Designate clades 24H (LF.7) and 24I (MV.1)

[corneliusroemer]

With this PR, we are designating clade 24H (lineage LF.7) and 24I (lineage MV.1). Both clades are notable in that they do not descend from JN.1.11.1 in contrast to the clades currently dominating circulation in Europe and North America: lineages KP.3.1.1 and XEC (the RBD of this recombinant descends from KP.3)

The trial build shows the prevalence of both clades in West and South East Asia, respectively:

https://nextstrain.org/staging/ncov/gisaid/trial/clades-2023-10/global/2m?label=clade:23I%20%28BA.2.86%29

Clade 24H, lineage LF.7

Clade 24H, lineage LF.7, descends from JN.1 by a relatively long branch with 15 substitutions, of which 7 cause Spike amino acid substitutions: T22N, S31P, K182R, R190S, R346T, K444R, F456L. It also has acquired ORF9b:I5T, a mutation that appeared in a number of XBB lineages.

The lack of obvious ancestral sequences has caused it to be designated as LF.7 (JN.1.16.1.7) - LF are all JN.1 lineages with R346T and F456L and no obvious ancestors distinguishing from JN.1. Of note is that this year's US mRNA vaccine strain KP.2 is similar to JN.1.16.1 with KP.2 just having an extra V1104L.

S:K444R has been seen a few times in the past, most commonly in BA.2.3.20. A higher worldwide proportion of a mutation at Spike site 444 was reached by S:K444T in BQ.1.1 and CH.1.1.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=lf.7*&

It has been dominant in Qatar since September 2024 and on the rise globally, including the US. It is at above 5% in several countries in West Asia: Kazakhstan, Kuwait, Uzbekistan and has been growing with around 5% per day in Asia and thus can be interpreted to satisfy clade criterion 4. Sparse sequencing in West Asia and North Africa make it difficult to satisfy the criterion to the letter in this case.

Clade 24I, lineage MV.1

Clade 24I, lineage MV.1 (JN.1.49.1.1.1.1.1, MB.1.1.1.1), is a descendant of MB.1.1 (JN.1.49.1.1.1, R346T, L456V, S31F) which reached 30-40% in India in July 2024. MV.1 is likely most common in South and South East Asia. It is on track to become dominant in Singapore where it surpassed 30% in early October 2024. Also growing in Europe and North America where it is at around 1% in sequences collected end of September 2024.

The reversion of 478K to wild type T is interesting: 478K was part of both Delta and Omicron and has hence been the variant at this position that most people have been exposed to through infections since mid-2021. The other amino acid that was common at this position was R which reached around 35% of global circulation in mid 2023 as part of XBB sublineages XBB.1.16 and FL.1.5.1.

Spike mutation 456V is less common than 456L, possibly due to a combination of being due to less frequent T->G mutations (as opposed to T->C).

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=mv.1*&

It satisfied 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 October in Asia.

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 (no longer necessary since we're defaulting to Omicron - only necessary for non-Omicrons)
• Explain in PR why we are elevating
• Check trial builds:
  • https://nextstrain.org/staging/ncov/gisaid/trial/clades-2023-10/north-america/all-time
  • https://nextstrain.org/staging/ncov/open/trial/clades-2023-10/north-america/all-time
• 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

[xz-keg]

MV.1 (or MB.1.1) seems also meet the 5% prevalence- 5% daily growth criteria in Asia now.