EG.5.1.2 with S:T76A (103 seqs from #512) with further S:M153I (17 seqs)

[FedeGueli]

Edited proposal by @aviczhl2 : focusing on branch 2

EG.5.1.2+T9127C,A21788G(S:T76A),A27330C

GISAID query: G18397A,A21788G, T22930A (Edited) Query for S:M153I branch: G18397A,A21788G, G22021T

No. of seqs: 4( Iceland 2 Sweden 1 UK 1)

First: EPI_ISL_17952040, 2023-6-13,UK Latest: EPI_ISL_17990591, 2023-7-13, Sweden

usher

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Here i want to sum the work of different variant spotters and of the ones tracking variants.

EG.5.1.2 has already 4 clear branches defined by spike mutations: as you could see from the Usher tree; https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f002_b7bc40.json?label=id:node_6753974

So i am proposing to designate them all starting from the bigger one:

Branch 1 S:R158G proposed by @krosa1910 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/301 EG.5.1.2 > T20631C > S:R158G (A22034G) Query: G18397A, G21718T, A22034G (edited by @NkRMnZr)
Samples : 54 Countries : Japan, Texas

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Branch 2 S:T883I proposed by @aviczhl2 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/511 EG.5.1.2 > Orf6:E54D (A27363C), S:T883I (C24210T) Query: A27363C,C24210T Samples: 9 Countries : Japan

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Branch 3 S:T76A proposed by @aviczhl2 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/512 EG.5.1.2 > S:T76A (A21788G) Query: G18397A,A21788G, T22930A, Samples : 5 Countries: Iceland, Portugal , Sweden, Uk

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Branch 4 S:V687L EG.5.1.2 >T1252C, C3787T > G4255A, S:V687L (G23621T) Query: T1252C, C3787T ,G4255A Samples : 6 Note that half of sequences of this lineage got also S:G485S FCS Flanking sequence with this mutation should be SYQTQTKSHRRARSLASQSIIA

[FedeGueli]

Tracking: EG.5.1.2+S:R158G +6 EG.5.1.2+S:T883I - EG.5.1.2+S:V76A +1 EG.5.1.2+S:V687L +5

Apparently branch 4 is doubling very fastly. lets keep it checked.

[FedeGueli]

Branch 1 and 4 growing but not suoer fastly considering they are EG.5.1

[FedeGueli]

Branch one is quite big and at least in Japan it is significant. branch 2-3 not showing any growth. branch 4 interesting but likely not fast enough.

so @corneliusroemer i suggest deignation og EG.5.1.2 +S: R158G then we can track back the others in the secondary repo.

[FedeGueli]

These ones still circualating but look at the biggest: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=T1252C%2CC3787T%2CG4255A&analysisMode=CompareToBaseline& no chance to compete with HK.3

[FedeGueli]

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_aef5_637770.json?c=gt-S_6&gmax=25384&gmin=21563&label=id:node_6961220

Updated tree;

the Branch 4 with S;V687L got also S:T470I.

[FedeGueli]

While branch 4 showed some fitness recent samples are rare except for Branch 3 . i will close this one and reopen in the other repo Branch 3 issue

[FedeGueli]

103/17

[FedeGueli]

2 only samples from December closing it.