JN.1.39+S:F456L mostly misplaced under JN.1.16 (456 seqs, 250 with S:R346T(designated JN.1.39.1), 16 with S:T572I and S:478Q)

[xz-keg]

From branch 11 of sars-cov-2-variants/lineage-proposals#1253

JN.1.39+T22928C(S:F456L)

GISAID query: G2782T,T22926C,T22928C,-T111C,-23601,-C1594T,-26873, -10369
GISAID query for S:T572I, K478Q branch: C6781T, C12733T,C23277T (By @FedeGueli )
No. of seqs: 43( Germany 2 China 1 Japan 1 USA 39(1 from Japan, 1 from Switzerland, 1 from UAE)

First: EPI_ISL_18695414, USA, 2023-12-16
Latest: EPI_ISL_19005864, Japan, 2024-3-13

Mostly misplace as JN.1.16+G2782T, as S:F456L(T22928C) is much more of a convergent mutation than G2782T this shall be JN.1.39+S:F456L(T22928C). Seqs placed on other branches are excluded, maybe recombs.

@AngieHinrichs @corneliusroemer

usher

[Mydtlwn]

@corneliusroemer

[xz-keg]

57, Canada,Australia

[xz-keg]

68, Ireland

[FedeGueli]

it has now a FLiRS branch of 2
[JN.1.16> G2782T ] = JN.1.39 > S:F456L > S:R346S (A22600C), T25054C
Query: G2782T,T3565C,A22600C, T25054C

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_1b8fb_26cb10.json?c=userOrOld&label=id:node_11429162

Note that there is another likely misplaced JN.1.39 with S:S346S but this time it is anticipated by S:S31F and it chould not be the same lineage of the one found here even if there is Geographical contiguity (US):
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1cd44_2abef0.json?label=id:node_6934825

[xz-keg]

96, Singapore

[xz-keg]

The 21034 shall also be part of this branch. The S:R346T branch is designated JN.1.39.1.

[AngieHinrichs]

I did a force move so the branch with USA/NY-CDC-LC1094418/2024 is now JN.1.39 > T22928C (S:F456L), so far matOptimize left it there.

[xz-keg]

265 seqs now.

[FedeGueli]

308

[FedeGueli]

Branch 11 designated JN.1.39.a.b = LZ.b

what do you mean?

[FedeGueli]

the tree looks like this now:

the top branch is JN.1.39.1

the bottom one is still undesignated .

Interestingly it got S:T572I and S:T478Q

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_41918_3ecf40.json?f_userOrOld=uploaded%20sample&label=id:node_12184780

So i suggest @aviczhl2 to modify the query to: G2782T,T22926C,T22928C,-G22599C,-T111C,-23601,-C1594T,-26873, -10369

and adding two sublineages to the proposal:
JN.1.39 > S:F456L (T22928C) > orf1b:T634I (C15368T) > C6781T, C12733T, S:T572I C23277T, C24157T >
Query :C6781T, C12733T,C23277T
Samples: 9 ( 7 with S:T478Q and 2 with S:G213R)

And
JN.1.39> S:F456L (T22928C) > S:R346S (A22600C), T25054C
Query: A22600C, T25054C
Samples: 7

[DailyCovidCases]

304 seqs, the tree looks like this now:
usher

[FedeGueli]

Another sublineage of this has emerged this time in Portorico:
#2543>> G29134A > Orf1a:T1168I (C3768T), A9337G, S:N641T (A23484C)
Query:C3768T, A9337G
Samples: 15

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice17_genome_test_1041f_236200.json?label=id:node_7155768

[DailyCovidCases]

Tracked in tracker11
Is it worth to be designated? @corneliusroemer

[xz-keg]

It seems that seqs outside JN.1.39.1 is close to stopped growing. Close this.

[DailyCovidCases]

482 seqs now

[xz-keg]

Re-open it to track the 456L-572I-478Q sub-branch

sars-cov-2-variants/lineage-proposals#1839

[FedeGueli]

Why isn't this branch be designated, though it has nearly 500 seqs?

sometimes a branch can being not designated even if it is quite big, likely if there is no fast offspring even if it is 500 or even it was 1000 but slowing down it won't be designated.

[xz-keg]

It seems that the T572I-478Q branch has also stopped growing. Close down.

[DailyCovidCases]

@corneliusroemer This branch got significant proportion between March and May in France:
https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/covid-19/documents/bulletin-national/covid-19-en-france.-point-au-21-aout-2024
usher

[DailyCovidCases]

513 seqs now, 2 new sample from USA and Sweden in August, please update the title

[FedeGueli]

The query was not updated to the suggested one, with it it is 222, but i added further -s to be excluded :
the only query catching JN.1.39 + 456L is : G2782T,T22926C,T22928C,-G25647T,-C23039G,-G24872T,-T6913C,-G22599C,-T111C,-23601,-C1594T,-26873, -10369 and the count is 204
10/204 have been collected in July this means it is dying off and can be kept closed.
@DailyCovidCases i don't understa nd why don't you do this kind of analysis that are the utmost important because doing that you can find small growing lineages hidden in old stale or dying proposed sublineages.

[FedeGueli]

Interestingly 3/10 of the ost recent samples of it are from the Trio sublineage with S:K478Q
New Query: C6781T,C24157T, C15368T,C12733T
Samples: 19
countries : 5
tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4f14d_b8fe90.json?label=id:node_7234738

Even if it has low chance to compete: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?%2FAllSamples%2FPast3M%2Fvariants%3FnextcladePangoLineage=JN.1*&nextcladePangoLineage=KP.3*&nucMutations1=C6781T%2CC24157T%2CC15368T%2CC12733T&analysisMode=CompareToBaseline&
i would consider to rearrange the proposal around it

[FedeGueli]

@aviczhl2 Now 520 seqs, please update the title

it is 205 see the comments above . cc @corneliusroemer
correct query is G2782T,T22926C,T22928C,-G25647T,-C23039G,-G24872T,-T6913C,-G22599C,-T111C,-23601,-C1594T,-26873, -10369

[DailyCovidCases]

@aviczhl2 Now 520 seqs, please update the title

it is 205 see the comments above . cc @corneliusroemer correct query is G2782T,T22926C,T22928C,-G25647T,-C23039G,-G24872T,-T6913C,-G22599C,-T111C,-23601,-C1594T,-26873, -10369

I think this branch should be designated ping @corneliusroemer

[FedeGueli]

206

[FedeGueli]

22 w 478Q now

[DailyCovidCases]

Tree now:
usher

ping @corneliusroemer worth a designation this one

[FedeGueli]

G2782T,T22926C,T22928C,-G25647T,-C23039G,-G24872T,-T6913C,-G22599C,-T111C,-23601,-C1594T,-26873, -10369 finds 220
It is circulating in August at low levels in Hubei in a branch defined by a silent C>G mutation (C22450G=S:L296L) with further S:S31F and PLPro_V66A (Orf1a:V1629A) ( PLPro_E67A was shown to reduced PLPRO activity )
Query: T5151C ,C21654T
tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_23548_944f20.json?c=gt-S_31,478&gmax=25384&gmin=21563&label=id:node_7320489

25 with 478Q using C6781T,C24157T, C15368T,C12733T with a Louisiana cluster that added S:S256L