GK.1.10: two branches with S:A475V (65 and 28 samples)

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GK.1+A1982G(Orf1a:I573V)+T8167C+C12651T, C28087T, C28567T(Orf1a:T4129I,Orf8:A65V, Orf9b:T95M)

GISAID query: C12651T, C28087T, C28567T
No. of seqs: 43(Brazil 27 USA 16)

First:EPI_ISL_18125506, Brazil, 2023-6-28
Latest: EPI_ISL_18237072, USA, 2023-8-30

Orf9b:T95M was in BA.5.1.33, and also appears in a large undesignated Brazilian BA.5 cov-lineages/pango-designation#1041

usher

Credit to @oobb45729 for these two subbranches with S:A475V:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5ac30_32e880.json?c=gt-S_475&gmax=25384&gmin=21563&label=id:node_3675253

Branch 1:
#814 > S:A475V (C22986T) Proposed in cov-lineages/pango-designation#2479
Query: C12651T, C28567T,C22986T,-T7049C
Samples: EPI_ISL_18415625, EPI_ISL_18453864, EPI_ISL_18464176,
EPI_ISL_18489082, EPI_ISL_18498414

Branch 2:
#814 > ORF1a:Y2262H (T7049C) >C1645T, C29272T > ORF1b:T2432I (C20762T), S:A475V (C22986T), ORF7a:L17F (C27442T)
Query: C20762T, C22986T,C1645T (new ) C20762T, C22986T, C27442T (former) EDITED
Samples: 7
EPI_ISL_18416001, EPI_ISL_18417773, EPI_ISL_18449316,
EPI_ISL_18464666, EPI_ISL_18471130, EPI_ISL_18494298-18494299,
Tree: (NEW)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_62cd1_309b40.json?label=id:node_3736558

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52, France, Ireland

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60, Israel

[FedeGueli]

67

[FedeGueli]

Apparently slow or due the fact it emerged in Brazil that is not uploading fast.

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69, Sweden

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71, Australia

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85, Denmark, Netherlands

[FedeGueli]

This seems to have some sort of prevalence in Rio de Janeiro. ping @corneliusroemer it cannot compete but a 3% in the area where it emerged.

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105, Belgium, Peru

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110, Austria, Canada, UK

[FedeGueli]

this is now a 2% of Brazilian recent samples

[FedeGueli]

C20762T, C22986T, C27442T

Brnach 2 is still 8 and seems slowed. i ve reopened it to track for a while more. only two sequences from November tough.

[oobb45729]

C20762T, C22986T, C27442T

Brnach 2 is still 8 and seems slowed. i ve reopened it to track for a while more. only two sequences from November tough.

Many new sequences from Branch 2 don't have C27442T.

[FedeGueli]

C20762T, C22986T, C27442T

Brnach 2 is still 8 and seems slowed. i ve reopened it to track for a while more. only two sequences from November tough.

Many new sequences from Branch 2 don't have C27442T.

thanks later i will re look at it for a new query thx!

[FedeGueli]

New query for Branch 2 : C20762T, C22986T,C1645T finds 16

[FedeGueli]

query and tree and count updated in the proposal

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Branch 1 becomes 44,

12/24=50% in Amazona, Brazil's 1/17 batch.

In 11/29 batch it was 7/47=15%

[FedeGueli]

Branch 1 it is also 50% in December samples from Amazonas while it was 6/27 from October 1 to November 30

[FedeGueli]

65 for branch 1 28 for Branch 2 .
Branch 1 seems quite good in Para too.

[ryhisner]

Is the S:N450D part of the S:Y200C branch known? 18 were uploaded from Brazil today. They all also have S:L5F, which seems specific to this branch and is still masked by Usher. One branch of it (which includes 10/18 sequences uploaded today) has N:L13I/ORF9b:H9Q.

[FedeGueli]

Is the S:N450D part of the S:Y200C branch known? 18 were uploaded from Brazil today. They all also have S:L5F, which seems specific to this branch and is still masked by Usher. One branch of it (which includes 10/18 sequences uploaded today) has N:L13I/ORF9b:H9Q.

thank you! i missed that personally . cc @corneliusroemer this should be designated and subdesignated. @aviczhl2 please propose it with the sublineages spotted by Ryan! Thank you

[FedeGueli]

Query for the S:Y200C branch : C12651T, C29668T,A22161G finds 40
Query for the Y200C S:N450D branch: C12651T, C5526T,A22910G finds 19
This last branch has also Orf1a:T1574I that corresponds to NSP3_T936I = PLPro_T191I

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thank you! i missed that personally . cc @corneliusroemer this should be designated and subdesignated. @aviczhl2 please propose it with the sublineages spotted by Ryan! Thank you

Yeah I find it too. Stepwise GK.1.10->475V->200C->450D

[FedeGueli]

branch 1 is GK.1.10.1 now via cov-lineages/pango-designation@f39ed9e

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Branch 2 is not fast, close down.

[FedeGueli]

subbranches of GK.1.10.1 got designated KN.1 and KN.1.1 via cov-lineages/pango-designation@2fcf851