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JN.1.4+C28201T（ORF8:S103L）（5678seqs）【JN.1.4.5】 #2426

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Memorablea opened this issue Dec 24, 2023 · 26 comments
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JN.1.4+C28201T（ORF8:S103L）（5678seqs）【JN.1.4.5】 #2426

Memorablea opened this issue Dec 24, 2023 · 26 comments

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@Memorablea
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Memorablea commented Dec 24, 2023 •
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from github.com/sars-cov-2-variants/lineage-proposals/issues/1171
GISAID seach ：T18453C,C28201T,A7842, C8293T, G8393A
On the basis of sars-cov-2-variants/lineage-proposals#1155 T18471C.
image
@Memorablea Memorablea changed the title JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（699 seqs） JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（701 seqs） Dec 24, 2023
@Memorablea Memorablea changed the title JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（701 seqs） JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（888seqs） Dec 24, 2023
@Mydtlwn
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Mydtlwn commented Dec 25, 2023

@corneliusroemer

@Memorablea Memorablea changed the title JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（888seqs） JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（928seqs） Dec 25, 2023
@Memorablea Memorablea changed the title JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（928seqs） JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（933seqs） Dec 26, 2023
@Memorablea
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Add the latest UshER tree
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b916_a664f0.json?f_userOrOld=uploaded%20sample
image

@Memorablea Memorablea changed the title JN.1+T18453C（#1155 ）with C28201T（ORF8:S103L）（933seqs） JN.1+T18453C,C28201T（ORF8:S103L）（933seqs） Dec 26, 2023
@ryhisner
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ryhisner commented Dec 29, 2023 •
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There's a 68-sequence lineage with the classic 3-nucleotide ORF1b TRS mutation in this branch that is either entirely confined or almost entirely confined to Israel. First sequences was November 29, and 54/68 have collection dates of Dec 10 or later. 28/68 were collected on or after Dec 15.
image

GISAID Nucleotide Query: C774T, C21302T, C21304A, T27810C, -C1762A, -A13278G, -C28528T
Usher Tree: https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1__C21302T_C21304A_G21305A_C28201T.json?c=gt-nuc_21302&gmax=22302&gmin=20302&label=id:node_6810451
image

Genomes

Genomes EPI_ISL_18616083, EPI_ISL_18616126, EPI_ISL_18673123, EPI_ISL_18673128, EPI_ISL_18673134, EPI_ISL_18673138, EPI_ISL_18673142, EPI_ISL_18673146, EPI_ISL_18673148, EPI_ISL_18673151, EPI_ISL_18673153-18673155, EPI_ISL_18673160, EPI_ISL_18673165, EPI_ISL_18673167, EPI_ISL_18673172, EPI_ISL_18673175-18673176, EPI_ISL_18673182, EPI_ISL_18673186, EPI_ISL_18673200, EPI_ISL_18673204, EPI_ISL_18683452, EPI_ISL_18683454, EPI_ISL_18683474, EPI_ISL_18683480, EPI_ISL_18683482, EPI_ISL_18683491, EPI_ISL_18683493, EPI_ISL_18683496-18683497, EPI_ISL_18683520, EPI_ISL_18683524, EPI_ISL_18683526, EPI_ISL_18683538, EPI_ISL_18683542, EPI_ISL_18683546-18683548, EPI_ISL_18683571-18683572, EPI_ISL_18683574-18683575, EPI_ISL_18683577-18683578, EPI_ISL_18683584, EPI_ISL_18683595, EPI_ISL_18700196, EPI_ISL_18700203, EPI_ISL_18700218-18700220, EPI_ISL_18700228, EPI_ISL_18700231, EPI_ISL_18700233, EPI_ISL_18700239-18700240, EPI_ISL_18700242, EPI_ISL_18700251-18700252, EPI_ISL_18700257, EPI_ISL_18700261, EPI_ISL_18700267-18700268, EPI_ISL_18700270, EPI_ISL_18700272, EPI_ISL_18701887,

@FedeGueli
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There's a 68-sequence lineage with the classic 3-nucleotide ORF1b TRS mutation in this branch that is either entirely confined or almost entirely confined to Israel. First sequences was November 29, and 54/68 have collection dates of Dec 10 or later. 28/68 were collected on or after Dec 15. image

GISAID Nucleotide Query: C774T, C21302T, C21304A, T27810C, -C1762A, -A13278G, -C28528T Usher Tree: https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1__C21302T_C21304A_G21305A_C28201T.json?c=gt-nuc_21302&gmax=22302&gmin=20302&label=id:node_6810451 image

Genomes

Genomes

most of them with PLPro_T277I too.

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（933seqs） JN.1+T18453C,C28201T（ORF8:S103L）（1212seqs） Dec 30, 2023
@Memorablea
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1212seqs now

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（1212seqs） JN.1+T18453C,C28201T（ORF8:S103L）（1272seqs） Jan 3, 2024
@Memorablea
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1272 now

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（1272seqs） JN.1+T18453C,C28201T（ORF8:S103L）（1301seqs） Jan 4, 2024
@Memorablea
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1301now

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（1301seqs） JN.1+T18453C,C28201T（ORF8:S103L）（1354seqs） Jan 6, 2024
@Memorablea
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1354now @AngieHinrichs @corneliusroemer

@Memorablea
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1674now @corneliusroemer @FedeGueli

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（1354seqs） JN.1+T18453C,C28201T（ORF8:S103L）（1674seqs） Jan 9, 2024
@FedeGueli
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1674now @corneliusroemer @FedeGueli

I think it will be designated along with spike mutated sublineages if they will become big , dont worry it is under scrutiny for sure.

@Memorablea Memorablea changed the title JN.1+T18453C,C28201T（ORF8:S103L）（1674seqs） JN.1+C28201T（ORF8:S103L）（1744seqs） Jan 11, 2024
@aviczhl2 aviczhl2 mentioned this issue Jan 12, 2024
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@Memorablea Memorablea changed the title JN.1+C28201T（ORF8:S103L）（1744seqs） JN.1+C28201T（ORF8:S103L）（1851seqs） Jan 12, 2024
@Memorablea
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1851now

@Memorablea
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2459 now

@Memorablea Memorablea changed the title JN.1+C28201T（ORF8:S103L）（1851seqs） JN.1+C28201T（ORF8:S103L）（2459seqs） Jan 21, 2024
@Memorablea Memorablea changed the title JN.1+C28201T（ORF8:S103L）（2459seqs） JN.1.4+C28201T（ORF8:S103L）（2459seqs） Jan 31, 2024
@Memorablea
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3596

@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（2459seqs） JN.1.4+C28201T（ORF8:S103L）（3596seqs） Feb 1, 2024
@Mydtlwn
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Mydtlwn commented Feb 2, 2024

@corneliusroemer

@Memorablea
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3866

@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（3596seqs） JN.1.4+C28201T（ORF8:S103L）（3866seqs） Feb 4, 2024
@Memorablea
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@corneliusroemer @FedeGueli @AngieHinrichs

@Memorablea
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4063

@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（3866seqs） JN.1.4+C28201T（ORF8:S103L）（4063seqs） Feb 6, 2024
@Mydtlwn
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Mydtlwn commented Feb 7, 2024

This one may need to be designated quickly, plus there are some sub-branches of this branch that are also very interesting. @corneliusroemer

@Memorablea
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@corneliusroemer

@Memorablea
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5067

@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（4063seqs） JN.1.4+C28201T（ORF8:S103L）（5067seqs） Feb 22, 2024
@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（5067seqs） JN.1.4+C28201T（ORF8:S103L）（5678seqs） Mar 2, 2024
@Memorablea
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5678

@Memorablea
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Currently 6598 seqs, due to excessive total number, it may not be specified, so the update will be stopped @FedeGueli

@FedeGueli
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Currently 6598 seqs, due to excessive total number, it may not be specified, so the update will be stopped @FedeGueli

thank you @Memorablea for tracking this, not sure if @corneliusroemer wants to designate it

FedeGueli referenced this issue Mar 14, 2024
@corneliusroemer
Designate JN.1.4.5 (ORF8:S103L)
72ac258
@FedeGueli
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Designated JN.1.4.5 via 72ac258

@Memorablea
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THX

@Memorablea
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There's a 68-sequence lineage with the classic 3-nucleotide ORF1b TRS mutation in this branch that is either entirely confined or almost entirely confined to Israel. First sequences was November 29, and 54/68 have collection dates of Dec 10 or later. 28/68 were collected on or after Dec 15. image

GISAID Nucleotide Query: C774T, C21302T, C21304A, T27810C, -C1762A, -A13278G, -C28528T Usher Tree: https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1__C21302T_C21304A_G21305A_C28201T.json?c=gt-nuc_21302&gmax=22302&gmin=20302&label=id:node_6810451 image

Genomes

Genomes
EPI_ISL_18616083, EPI_ISL_18616126, EPI_ISL_18673123, EPI_ISL_18673128, EPI_ISL_18673134, EPI_ISL_18673138, EPI_ISL_18673142, EPI_ISL_18673146, EPI_ISL_18673148, EPI_ISL_18673151, EPI_ISL_18673153-18673155, EPI_ISL_18673160, EPI_ISL_18673165, EPI_ISL_18673167, EPI_ISL_18673172, EPI_ISL_18673175-18673176, EPI_ISL_18673182, EPI_ISL_18673186, EPI_ISL_18673200, EPI_ISL_18673204, EPI_ISL_18683452, EPI_ISL_18683454, EPI_ISL_18683474, EPI_ISL_18683480, EPI_ISL_18683482, EPI_ISL_18683491, EPI_ISL_18683493, EPI_ISL_18683496-18683497, EPI_ISL_18683520, EPI_ISL_18683524, EPI_ISL_18683526, EPI_ISL_18683538, EPI_ISL_18683542, EPI_ISL_18683546-18683548, EPI_ISL_18683571-18683572, EPI_ISL_18683574-18683575, EPI_ISL_18683577-18683578, EPI_ISL_18683584, EPI_ISL_18683595, EPI_ISL_18700196, EPI_ISL_18700203, EPI_ISL_18700218-18700220, EPI_ISL_18700228, EPI_ISL_18700231, EPI_ISL_18700233, EPI_ISL_18700239-18700240, EPI_ISL_18700242, EPI_ISL_18700251-18700252, EPI_ISL_18700257, EPI_ISL_18700261, EPI_ISL_18700267-18700268, EPI_ISL_18700270, EPI_ISL_18700272, EPI_ISL_18701887,

316 seqs now,suggest proposing it! @ryhisner

@Memorablea Memorablea changed the title JN.1.4+C28201T（ORF8:S103L）（5678seqs） JN.1.4+C28201T（ORF8:S103L）（5678seqs）【JN.1.4.5】 Mar 16, 2024
@Memorablea Memorablea mentioned this issue Mar 16, 2024
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@ryhisner @Mydtlwn @FedeGueli @Memorablea