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Repository for suggesting new lineages that should be added to the current scheme
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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) #2543

Closed xz-keg closed 3 months ago

xz-keg commented 7 months ago

From branch 11 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/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

image

Mydtlwn commented 7 months ago

@corneliusroemer

xz-keg commented 7 months ago

57, Canada,Australia

xz-keg commented 6 months ago

68, Ireland

FedeGueli commented 6 months ago

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

Screenshot 2024-05-01 alle 23 01 29

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

Screenshot 2024-05-01 alle 23 05 44 Screenshot 2024-05-01 alle 23 05 58
xz-keg commented 6 months ago

96, Singapore

xz-keg commented 6 months ago

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

AngieHinrichs commented 5 months ago

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 commented 5 months ago

265 seqs now.

FedeGueli commented 5 months ago

308

FedeGueli commented 4 months ago

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

what do you mean?

FedeGueli commented 4 months ago

the tree looks like this now:

Screenshot 2024-06-20 alle 11 06 57

the top branch is JN.1.39.1

the bottom one is still undesignated .

Interestingly it got S:T572I and S:T478Q

Screenshot 2024-06-20 alle 11 07 48

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)

Screenshot 2024-06-20 alle 11 12 47

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

DailyCovidCases commented 4 months ago

304 seqs, the tree looks like this now: usher Screenshot (126)

FedeGueli commented 4 months ago

Another sublineage of this has emerged this time in Portorico:

2543>> G29134A > Orf1a:T1168I (C3768T), A9337G, S:N641T (A23484C)

Query:C3768T, A9337G Samples: 15

Screenshot 2024-07-01 alle 07 31 08

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

DailyCovidCases commented 4 months ago

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

xz-keg commented 3 months ago

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

DailyCovidCases commented 3 months ago

482 seqs now

xz-keg commented 3 months ago

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

https://github.com/sars-cov-2-variants/lineage-proposals/issues/1839

FedeGueli commented 3 months ago

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 commented 3 months ago

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

DailyCovidCases commented 2 months ago

@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 Screenshot (183) Screenshot (173) Screenshot (174)

DailyCovidCases commented 2 months ago

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

FedeGueli commented 2 months ago

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 commented 2 months ago

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

Screenshot 2024-08-25 alle 22 21 11

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 commented 2 months ago

@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 commented 2 months ago

@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 commented 2 months ago

206

FedeGueli commented 2 months ago

22 w 478Q now

DailyCovidCases commented 1 month ago

Tree now: usher Screenshot (210) ping @corneliusroemer worth a designation this one

FedeGueli commented 1 month ago

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:

Screenshot 2024-09-17 alle 11 06 55

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

DailyCovidCases commented 2 weeks ago

@corneliusroemer This branch should be designated

FedeGueli commented 2 weeks ago

@corneliusroemer This branch should be designated

one only sample from September