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JN.1 + ORF6:P57L (C27371T) (39) and JN.1 + ORF1a:F499L (C1762A) (427) and JN.1 + ORF1a:T170I (T18453C)(103) #987

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Fearuncle opened this issue Oct 18, 2023 · 13 comments
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JN.1 + ORF6:P57L (C27371T) (39) and JN.1 + ORF1a:F499L (C1762A) (427) and JN.1 + ORF1a:T170I (T18453C)(103) #987

Fearuncle opened this issue Oct 18, 2023 · 13 comments
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BA.2.86 designated JN.1 Multiple lineages Orf6 S:455
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JN.1.1 JN.1.4 JN....

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@Fearuncle
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image
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e2c9_28f70.json

gisaid query: T27810C, C18894T

First Seq: 2023-08-25
Most Recent: 2023-10-04
@FedeGueli
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Yeah the Orf6:P57L was mentioned by me in the open discussion, worth remembering Orf6:P57L was defining of a large undesignated BA.5.2.1 branch emerged in Africa and had in BF.15 its most interesting sublineage.

@FedeGueli FedeGueli added the Orf6 label Oct 18, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (16) and JN.1 + ORF1a:F499L (C1762A) (21) JN.1 + ORF6:P57L (C27371T) (16) and JN.1 + ORF1a:F499L (C1762A) (28) Oct 19, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (16) and JN.1 + ORF1a:F499L (C1762A) (28) JN.1 + ORF6:P57L (C27371T) (16) and JN.1 + ORF1a:F499L (C1762A) (30) Oct 21, 2023
@Fearuncle Fearuncle mentioned this issue Oct 21, 2023
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@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (16) and JN.1 + ORF1a:F499L (C1762A) (30) JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (34) Oct 22, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (34) JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (35) Oct 24, 2023
@RajLABN
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RajLABN commented Oct 24, 2023

JN.1 + NSP2_F319L grows to 61

@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (35) JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (61) Oct 24, 2023
@Fearuncle
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@FedeGueli JN.1 + ORF1a:F499L passed 60 seq.

@FedeGueli
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Yes they are the two main branches of JN.1 i think @corneliusroemer is already aware of them

@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (61) JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (63) Oct 28, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (22) and JN.1 + ORF1a:F499L (C1762A) (63) JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (63) Oct 29, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (63) JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (66) Oct 29, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (66) JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (97) Oct 30, 2023
@Fearuncle
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13 with s:157f

@Memorablea Memorablea mentioned this issue Oct 30, 2023
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@FedeGueli
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13 with s:157f

have you the IDs it is likely artefact reversion

@RajLABN
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RajLABN commented Oct 30, 2023

JN.1 + NSP2 F319L grows to 117

@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (23) and JN.1 + ORF1a:F499L (C1762A) (97) JN.1 + ORF6:P57L (C27371T) (25) and JN.1 + ORF1a:F499L (C1762A) (97) Nov 1, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (25) and JN.1 + ORF1a:F499L (C1762A) (97) JN.1 + ORF6:P57L (C27371T) (25) and JN.1 + ORF1a:F499L (C1762A) (124) Nov 1, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (25) and JN.1 + ORF1a:F499L (C1762A) (124) JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (127) Nov 2, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (127) JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (131) Nov 4, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (131) JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (169) Nov 5, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (169) JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (172) Nov 6, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (172) JN.1 + ORF6:P57L (C27371T) (26) and JN.1 + ORF1a:F499L (C1762A) (174) Nov 7, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (33) and JN.1 + ORF1a:F499L (C1762A) (279) and JN.1 + ORF1a:T170I (T18453C)(58) JN.1 + ORF6:P57L (C27371T) (33) and JN.1 + ORF1a:F499L (C1762A) (293) and JN.1 + ORF1a:T170I (T18453C)(59) Nov 15, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (33) and JN.1 + ORF1a:F499L (C1762A) (293) and JN.1 + ORF1a:T170I (T18453C)(59) JN.1 + ORF6:P57L (C27371T) (37) and JN.1 + ORF1a:F499L (C1762A) (346) and JN.1 + ORF1a:T170I (T18453C)(67) Nov 16, 2023
@FedeGueli
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Please propose in the main page as JN.1 Branches

@FedeGueli FedeGueli added the To be proposed Green light for proposal label Nov 16, 2023
@FedeGueli FedeGueli mentioned this issue Nov 16, 2023
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@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (37) and JN.1 + ORF1a:F499L (C1762A) (346) and JN.1 + ORF1a:T170I (T18453C)(67) JN.1 + ORF6:P57L (C27371T) (37) and JN.1 + ORF1a:F499L (C1762A) (361) and JN.1 + ORF1a:T170I (T18453C)(73) Nov 17, 2023
@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (37) and JN.1 + ORF1a:F499L (C1762A) (361) and JN.1 + ORF1a:T170I (T18453C)(73) JN.1 + ORF6:P57L (C27371T) (38) and JN.1 + ORF1a:F499L (C1762A) (373) and JN.1 + ORF1a:T170I (T18453C)(74) Nov 19, 2023
@Fearuncle Fearuncle mentioned this issue Nov 19, 2023
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@Fearuncle Fearuncle changed the title JN.1 + ORF6:P57L (C27371T) (38) and JN.1 + ORF1a:F499L (C1762A) (373) and JN.1 + ORF1a:T170I (T18453C)(74) JN.1 + ORF6:P57L (C27371T) (39) and JN.1 + ORF1a:F499L (C1762A) (427) and JN.1 + ORF1a:T170I (T18453C)(103) Nov 20, 2023
@Fearuncle Fearuncle mentioned this issue Nov 27, 2023
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@xz-keg
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xz-keg commented Nov 28, 2023

The Orf1a:F499L branch is designated JN.1.1

@xz-keg xz-keg added this to the JN.1.1 milestone Nov 28, 2023
@FedeGueli FedeGueli added partially designated and removed To be proposed Green light for proposal labels Nov 28, 2023
@FedeGueli
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Orf1a:F499L Designated JN.1.1 via cov-lineages/pango-designation@ad90952

FedeGueli referenced this issue in cov-lineages/pango-designation Nov 28, 2023
@corneliusroemer
Designate JN.1.1 (ORF1a:F499L, C11747T, France)
ad90952
@alurqu alurqu mentioned this issue Dec 7, 2023
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This was referenced Jan 8, 2024
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@FedeGueli FedeGueli modified the milestones: JN.1.1, JN.1.1 JN.1.4 Jan 8, 2024
@FedeGueli
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JN.1 + ORF1a:T170I (T18453C) now Designated JN.1.4 via cov-lineages/pango-designation@20ddbad

@xz-keg xz-keg mentioned this issue Jan 12, 2024
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@xz-keg
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xz-keg commented Mar 25, 2024 •
edited by FedeGueli
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The Orf6:P57L branch is designated JN.1.44 via cov-lineages/pango-designation@8aa6137

FedeGueli referenced this issue in cov-lineages/pango-designation Mar 25, 2024
@corneliusroemer
Designate JN.1.44 (ORF6:P57L)
8aa6137
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BA.2.86 designated JN.1 Multiple lineages Orf6 S:455
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