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XBB.1.9.1 with N:P122S and S:T76I (41 seqs, mainly in Japan, 4 countries) #626

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NkRMnZr opened this issue Aug 16, 2023 · 2 comments
Closed

XBB.1.9.1 with N:P122S and S:T76I (41 seqs, mainly in Japan, 4 countries) #626

NkRMnZr opened this issue Aug 16, 2023 · 2 comments
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Convergent evolution Lineages with convergent mutations It can not compete It means it has growth disadvantage versus dominant lineages but worth tracking

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@NkRMnZr
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NkRMnZr commented Aug 16, 2023

Defining Mutations: XBB.1.9.1 > C28637T(N:P122S) > C11020T > T29131C > C21789T(S:T76I)
Query: C11020T, C21789T, C28637T
Earliest seq: 2023-06-01 (EPI_ISL_17952661, Hiroshima, Japan)
Latest seq: 2023-07-21 (EPI_ISL_18101037, Kagoshima, Japan)
Sampled Countries: Japan (24), USA (2, California, ex. Japan), China (1, Shanghai, ex. Japan)

Genomes:

EPI_ISL_17950309, EPI_ISL_17950372, EPI_ISL_17952661, EPI_ISL_17952663, EPI_ISL_17956852, EPI_ISL_17978057, EPI_ISL_17978796, EPI_ISL_17979662, EPI_ISL_17980747, EPI_ISL_17982136, EPI_ISL_17996455, EPI_ISL_18000614, EPI_ISL_18006556, EPI_ISL_18040754, EPI_ISL_18040801, EPI_ISL_18051328, EPI_ISL_18051992, EPI_ISL_18065192, EPI_ISL_18071779, EPI_ISL_18100464, EPI_ISL_18100890, EPI_ISL_18101002, EPI_ISL_18101037, EPI_ISL_18101050, EPI_ISL_18101139, EPI_ISL_18101159, EPI_ISL_18101166

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_36d69_cbf9e0.json?f_userOrOld=uploaded%20sample&label=id:node_6774421
details

Trivia:

  • S:T76I is the definition of BA.5.5 and HU.2 (XBB.1.22.2.2)
@NkRMnZr NkRMnZr mentioned this issue Aug 13, 2023
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@FedeGueli FedeGueli added the Convergent evolution Lineages with convergent mutations label Aug 16, 2023
@NkRMnZr
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NkRMnZr commented Sep 2, 2023

Tracking updates

09-02, 3 seqs from Finland and Japan

EPI_ISL_18146216, EPI_ISL_18164829, EPI_ISL_18166665

@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with N:P122S and S:T76I (27 seqs, Japan) XBB.1.9.1 with N:P122S and S:T76I (30 seqs, mainly in Japan, 3 countries) Sep 2, 2023
@FedeGueli
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It cant compete : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C11020T%2CC21789T%2CC28637T&analysisMode=CompareToBaseline&
i am closing it.

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 2, 2023
@FedeGueli FedeGueli added the It can not compete It means it has growth disadvantage versus dominant lineages but worth tracking label Sep 2, 2023
@NkRMnZr NkRMnZr changed the title XBB.1.9.1 with N:P122S and S:T76I (30 seqs, mainly in Japan, 3 countries) XBB.1.9.1 with N:P122S and S:T76I (41 seqs, mainly in Japan, 4 countries) Oct 1, 2023
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