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XBB.2.3.15 [ORF1a:I4308V (nsp10_I55V)] with ORF1a:M3669I (nsp6_M100I) and S:T323I (62 seqs, 4 countries) #722

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NkRMnZr opened this issue Aug 30, 2023 · 8 comments
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XBB.2.3.15 [ORF1a:I4308V (nsp10_I55V)] with ORF1a:M3669I (nsp6_M100I) and S:T323I (62 seqs, 4 countries) #722

NkRMnZr opened this issue Aug 30, 2023 · 8 comments
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S:323 S:521 To be proposed Green light for proposal
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XBB.2.3.15 JS.2

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@NkRMnZr
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NkRMnZr commented Aug 30, 2023 •
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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: 2023-08-16 (EPI_ISL_18162845, New Jersey, USA)
Sampled Countries: USA (25: CA/14; TX/4; NJ/3; AZ/2; NV/1; NY/1), Guatemala (4), Canada (3: ON/2; AB/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

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1303f_f8f520.json?label=id:node_7380459

view from ORF1a:I4308V branch, neighbouring to #607 and recombinant #711
poly

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@NkRMnZr NkRMnZr mentioned this issue Aug 30, 2023
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@FedeGueli FedeGueli added New mutations Lineage with an unusual/new/interesting mutation Rapid review needed labels Aug 31, 2023
@FedeGueli
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It seems quite fast lets see

@NkRMnZr
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NkRMnZr commented Sep 2, 2023 •
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Tracking updates

09-02, 5 seqs from USA EPI_ISL_18163822-18163823, EPI_ISL_18164188, EPI_ISL_18164415, EPI_ISL_18212770
09-08, 8 seqs from Canada, Singapore and USA
09-15, 17 seqs from USA

@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (32 seqs, Canada, Guatemala and USA) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (37 seqs, Canada, Guatemala and USA) Sep 2, 2023
@FedeGueli FedeGueli added the S:521 label Sep 2, 2023
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tracker: https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=G11272T%2CA13187G%2CC22530T&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli added S:323 and removed New mutations Lineage with an unusual/new/interesting mutation labels Sep 2, 2023
@NkRMnZr NkRMnZr mentioned this issue Sep 3, 2023
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@NkRMnZr
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NkRMnZr commented Sep 9, 2023

09-08, 8 seqs from Canada, Singapore and USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2edfb_c52200.json?f_userOrOld=uploaded%20sample&label=id:node_7410195
image

EPI_ISL_18222404, EPI_ISL_18222708, EPI_ISL_18223158, EPI_ISL_18224516, EPI_ISL_18229868, EPI_ISL_18232976, EPI_ISL_18233198, EPI_ISL_18234987

@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (37 seqs, Canada, Guatemala and USA) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (45 seqs, 4 countries) Sep 9, 2023
@NkRMnZr
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NkRMnZr commented Sep 15, 2023

09-15, 17 seqs from USA

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_32554_43eec0.json?f_userOrOld=uploaded%20sample&label=id:node_7439035
image

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

@NkRMnZr NkRMnZr changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (45 seqs, 4 countries) XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (62 seqs, 4 countries) Sep 15, 2023
@FedeGueli
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Please propose it

@FedeGueli FedeGueli added To be proposed Green light for proposal and removed Rapid review needed labels Sep 15, 2023
@NkRMnZr NkRMnZr mentioned this issue Sep 18, 2023
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@NkRMnZr
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NkRMnZr commented Sep 18, 2023

Transferred to cov-lineages/pango-designation#2291

@NkRMnZr NkRMnZr closed this as completed Sep 18, 2023
@FedeGueli
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Parental lineage described by you here Designated XBB.2.3.15 via cov-lineages/pango-designation@2fe3c52

@FedeGueli FedeGueli added this to the XBB.2.3.15 milestone Oct 13, 2023
@FedeGueli FedeGueli changed the title XBB.2.3 with ORF1a:I4308V (nsp10_I55V), ORF1a:M3669I (nsp6_M100I) and S:T323I (62 seqs, 4 countries) XBB.2.3.15 [ORF1a:I4308V (nsp10_I55V)] with ORF1a:M3669I (nsp6_M100I) and S:T323I (62 seqs, 4 countries) Oct 13, 2023
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