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XBC.1.6 with S:V445A (39 seqs- South Australia) #203

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FedeGueli opened this issue Jun 16, 2023 · 10 comments
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XBC.1.6 with S:V445A (39 seqs- South Australia) #203

FedeGueli opened this issue Jun 16, 2023 · 10 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Convergent evolution Lineages with convergent mutations designated S:445
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JT.1

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@FedeGueli
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FedeGueli commented Jun 16, 2023 •
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I spotted a little interesting recent cluster of XBC.1.6 carrying additional mutation at S:445 , this time to A.

Defining mutations: XBC.1.6 >>T8707C, C26735T > C10156T > C29762T > S:V445A (T22896C)

Tree:
Schermata 2023-06-16 alle 11 48 33
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_15f98_c04500.json?label=id:node_6127573

Gisaid query : T8707C,T22896C,C10156T (edited)
Samples 6

EPI_ISL_17703905, EPI_ISL_17793665, EPI_ISL_17793682,
EPI_ISL_17793695, EPI_ISL_17793826, EPI_ISL_17793913,
@FedeGueli FedeGueli added Convergent evolution Lineages with convergent mutations S:445 labels Jun 16, 2023
@HynnSpylor
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6 more seqs updated today (also from SA, Australia)

@FedeGueli FedeGueli changed the title XBC.1.6 with S:V445A (6seqs) XBC.1.6 with S:V445A (12 seqs- South Australia) Jun 27, 2023
@HynnSpylor HynnSpylor mentioned this issue Jul 3, 2023
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@FedeGueli
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It seems slow.

@FedeGueli
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no new seq in the last batch from Australia. lets wait a week more.

@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Jul 10, 2023
@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Jul 13, 2023
@HynnSpylor
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9 seqs updated and we can track it again.

@FedeGueli FedeGueli reopened this Jul 19, 2023
@FedeGueli FedeGueli changed the title XBC.1.6 with S:V445A (12 seqs- South Australia) XBC.1.6 with S:V445A (21 seqs- South Australia) Jul 19, 2023
@FedeGueli
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Closing this for now

@NkRMnZr
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NkRMnZr commented Aug 17, 2023

seems split in two sub-branches now
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f6a8_e609a0.json?c=gt-S_445&label=id:node_6399877
image

@FedeGueli FedeGueli changed the title XBC.1.6 with S:V445A (21 seqs- South Australia) XBC.1.6 with S:V445A (26 seqs- South Australia) Aug 17, 2023
@FedeGueli
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seems split in two sub-branches now https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f6a8_e609a0.json?c=gt-S_445&label=id:node_6399877 image

I bet they are the same.

@FedeGueli
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New query finds 39 : T8707C,T22896C,C10156T

@FedeGueli FedeGueli reopened this Aug 17, 2023
@FedeGueli FedeGueli changed the title XBC.1.6 with S:V445A (26 seqs- South Australia) XBC.1.6 with S:V445A (39 seqs- South Australia) Aug 17, 2023
@FedeGueli
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I am going to propose this one in the main page.

@FedeGueli FedeGueli mentioned this issue Aug 17, 2023
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@FedeGueli FedeGueli added this to the JT.1 milestone Oct 14, 2023
@FedeGueli
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JT.1 via cov-lineages/pango-designation@0f50930

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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Convergent evolution Lineages with convergent mutations designated S:445
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@FedeGueli @HynnSpylor @NkRMnZr