LP.8.1 (KP.1.1.3.8.1) sublineage with S:T22N (35 seqs in 7 countries)

[HynnSpylor]

*Transferred from sars-cov-2-variants/lineage-proposals#2353

Defining mutations:
LP.8.1>C21627A (S:T22N)

GISAID Query: C4999T, C21627A, C22120A, C23039G,
Earliest seq: 2024-10-21 (Taiwan, China-EPI_ISL_19522303)
Most recent seq: 2025-01-03 (NY, US-EPI_ISL_19666138)
Countries detected: US 14, China 6, Japan 3, Spain 2, France 1, Canada 1, Thailand 1(detected from Japan Intl Airport)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_2975a_762700.json

S:T22N is popular and convergent in almost with added NTD Glycan. the original LP.8.1 lineage gets S:Q493E while without S:T22N, maybe the added mutation can further increase the growth rate.

Genomes:
EPI_ISL_19522303, EPI_ISL_19574561, EPI_ISL_19601561, EPI_ISL_19602029, EPI_ISL_19615862, EPI_ISL_19623944, EPI_ISL_19629064, EPI_ISL_19629074, EPI_ISL_19639556, EPI_ISL_19640047, EPI_ISL_19640369, EPI_ISL_19643740, EPI_ISL_19643743, EPI_ISL_19643748, EPI_ISL_19643761, EPI_ISL_19650427, EPI_ISL_19651624, EPI_ISL_19651637, EPI_ISL_19656578-19656579, EPI_ISL_19657167, EPI_ISL_19658511-19658512, EPI_ISL_19658583, EPI_ISL_19660540, EPI_ISL_19663074, EPI_ISL_19664117, EPI_ISL_19666138

[HynnSpylor]

+1 from HK, China (with a rare mutation S:N679K->T)

[FedeGueli]

This is the first TRIDENT ( meaning with that it has three new N Glycans in the NTD) to reach the proposal in the main pango page.

[FedeGueli]

+1 from HK, China (with a rare mutation S:N679K->T)

It is quite trending in the very few last weeks with multiple lineages getting it.

[xz-keg]

This is the first TRIDENT ( meaning with that it has three new N Glycans in the NTD) to reach the proposal in the main pango page.

NG.1+S:R190T but not separately proposed and dies out early.

[HynnSpylor]

33 seqs now (US +4)

[FedeGueli]

35

[cvejris]

Sublineage with S:L5F (C21575T) + S:K679T (A23598C) (+C2773T, C4683T, G17721T, C20235T, C29545A):
1x Hong Kong, 1x Canada BC

[FedeGueli]

There are two branches under this lineage with S:K679R :
First one has been found by @cvejris but it doesnt seem growing:
Query : A9328G,23598G
Samples: 2 ( 1 with this query) Australia, Taiwan

Second one directly from Politomy (so it could be also seen as LP.8.1.1 + 22N):
Query: A23598G,C21627A,G1954A,-A9328G,-T16600C,-G12892A or A23598G,C21627A,del21653,-A9328G
Samples: 3 but 8 on Usher (no idea why not caught by the query)
Places: Alabama; Canada

Note that we should avoid to confound with the recombinant proposed by Ryan in sars-cov-2-variants/lineage-proposals#2323

cc @HynnSpylor @xz-keg ping @corneliusroemer i think some designations would be helpful to avoid a full mess mode with convergence toward 679R (or 22N)

[FedeGueli]

39

[FedeGueli]

LP.8.1.6 via 841d847