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XBB.1.5.110+S:T573I (92 seqs, mainly in USA, 4 countries) #621

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NkRMnZr opened this issue Aug 16, 2023 · 4 comments
Closed

XBB.1.5.110+S:T573I (92 seqs, mainly in USA, 4 countries) #621

NkRMnZr opened this issue Aug 16, 2023 · 4 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 S:573

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@NkRMnZr
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NkRMnZr commented Aug 16, 2023

Defining Mutations: XBB.1.5 [pre-T17124C] > C12651T(ORF1a:T4129I) > A5116G > C23280T(**S:T573I**)
Query: A5116G, C12651T, C23280T
Earliest seq: 2023-03-28 (EPI_ISL_17412081, California, USA)
Latest seq: 2023-07-28 (EPI_ISL_18078835, Arizona, USA)
Sampled Countries: USA (56: California/49; Arizona/4; Colorado/1; New Mexico/1; Nevada/1), Spain (2, Canary Islands), Japan (1)

Genomes:

EPI_ISL_17412081, EPI_ISL_17486904, EPI_ISL_17582593, EPI_ISL_17694105, EPI_ISL_17767930, EPI_ISL_17783184-17783185, EPI_ISL_17783441, EPI_ISL_17791528, EPI_ISL_17815322, EPI_ISL_17854153, EPI_ISL_17856443, EPI_ISL_17856775, EPI_ISL_17887178, EPI_ISL_17951107, EPI_ISL_17965297-17965300, EPI_ISL_17965688, EPI_ISL_17976661, EPI_ISL_17977777, EPI_ISL_17981054, EPI_ISL_17986245, EPI_ISL_17997618, EPI_ISL_17997626, EPI_ISL_17997628, EPI_ISL_17997634, EPI_ISL_17997641, EPI_ISL_17997981, EPI_ISL_17997983, EPI_ISL_17997985, EPI_ISL_17997988, EPI_ISL_17997991, EPI_ISL_18043211, EPI_ISL_18045413, EPI_ISL_18046102, EPI_ISL_18046135, EPI_ISL_18050227-18050228, EPI_ISL_18050241, EPI_ISL_18078835, EPI_ISL_18079296, EPI_ISL_18079450, EPI_ISL_18079462, EPI_ISL_18079480, EPI_ISL_18079543, EPI_ISL_18079590, EPI_ISL_18079809, EPI_ISL_18079892, EPI_ISL_18080010, EPI_ISL_18080631, EPI_ISL_18080758, EPI_ISL_18081422, EPI_ISL_18093562, EPI_ISL_18105265-18105267, EPI_ISL_18106318

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41f46_c9a1c0.json?f_userOrOld=uploaded%20sample&label=id:node_6874732

  • view from ORF1a:T4129I branch
    poly

  • details
    details

Trivia:

  • At the moment, all XBB.1.5 pre-T17124C has been misplaced under XBB.1.22 > C28297T_reversion (ORF9b:T5I_reversion)
@NkRMnZr NkRMnZr mentioned this issue Aug 16, 2023
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@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Aug 16, 2023
@FedeGueli
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Interesting but it will have hard life from now ahead: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A5116G%2CC12651T%2CC23280T&analysisMode=CompareToBaseline&

@FedeGueli FedeGueli added the Convergent evolution Lineages with convergent mutations label Aug 16, 2023
@NkRMnZr
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NkRMnZr commented Aug 19, 2023 •
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Tracking updates:

08-18, 3 seqs from USA (CA): EPI_ISL_18107488, EPI_ISL_18110822, EPI_ISL_18113902
08-26, 3 seqs from USA (CA, AZ)

@NkRMnZr NkRMnZr changed the title XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (59 seqs, mainly in USA, 3 countries) XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (62 seqs, mainly in USA, 3 countries) Aug 19, 2023
@NkRMnZr
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NkRMnZr commented Aug 26, 2023

08-26, 3 seqs from California and Arizona: EPI_ISL_18120362, EPI_ISL_18120627, EPI_ISL_18120739

@NkRMnZr NkRMnZr changed the title XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (62 seqs, mainly in USA, 3 countries) XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (65 seqs, mainly in USA, 3 countries) Aug 26, 2023
@FedeGueli
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https://cov-spectrum.org/explore/United%20States/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=A5116G%2CC12651T%2CC23280T&analysisMode=CompareToBaseline&

closing this for now.

@NkRMnZr NkRMnZr changed the title XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (65 seqs, mainly in USA, 3 countries) XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (92 seqs, mainly in USA, 4 countries) Oct 1, 2023
@xz-keg xz-keg changed the title XBB.1.5 (pre-T17124C) with ORF1a:T4129I and S:T573I (92 seqs, mainly in USA, 4 countries) XBB.1.5.110 and S:T573I (92 seqs, mainly in USA, 4 countries) Dec 17, 2023
@xz-keg xz-keg changed the title XBB.1.5.110 and S:T573I (92 seqs, mainly in USA, 4 countries) XBB.1.5.110+S:T573I (92 seqs, mainly in USA, 4 countries) Dec 17, 2023
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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 S:573
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