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XBB.2.3.11 with S:T470N (15 seqs, Singapore, Brunei) #93

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NkRMnZr opened this issue May 23, 2023 · 8 comments
Closed

XBB.2.3.11 with S:T470N (15 seqs, Singapore, Brunei) #93

NkRMnZr opened this issue May 23, 2023 · 8 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated New mutations Lineage with an unusual/new/interesting mutation
Milestone
GS.2

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@NkRMnZr
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NkRMnZr commented May 23, 2023 •
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Defining mutations: (On top of XBB.2.3.11's defining C22995G/S:T478R) > T16389C > C22971A(S:T470N)

Query: C4234T, G6536A, C22971A, -G22113T

Earliest seq: 2023-04-24 (EPI_ISL_17631534, Singapore)
Latest seq: 2023-05-12 (EPI_ISL_17694915, Singapore)

Genomes: EPI_ISL_17631534, EPI_ISL_17670285, EPI_ISL_17694915, EPI_ISL_17694916

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c66d_ca5bd0.json?c=gt-S_470&f_userOrOld=uploaded%20sample&label=id:node_7166365&showBranchLabels=all
downsampled
XBB 2 3 11+S_T470N
detailed
XBB 2 3 11+S_T470N_Detailed

Trivia:

  • S:T470N is somewhat less popular but convergent, popped up on BN.1.2.1, XBB.4.1 before.
  • There's a sequence (EPI_ISL_17631534) acuires a premature stop codon C27972T(ORF8:Q27*) to get ORF8 truncated, we have seen G27915T(ORF8:G8*) success on XBB.1*, wondering what may be happening on XBB.2*, despite it is a pretty new yet small cluster, it may be interesting to watch.
@FedeGueli FedeGueli added the Convergent evolution Lineages with convergent mutations label May 23, 2023
@FedeGueli
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Thx i ve spotted in the last week upload!
Schermata 2023-05-23 alle 23 29 51
Thx for getting it proposed.
S:T470N was a key residue in Sars 1 RBD too.

@ryhisner finally XBB.2.3 got Orf8 truncated too (singlet)

@FedeGueli FedeGueli added New mutations Lineage with an unusual/new/interesting mutation Mutations outside spike Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Convergent evolution Lineages with convergent mutations Mutations outside spike labels May 23, 2023
@FedeGueli
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Closing this one for now

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jun 4, 2023
@NkRMnZr
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NkRMnZr commented Jun 21, 2023

Tracking updates:

3 additional seqs (23-06-21) 3 seqs from Brunei: EPI_ISL_17811902, EPI_ISL_17811903, EPI_ISL_17811909

@NkRMnZr NkRMnZr changed the title XBB.2.3.11 with S:T470N (4 seqs, Singapore) XBB.2.3.11 with S:T470N (7 seqs, Singapore, Brunei) Jun 21, 2023
@FedeGueli FedeGueli reopened this Jun 24, 2023
@FedeGueli
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ok lets monitor it for a longer period

@NkRMnZr
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NkRMnZr commented Jul 2, 2023

Too slow.

@NkRMnZr NkRMnZr closed this as not planned Won't fix, can't repro, duplicate, stale Jul 2, 2023
@FedeGueli FedeGueli changed the title XBB.2.3.11 with S:T470N (7 seqs, Singapore, Brunei) XBB.2.3.11 with S:T470N (9 seqs, Singapore, Brunei) Jul 5, 2023
@FedeGueli
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FedeGueli commented Jul 5, 2023 •
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3 more seqs from Singapore uploaded yesterday worth monitoring for a couple of weeks more. (one for some reason is not caught by the query.

@FedeGueli FedeGueli changed the title XBB.2.3.11 with S:T470N (9 seqs, Singapore, Brunei) XBB.2.3.11 with S:T470N (10 seqs, Singapore, Brunei) Jul 5, 2023
@NkRMnZr
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NkRMnZr commented Jul 6, 2023

3 more seqs from Singapore uploaded yesterday worth monitoring for a couple of weeks more. (one for some reason is not caught by the query.

Guess I'll reopen it once it reaches 20 seqs.

@NkRMnZr NkRMnZr mentioned this issue Jul 13, 2023
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@NkRMnZr NkRMnZr changed the title XBB.2.3.11 with S:T470N (10 seqs, Singapore, Brunei) XBB.2.3.11 with S:T470N (15 seqs, Singapore, Brunei) Aug 11, 2023
@FedeGueli FedeGueli added this to the GS.2 milestone Aug 23, 2023
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Designated GS.2 from cov-lineages/pango-designation@b2febbe

FedeGueli referenced this issue in cov-lineages/pango-designation Aug 23, 2023
@corneliusroemer
Designate GS.2 (XBB.2.3.11.2, S:T470N, Singapore/Brunei) with 20 seqs
b2febbe
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. designated New mutations Lineage with an unusual/new/interesting mutation
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