Doubling time of sequences in GISAID, by submission date of JN.1.11.1 + S:R346T

N	Submission Date of Nth sequence	Days between doublings
1	2024-01-20
2	2024-02-20	0
4	2024-02-21	1
8	2024-02-26	4
16	2024-03-01	3
32	2024-03-06	6
64	2024-03-12	6
128	2024-03-18	6
256	2024-03-27	9
(399)	2024-04-04	(8)

This is the growth of JN.1.11.1* per https://nextstrain.github.io/forecasts-ncov/

JN.1.11.1 is clearly fitter than JN.1

There are other JN.1* + 346T + 456L but none are as frequent globally as JN.1.11.1 is.

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-2024-03/global/1m
  • https://nextstrain.org/staging/ncov/gisaid/21L/trial/clades-2024-03/global/1m
  • https://nextstrain.org/staging/ncov/open/trial/clades-2024-03/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

[AngieHinrichs]

Changes look good but the PR title should say 24A instead of 23A. 🙂

[corneliusroemer]

Changes look good but the PR title should say 24A instead of 23A. 🙂

Done, thanks @AngieHinrichs! I've made that mistake about 5 times already, I caught it 3 times 🙃