cov-lineages / pango-designation

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

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JN.1.4+Orf1a:T4087I,Orf1b:S1512N+S:F456L(259 seqs, 18 countries, 12 with S:T572I) #2517

Open aviczhl2 opened 3 months ago

aviczhl2 commented 3 months ago

From branch 7 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

JN.1.4+Orf1a:T4087I(C12525T)+Orf1b:S1512N(G18002A)+S:F456L (T22928C)

GISAID Query: T18453C, C12525T,T22928C No. of seqs: 53(Australia 2 USA 18 Canada 33)

First: EPI_ISL_18681708,USA,2023-12-12 Latest: EPI_ISL_18967410, Australia, 2024-3-3

usher

aviczhl2 commented 3 months ago

58, New Zealand via GBW

FedeGueli commented 3 months ago

this seems quite fast ping @corneliusroemer

aviczhl2 commented 3 months ago

64, Japan, Taiwan via unknown, GBW via Vietnam, GBW via Taiwan

FedeGueli commented 3 months ago

It seems fast.

aviczhl2 commented 3 months ago

+49 Canada, 121 now @corneliusroemer

aviczhl2 commented 3 months ago

49/241=20% in Ontario 2024-4-2 batch

Mydtlwn commented 3 months ago

@corneliusroemer

aviczhl2 commented 2 months ago

126, South Korea

FedeGueli commented 2 months ago

@corneliusroemer this should be designated:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_6a95_a9caf0.json?label=id:node_7049073

Its growth advantage likely unreliable due to canadian clusters but still quite big in the last weeks

aviczhl2 commented 2 months ago

159, Spain, France

FedeGueli commented 2 months ago

this should be designated @corneliusroemer

aviczhl2 commented 2 months ago

164, China, Ukraine

aviczhl2 commented 1 month ago

199, Thailand, Qatar

DailyCovidCases commented 1 month ago

https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=T18453C%2CC12525T%2CT22928C&nextcladePangoLineage=JN.1.4*&

aviczhl2 commented 1 month ago

227, Israel,

aviczhl2 commented 1 month ago

@corneliusroemer This branch also exceeds 200,

aviczhl2 commented 3 weeks ago

238,Singapore

FedeGueli commented 1 week ago

253 with an interesting combo branch with S:T572I:

2517>> ORF1a:T2124I (C6636T) >Orf1a:Q1759L (A5541T =PLPro_Q196L)> Orf1a:V4266I(G13061A), ORF1b:A1443V (C17795T), S:T572I (C23277T)

Query: A5541T ,G13061A,C17795T Samples: 10 ( 2 GBW from Portugal and Thailand) Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_205a6_3f5100.json?c=userOrOld&label=id:node_12205827

DailyCovidCases commented 6 days ago

254 seqs now, this should be designated @corneliusroemer

aviczhl2 commented 1 day ago

259,Cambodia, Netherlands