JN.1+M:L46F+S:F456L(1922 seqs, 38 countries, 28% China, 22 with S:R346T, 51 with S:S31F, 6 with S:T22N)

[xz-keg]

From branch 26 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C)

GISAID query:G26660T, G4162A ,T22928C,T3565C (26 seqs) GISAID supplementary query: G4162A,-22928,G1126A,T3565C (2 seqs, for seqs with no coverage at S:F456 but share mutation) No. of seqs: 28(USA 4(2 from Singapore, 2 from South Korea) China 24(Hubei, Shanxi, Heilongjiang, Gansu, Henan, Hong Kong, Fujian from Taiwan, 1 from Malaysia 1 from Australia 1 from Thailand))

GISAID query for S:R346T branch: G26660T, G4162A ,T22928C,T3565C,G22599C (1 seq) GISAID query for S:S31F branch: G26660T, G4162A ,T22928C,T3565C, C21654T

First: EPI_ISL_18872894, Hong Kong, 2024-1-27 Latest: EPI_ISL_18999287, USA from South Korea, 2024-3-12

Seems widely distributed in China and SE Asian countries. Usher splits into two branches but the G1126A is separated by 2 Hong Kong seqs with no coverage on S:456, they shall have S:F456L too. usher

[FedeGueli]

@corneliusroemer designation required here

[FedeGueli]

2 FLiRT of this uploaded today from Hong Kong total 3 ( 1 Anhui, 2 HK) Query: G26660T, G4162A ,G22599C,G1126A

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5e3eb_ff05a0.json?c=userOrOld&label=id:node_11491539

[NkRMnZr]

it's getting further key spike mutations like R346T, A475V, T572I etc.

[Mydtlwn]

@corneliusroemer @FedeGueli

[Mydtlwn]

@ryhisner

[FedeGueli]

it's getting further key spike mutations like R346T, A475V, T572I etc.

Also in the NTD: here a recent cluster from Hubei with S:T22N: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_442aa_217ce0.json?label=id:node_7021832

[FedeGueli]

Flirt went to 4 with a sample from Netherlands. @aviczhl2

[FedeGueli]

2 samples from GBW interestingly both coming from Oceania: from Fiji with S:L441F and from NZL

[Memorablea]

China +95.7 get S:I794T,3 get S:S31F,1 get S:N282S, S:S680F.

[FedeGueli]

China +95.7 get S:I794T,3 get S:S31F,1 get S:N282S, S:S680F.

@corneliusroemer ping

[DailyCovidCases]

This branch should be designated now

[xz-keg]

1170 now,

[xz-keg]

30/120 in Chinese seqs after 6-1, stable at 25%. @corneliusroemer

[Over-There-Is]

1197+73+2+18+2=1292

[xz-keg]

1214, Spain

[Memorablea]

China+135

[FedeGueli]

5 in the FLiRT lineage with G26660T, G4162A ,G22599C,G1126A, last sample from France 8 with G26660T, G4162A ,T22928C,T3565C,G22599C last sample from Arizona

[xz-keg]

5 in the FLiRT lineage with G26660T, G4162A ,G22599C,G1126A, last sample from France 8 with G26660T, G4162A ,T22928C,T3565C,G22599C last sample from Arizona

So 2 FLiRTs already?

[xz-keg]

1356, Russia

64/228=28% in Chinese seqs after 6-1.

[xz-keg]

@corneliusroemer This one seems to be ignored from designation for quite a long time.

[FedeGueli]

5 in the FLiRT lineage with G26660T, G4162A ,G22599C,G1126A, last sample from France 8 with G26660T, G4162A ,T22928C,T3565C,G22599C last sample from Arizona

So 2 FLiRTs already?

I have to check i was thinking my query was just not good i'll update later!

[FedeGueli]

G26660T, G4162A ,G22599C,G1126A

checked they are the same FLiRT

[FedeGueli]

This branch should be designated, one possibility is JN.1.65 or JN.1.66

please don't write possible designation numbers because someone could then be fooled finding this issue in the issue instead the correct one so call it JN.1.X please

[xz-keg]

1479, Sweden, Laos, Switzerland, Germany, Slovenia, 10 with S:R346T, 38 with S:S31F

[xz-keg]

@corneliusroemer

[DailyCovidCases]

Tracked in tracker26a Is it worth to be designated? @corneliusroemer

[Over-There-Is]

@corneliusroemer

[xz-keg]

1574 seqs now. Italy, Iceland

40 for S:S31F and 11 for S:R346T

[DailyCovidCases]

@corneliusroemer This one seems to be ignored from designation for quite a long time

[FedeGueli]

@corneliusroemer This one seems to be ignored from designation for quite a long time

@dailycovidcases consider that each designation means work for all the chain of people involved, Cornelius knows when designating something. If he doesn't he will have his reasons, wrong or right. So until nothing new happens better wait calmly. This is big but not fast. So while i would prefer to see it designated it could happen that designations miss a lineage.

[xz-keg]

1595, Qatar, Israel

[xz-keg]

1632, Denmark and GBW from India

[xz-keg]

1718 seqs, Luxembourg,

[FedeGueli]

@corneliusroemer This one seems to be ignored from designation for quite a long time

a bit a pity maybe now it is not that relevant even if we have no clear picture of what is happening in China where this had and has a good share @corneliusroemer

[DailyCovidCases]

Why isn't this branch be designated, though it has more than 1700 seqs?

[DailyCovidCases]

Ping @corneliusroemer rapid designation needed

[xz-keg]

@corneliusroemer This lineage is very prevalent in China. Most of the "JN.1"(yellow bar) in the unreleased CCDC data actually belong to this branch. This branch shall get designated to distinguish from vanilla JN.1.

[FedeGueli]

also on Gisaid it represents more than 15% (54/330) of samples collected in or related to China after July 15

[DailyCovidCases]

@corneliusroemer suggest to designate some trajectory of this

[Memorablea]

For now, I don't think this branch will be specified.Although this branch is very broad.

However, attention should be paid to the emergence and development of noteworthy mutations in the branch.

If we can.

[xz-keg]

For now, I don't think this branch will be specified.Although this branch is very broad.

However, attention should be paid to the emergence and development of noteworthy mutations in the branch.

If we can.

Still I think this needs designation. It is very large, and most of the sequences actually come from an underrepresented region (China and around).

Given its prevalence infection toll can be more than 100 million.

[Memorablea]

For now, I don't think this branch will be specified.Although this branch is very broad. However, attention should be paid to the emergence and development of noteworthy mutations in the branch. If we can.

Still I think this needs designation. It is very large, and most of the sequences actually come from an underrepresented region (China and around).

Given its prevalence infection toll can be more than 100 million.

Yes,you are right.I understand that the epidemic of this disease is very wide.I have also been paying attention to the monthly report of China CDC.In China, we have found too much of this branch.

Of course, I would very much like you to be designated.Because it will help the research further.

[FedeGueli]

In August this has been over 30% of samples in Gansu, i think we should designate it. China has two lineages that are leading and co-leading the epidemic there, XDV.1 and this one, being both very different from what we see outside China it would be of special interest to follow them both. more: M:L46F is acquiring more spike mutations.

[xz-keg]

1922 seqs now. Still very prevalent in China. New sample from GBW from Cayman Islands,

51 with S:S31F 22 with S:R346T 6 with S:T22N

[FedeGueli]

Designated JN.1.67 and JN.1.67.1 via https://github.com/cov-lineages/pango-designation/commit/477df9d9f6baf6c4809cebcfcb6c46714fb323ee

[Memorablea]

THX

[Over-There-Is]

S:F59S, R346T mainly in China: sars-cov-2-variants/lineage-proposals#1971

[xz-keg]

The S31F sub-branch is designated MZ.1