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XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (102 seqs, mainly in USA, 5 countries) #2291

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NkRMnZr opened this issue Sep 18, 2023 · 2 comments
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XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (102 seqs, mainly in USA, 5 countries) #2291

NkRMnZr opened this issue Sep 18, 2023 · 2 comments

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@NkRMnZr
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NkRMnZr commented Sep 18, 2023

Transferred from sars-cov-2-variants/lineage-proposals#722

Defining Mutations: XBB.2.3 > A13187G(ORF1a:I4308V) > G11272T(ORF1a:M3669I), C22530T(S:T323I)
Query: G11272T, A13187G, C22530T
Earliest seq: 2023-06-20 (EPI_ISL_17952263, Arizona, USA)
Latest seq: 2023-09-06 (EPI_ISL_18264320, Texas, USA)
Sampled Countries: USA (66: CA/36; TX/16; NJ/3; AZ/2; NV/2; NY/2; VA/2; MD/1; NC/1; OH/1), Canada (4: ON/3; AB/1), Guatemala (4), Singapore (1)

Genomes:

EPI_ISL_17952263, EPI_ISL_18038125, EPI_ISL_18045676, EPI_ISL_18045918, EPI_ISL_18062539, EPI_ISL_18069595, EPI_ISL_18072544, EPI_ISL_18072550, EPI_ISL_18080828, EPI_ISL_18081484, EPI_ISL_18098781, EPI_ISL_18098973, EPI_ISL_18099421, EPI_ISL_18104565, EPI_ISL_18105243, EPI_ISL_18119806, EPI_ISL_18119822, EPI_ISL_18122247, EPI_ISL_18124435, EPI_ISL_18124514, EPI_ISL_18126244, EPI_ISL_18144756, EPI_ISL_18144841, EPI_ISL_18144861, EPI_ISL_18144878, EPI_ISL_18145021, EPI_ISL_18162749-18162750, EPI_ISL_18162845, EPI_ISL_18163531, EPI_ISL_18163551-18163552, EPI_ISL_18163822-18163823, EPI_ISL_18164188, EPI_ISL_18164415, EPI_ISL_18212770, EPI_ISL_18222404, EPI_ISL_18222708, EPI_ISL_18223158, EPI_ISL_18224516, EPI_ISL_18229868, EPI_ISL_18232976, EPI_ISL_18233198, EPI_ISL_18234987, EPI_ISL_18246609, EPI_ISL_18251782, EPI_ISL_18251799, EPI_ISL_18252612, EPI_ISL_18252685, EPI_ISL_18253599, EPI_ISL_18253639, EPI_ISL_18256110, EPI_ISL_18256196, EPI_ISL_18257353, EPI_ISL_18257454, EPI_ISL_18257467, EPI_ISL_18257481, EPI_ISL_18260471, EPI_ISL_18260794, EPI_ISL_18261335, EPI_ISL_18261390, EPI_ISL_18264164, EPI_ISL_18264244, EPI_ISL_18264290, EPI_ISL_18264320, EPI_ISL_18264387, EPI_ISL_18264500, EPI_ISL_18265779, EPI_ISL_18265828, EPI_ISL_18267296, EPI_ISL_18270432, EPI_ISL_18270702, EPI_ISL_18270903, EPI_ISL_18271244

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ac71_84b310.json?f_userOrOld=uploaded%20sample&label=id:node_7445541

view from ORF1a:I4308V branch, neighbouring to sars-cov-2-variants/lineage-proposals#607 and recombinant sars-cov-2-variants/lineage-proposals#711
poly

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@NkRMnZr NkRMnZr mentioned this issue Sep 18, 2023
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NkRMnZr commented Sep 23, 2023 •
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Tracking updates

09-23, 5 seqs from USA EPI_ISL_18276317, EPI_ISL_18276342, EPI_ISL_18284370, EPI_ISL_18291643, EPI_ISL_18298877

09-29, 13 seqs from USA

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_13be8_693940.json?f_userOrOld=uploaded%20sample&label=id:node_7350523
image

EPI_ISL_18309112, EPI_ISL_18309877, EPI_ISL_18311924, EPI_ISL_18316134, EPI_ISL_18316518, EPI_ISL_18317368, EPI_ISL_18317373, EPI_ISL_18317821, EPI_ISL_18318217, EPI_ISL_18318929, EPI_ISL_18319240, EPI_ISL_18319473

10-08, 10 seqs from USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8191_2ca7a0.json?f_userOrOld=uploaded%20sample&label=id:node_3903662
image

EPI_ISL_18327966, EPI_ISL_18327988, EPI_ISL_18328057, EPI_ISL_18328239, EPI_ISL_18328847, EPI_ISL_18339478, EPI_ISL_18339530, EPI_ISL_18340520, EPI_ISL_18341795, EPI_ISL_18347401

@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (75 seqs, mainly in USA, 5 countries) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (80 seqs, mainly in USA, 5 countries) Sep 23, 2023
@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (80 seqs, mainly in USA, 5 countries) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (92 seqs, mainly in USA, 5 countries) Sep 29, 2023
@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (92 seqs, mainly in USA, 5 countries) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (102 seqs, mainly in USA, 5 countries) Oct 8, 2023
Over-There-Is referenced this issue Oct 13, 2023
@corneliusroemer
Desingate JS.2 (S:T323I) with 100 seqs
e5fbf04
FedeGueli referenced this issue Oct 13, 2023
@corneliusroemer
Designate XBB.2.3.15 (ORF1a:I4308V)
2fe3c52
@NkRMnZr
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NkRMnZr commented Oct 13, 2023

Designated as JS.2 via e5fbf04

@NkRMnZr NkRMnZr closed this as completed Oct 13, 2023
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