JN.1+C21762T(S:A67V) (36 sequences, at least 7 countries)

[yanjin1234]

Sub-lineage of:JN.1

First: EPI_ISL_18819543, Japan, 2023-11-28 Latest: EPI_ISL_18944034,China, 2024-02-20

No. of seqs: 36( China 20 USA 8 Germany 4 Singapore 1 Japan 1 Poland 1 Oman 1 ） Among the 20 sequences from China, 17 come from our laboratory. They were detected within a short timeframe. interesting fact is that S:A67V is a highly prevalent mutation in BA.1, located at the superantigen site of the S protein's N-terminal domain

IDs:EPI_ISL_18926250, EPI_ISL_18926252, EPI_ISL_18926251, EPI_ISL_18926254, EPI_ISL_18926253 EPI_ISL_18944034 GISAID query:T111C,C5512T,G2782T,C21762T,C18894T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1aa02_1ec780.json?f_userOrOld=uploaded%20sample

[FedeGueli]

Hi @yanjin1234 this was proposed yesterday by @aviczhl2 in the pre proposal repository : https://github.com/sars-cov-2-variants/lineage-proposals/issues/1395 If he agrees i suggest him to close that and to track the lineage together here . Thank you for proposing

[yanjin1234]

Among the 10 sequences that passed QC this week, 6 are JN.1+S:A67V. We will continue to track the prevalence of this variant strain locally.

[aviczhl2]

The proposed lineage shall be independent lineage with additional mutations of C5512T and G2782T as described in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1395?

Other ~40 seqs shall belong to other separate lineages I guess?

[FedeGueli]

@corneliusroemer this proposal embraces a various of lineage, the one emerging in Chonqqing, where is the lab that put out this proposal is found with C5512T,G2782T,C21762T,C18894T and described by @aviczhl2 in secondary report issue # 1395

[yanjin1234]

@FedeGueli @corneliusroemer As an addition, the JN.1+S:A67V lineage, identified in Chongqing, is characterized by the following sites: T111C, C5512T, G2782T, C21762T, and C18894T.

[yanjin1234]

The number of sequences with this characteristic mutation in Chongqing has increased to 19. Gisaid ID will be provided later.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_3c2e6_1793d0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

@corneliusroemer i suggest to designate this one.

[yanjin1234]

EPI_ISL ID： EPI_ISL_18944031- EPI_ISL_18944041

[aviczhl2]

@corneliusroemer i suggest to designate this one.

I think the designation show follow https://github.com/sars-cov-2-variants/lineage-proposals/issues/1395 as other branches here are separate branches getting S:A67V independently.

[yanjin1234]

@FedeGueli @corneliusroemer @aviczhl2 You've done a great job, but it is based on the sequences we specifically uploaded. It is recommended that the Pango committee grant naming rights to the laboratory that uploaded the data, in recognition of the hard work of the laboratory scientists. Thank you.

[FedeGueli]

@FedeGueli @corneliusroemer @aviczhl2 You've done a great job, but it is based on the sequences we specifically uploaded. It is recommended that the Pango committee grant naming rights to the laboratory that uploaded the data, in recognition of the hard work of the laboratory scientists. Thank you.

Yeah of course @aviczhl2 was just pointing out the correct definition of this lineage at the scope to designate it as soon as possible. our work is based on your efforts and we are pleased you took the time and the willing of describing and proposing this lineage . Thank you.

[yanjin1234]

+2 Yibin, another city 300 kilometers away from Chongqing.

[FedeGueli]

+2 Indonesia and Japan using the query : C5512T,G2782T,C21762T,C18894T by @aviczhl2 (44 total)

cc @corneliusroemer this is going very well i would designate it as soon as possible.

[yanjin1234]

+2 Indonesia and Japan using the query : C5512T,G2782T,C21762T,C18894T by @aviczhl2 (44 total)+2 印度尼西亚和日本使用查询 ： C5512T，G2782T，C21762T，C18894T by （44 总计）

cc @corneliusroemer this is going very well i would designate it as soon as possible.抄送：进展顺利，我会尽快指定它。

If the A67V lineage cannot have any sub-lineages, then should the sequence query include T111C?

[FedeGueli]

i suggest to start the designation from S:A67V not from T111C cause the sequences included seems really part of this lineage via nucleotides marker , not a big issue anyway cause the sequences not part of T111C seem quite older than the main branch https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2d411_5a5550.json?c=country&label=id:node_6911005

[FedeGueli]

45 with C5512T,G2782T,C21762T,C18894T today uploads from Japan, Thailandia and Indonesia

[FedeGueli]

52 including not T111C samples cc @corneliusroemer

[yanjin1234]

This week, there was an increase of 13,The sequence is shared afterwards.

[yanjin1234]

[FedeGueli]

now it is 67 with C5512T,G2782T,C21762T,C18894T @corneliusroemer ping this is fast.

[aviczhl2]

There is an S:F456L sub-branch of this lineage. Query : C21762T,C18894T,T22928C in France

[FedeGueli]

There is an S:F456L sub-branch of this lineage. Query : C21762T,C18894T,T22928C in France

one to watch

[yanjin1234]

@FedeGueli +10 All from China

[FedeGueli]

@FedeGueli +10 All from China

thx!! i see 77 with my query (by @aviczhl2 my to distinguish from yours lacking T111C) most or all the new ones from Sichuan right?

[FedeGueli]

@corneliusroemer designation needed this one has prevalence and actually widespread in multiple states of China

[FedeGueli]

and as @aviczhl2 noted, it likely recombined already with JN.1.18 to create branch 51 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

[aviczhl2]

and as @aviczhl2 noted, it likely recombined already with JN.1.18 to create branch 51 of sars-cov-2-variants/lineage-proposals#1089

Not recomb. It seems that this branch is misplaced in usher. It shall be under G2782A->T111C branch and be a sibling of B51 in the 346 repo.

Or this branch is a recomb of the G2782A->T111C branch and the C5512T branch?

[yanjin1234]

and as @aviczhl2 noted, it likely recombined already with JN.1.18 to create branch 51 of sars-cov-2-variants/lineage-proposals#1089如前所述，它可能已经与 JN.1.18 重新组合以创建 sars-cov-2-variants/lineage-proposals#1089 的分支 51

This branch does not carry S:A67V

[aviczhl2]

I checked seqs with S:A67V from this branch. 72 of them have 111C, 5 of them have 111 missing coverage, none of them have 111T.

So T111C is shared by all seqs of this branch.

The correct trajectory shall be JN.1->G2782T->T111C->C5512T, S:A67V.

[FedeGueli]

@aviczhl2 Thanks for the analysis .

[FedeGueli]

and as @aviczhl2 noted, it likely recombined already with JN.1.18 to create branch 51 of sars-cov-2-variants/lineage-proposals#1089如前所述，它可能已经与 JN.1.18 重新组合以创建 sars-cov-2-variants/lineage-proposals#1089 的分支 51

This branch does not carry S:A67V

yeah we thought it was a donor of the recombinant. But @aviczhl2 went further in the comments below.

[yanjin1234]

This week, the laboratory continued to detect an additional 11 cases.

[Memorablea]

please designation

[FedeGueli]

93

[aviczhl2]

Designated JN.1.33

[FedeGueli]

Designated JN.1.33 via https://github.com/cov-lineages/pango-designation/commit/98da9b23d589330f4a12657b75707c76f976fbbb

[FedeGueli]

21762T,C18894T,T22928C in France

this query now catches an unrelated sample from Brazil. I suiggest to use C13694T, C24718T ,T22928C to monitor it although the two samples appear to be quite old now so unlikely it is growing