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XBB.1.9.1 and UShER misplacement featuring S:T478R with a Georgian sublineage of ORF1b:A1377V/nsp13_A454V (113 seqs, 8 countries) #828

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NkRMnZr opened this issue Sep 17, 2023 · 2 comments
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XBB.1.9.1 and UShER misplacement featuring S:T478R with a Georgian sublineage of ORF1b:A1377V/nsp13_A454V (113 seqs, 8 countries) #828

NkRMnZr opened this issue Sep 17, 2023 · 2 comments
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designated help wanted Extra attention is needed S:478 Unclear tree Tree not much clear with reversions or flip/flop mutations
Milestone
FL.33.1

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@NkRMnZr
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NkRMnZr commented Sep 17, 2023 •
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Defining Mutations: XBB.1.9.1 > C22995G(S:T478R) > C17597T(ORF1b:A1377V)
Query: G5720A, C11956T, C17597T, C22995G, -C4345T
Earliest seq: 2023-04-03 (EPI_ISL_18042884, Greece)
Latest seq: 2023-09-05 (EPI_ISL_18263886, Georgia)
Sampled Countries: Georgia (102), Greece (4), France (2), Israel (2), China (1: SH), Slovenia (1), Sweden (1)

Genomes:

EPI_ISL_17850012, EPI_ISL_17876313, EPI_ISL_17876324, EPI_ISL_17876327, EPI_ISL_17876329, EPI_ISL_17885323, EPI_ISL_17885329, EPI_ISL_17885334, EPI_ISL_17885345-17885347, EPI_ISL_17885355, EPI_ISL_17885362, EPI_ISL_17885381, EPI_ISL_18042884, EPI_ISL_18072154, EPI_ISL_18072156, EPI_ISL_18072168, EPI_ISL_18072172, EPI_ISL_18072175, EPI_ISL_18072177, EPI_ISL_18072180-18072184, EPI_ISL_18072187-18072193, EPI_ISL_18072195, EPI_ISL_18096165, EPI_ISL_18096199, EPI_ISL_18096297, EPI_ISL_18161218, EPI_ISL_18208424, EPI_ISL_18215477, EPI_ISL_18246917, EPI_ISL_18249805, EPI_ISL_18258751, EPI_ISL_18263771-18263782, EPI_ISL_18263784-18263787, EPI_ISL_18263790-18263791, EPI_ISL_18263793-18263798, EPI_ISL_18263800-18263801, EPI_ISL_18263807, EPI_ISL_18263809, EPI_ISL_18263816-18263817, EPI_ISL_18263819, EPI_ISL_18263823, EPI_ISL_18263825, EPI_ISL_18263827-18263830, EPI_ISL_18263833, EPI_ISL_18263835-18263838, EPI_ISL_18263841-18263843, EPI_ISL_18263845, EPI_ISL_18263847-18263850, EPI_ISL_18263853-18263858, EPI_ISL_18263861-18263862, EPI_ISL_18263864-18263867, EPI_ISL_18263869-18263871, EPI_ISL_18263875-18263878, EPI_ISL_18263886

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ad68_6d8da0.json?f_userOrOld=uploaded%20sample&label=id:node_6931616
image

Trivia:

  • This branch seems to be split into 3 clusters of the tree, the major one is placed under XBB.1.9.1 > S:T478R, for some reason right now UShER places both XBB.1.9.1 and XBB.1.9.2 under C11956T (the latter via a T11956C_reversion), and the whole XBB.1.9.7 seems placed under XBB.1.9.1 > S:T478R as well, it could be served as a dump for all undesignated XBB.1.9* with S:T478R and S:F486P, the issue was ealier submitted at Issues in XBB.1.9* cluster yatisht/usher#350

  • Misplacement of XBB.1.9.7 under XBB.1.9.1 > S:T478R
    image

  • At that time that wasn't a big problem, but after a recent batch of Georgian samples, it represents the dominant lineage out there
    image

  • There seems to be a XBB.1.9.1 > C17597T(ORF1b:A1377V) branch too, there's a proportion of this lineage placed under it too, follows XBB.1.9.1 > C17597T(ORF1b:A1377V) > C21077T(ORF1b:T2537I) > C1929T(ORF1a:A555V), G8017T, C20178T, C29585T(ORF10:P10S) > C22995G(S:T478R), C27737T(ORF7a:T115I), where most Greek seqs are located.
    https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_ad68_6d8da0.json?c=gt-nuc_21077,22995&gmax=23995&gmin=20077&label=id:node_7056247
    image

  • The last proportion of this branch is located under an end-of-ORF1ab, probably-TRS-related series of mutations, that we have seen in many lineages, follows XBB.1.9.1 > G21305A(ORF1b:R2613H/nsp16_R216H) > C21304A(ORF1b:R2613N/nsp16_R216N) > C21302T(ORF1b:P2612L/nsp16_P215L) > C14649T, A17013T, C17597T(ORF1b:A1377V), C18086T(ORF1b:T1540I), C22995G(S:T478R), only small numbers so it probably won't matter.
@FedeGueli
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The fact is even harder to fix cause there is a big XBB.1.9.1 + orf1b:A1377V sublineage (C17597T) undesignated with 333 sequences :
Schermata 2023-09-18 alle 11 18 39
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2fc27_814fc0.json?c=gt-S_478&f_userOrOld=uploaded%20sample&label=id:node_7056025

and as highlighted in the tree a small part of it got 478R too.

cc @AngieHinrichs could you help here? ( it is the sam XBB.1.9.7 thing i highlighted you in another issue)

@FedeGueli FedeGueli added Unclear tree Tree not much clear with reversions or flip/flop mutations S:478 help wanted Extra attention is needed labels Sep 18, 2023
@AngieHinrichs
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I think I can get the A22995G > C17597T branch moved to C17597T, we'll find out in a couple days.

Over-There-Is referenced this issue in cov-lineages/pango-designation Sep 21, 2023
@corneliusroemer
Designate FL.33.1 (XBB.1.9.1.33.1, S:478R, Georgia) with 100 seqs
ab210f7 
Note for @AngieHinrichs: this lineage is not where it should be on the Usher tree
Need to prune/regraft - it gets pulled to EG due to 478R, but clearly it should be
within FL.33
@FedeGueli FedeGueli added this to the FL.33.1 milestone Sep 22, 2023
@NkRMnZr NkRMnZr closed this as completed Sep 24, 2023
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