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Repository for suggesting new lineages that should be added to the current scheme
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KU.2 (JN.1.30.1 + S:F456L) FLiRT sublineage got S:G213E and Orf1a:P2739L(19) in Uk, France, NZL #2514

Closed FedeGueli closed 1 month ago

FedeGueli commented 4 months ago

Formerly known as branch 28 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

JN.1.30.1 designated =

Branch 28: JN.1.30( G21255T) > T7789C > S:R346T (G22599C) Query:G21255T , G22599C,T3565C,G11727A Samples : 26 India

KU.2 designated=

With further S:F456L branch following: JN.1.30 (G21255T) > T7789C > S:R346T (G22599C) > S:F456L (T22928C) Query: G22599C,T22928C,G21255T,T3565C Samples : 4 Uk

KU.2 with further S:G213E NOW PROPOSED: KU.2>Orf1a:P2739L (C8481T), S:G213E (G22200A),C22432T Query: C8481T, C22432T,T22928C Samples: 13 Uk EPI_ISL_18969314, EPI_ISL_18969579, EPI_ISL_18969597, EPI_ISL_18987610, EPI_ISL_18987614, EPI_ISL_18987693, EPI_ISL_18987696, EPI_ISL_18987703, EPI_ISL_19002136, EPI_ISL_19002141, EPI_ISL_19002143, EPI_ISL_19006296, EPI_ISL_19006611

Tree:https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b36d_f0f8b0.json?c=gt-nuc_7789&gmax=8789&gmin=6789&label=id:node_6907783

Screenshot 2024-03-11 alle 15 29 04 Screenshot 2024-03-11 alle 15 29 30 Screenshot 2024-03-11 alle 15 29 55
Original proposal Samples: image Usher finds more sequences than Gisaid cause many samples have T7789C defining as missing nucleotide, T7789C is needed in the query cause there is a smaller branch bottom with G21255T > > S:R346T (G22599C) Manually checking it on Nextclade i found just three samples that has not T7789C and has no missing nuc in that position or very close to it , so to me likely it is there in the very most of them ( Query including sequences placed in the other branch by Usher: G21255T , T3565C, G22599C Screenshot 2024-03-11 alle 15 41 29 Screenshot 2024-03-11 alle 15 44 13
aviczhl2 commented 4 months ago

S:G213E is appeared together with S:R346T in XDK.1

FedeGueli commented 4 months ago

S:G213E is appeared together with S:R346T in XDK.1

yeah i thought the same not sure if a recombinant event happened in which direction from this to XDK.1 or from XDK.1 to this one. or none and just convergence

FedeGueli commented 3 months ago

32 for 346T and 6 for 456L ( GBW, Australia)

FedeGueli commented 3 months ago

S:R346T went to 35 with three samples from Australia ( 2 from NSW one from SA) The FLirt sublinegae up to 7 with one of the two samples coming from NSW being FLiRT and havig S:W64L too. S:W64L was previously defining mutation of BA.2.14 and BA.5.2.14 indicating some probable beneficial effect of it.

FedeGueli commented 3 months ago

Big upload from Uk 5 more sequence with 456L and 213E

FedeGueli commented 3 months ago

Now the total is 50 i ve updated the qeury with G21255T , G22599C,T3565C,G11727A , it catches also a flip flop branch that belongs to this :

Screenshot 2024-03-18 alle 13 46 01

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_540db_836390.json?label=id:node_6911800 Ping @corneliusroemer i suggest the designation of the three levels

aviczhl2 commented 3 months ago

Designated JN.1.30.1

FedeGueli commented 3 months ago

JN.1.30.1 via https://github.com/cov-lineages/pango-designation/commit/e03042f9c2bacc2d7f5bffce3194fd29ef2420b5

aviczhl2 commented 3 months ago

19 for S:F456L and 11 for S:G213E now.

FedeGueli commented 3 months ago

19 for S:F456L and 11 for S:G213E now.

Thx! @corneliusroemer i would designate them.

FedeGueli commented 3 months ago

the JN.1.30.1 branch with S:F456L designated KU.2 via https://github.com/cov-lineages/pango-designation/commit/1cda06ac97854e9a8e33c4340d91c599921f8490 Leaving this open to track the S:G213E branch

FedeGueli commented 3 months ago

+2

FedeGueli commented 2 months ago

17 for the G213E branch

FedeGueli commented 1 month ago

the sublineage is stale