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EG.2+S:Q675H(42 seqs, 7 countries) with a further sublineage with S:F490P (19 seqs, mainly Japan) #445

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xz-keg opened this issue Jul 20, 2023 · 5 comments
Closed

EG.2+S:Q675H(42 seqs, 7 countries) with a further sublineage with S:F490P (19 seqs, mainly Japan) #445

xz-keg opened this issue Jul 20, 2023 · 5 comments
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designated S:478 S:675
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EG.2.5

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@xz-keg
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xz-keg commented Jul 20, 2023 •
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EG.2+G4561A,G23587C(S:Q675H)

GISAID query: G4561A,G23587C,C22995G
No. of seqs:30( Indonesia 2 Japan 14 New Zealand 4 China 1 South Korea 4 (1 from USA) USA 3(1 from Japan))

First: EPI_ISL_17664308, Indonesia, 2023-4-17
Latest: EPI_ISL_17999344, Japan, 2023-6-27

Another S:Q675H lineage after S:478R.

usher

image

EDITED
Possible sublineage of interest with S:F490P
EG.2 >> S:Q675H > C24748T > A5725G >Orf1a:A2554V (C7926T), A10132T, T10135A >S:F490P (T23030C)
Gisaid query: T23030C,C7926T, T10135A
Samples: 14
tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_1de74_fdc20.json?c=userOrOld&label=id:node_6725008
Schermata 2023-07-26 alle 13 23 22
@xz-keg xz-keg changed the title EG.2+S:Q675H(30 seqs, 6 countries) EG.2+S:Q675H(31 seqs, 6 countries) Jul 22, 2023
@FedeGueli FedeGueli added Convergent evolution Lineages with convergent mutations S:613 labels Jul 22, 2023
@xz-keg
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xz-keg commented Jul 23, 2023

@FedeGueli It shouldn't have the S:613 label. You can create an S:675 label.

@FedeGueli FedeGueli added S:675 and removed S:613 labels Jul 23, 2023
@NkRMnZr NkRMnZr mentioned this issue Jul 23, 2023
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@xz-keg xz-keg changed the title EG.2+S:Q675H(31 seqs, 6 countries) EG.2+S:Q675H(32 seqs, 6 countries) Jul 24, 2023
@FedeGueli
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Interestingly a sub branch of it has S:F490P and seems spreading in japan:
Schermata 2023-07-26 alle 13 21 01
counting 13 samples.

@FedeGueli FedeGueli changed the title EG.2+S:Q675H(32 seqs, 6 countries) EG.2+S:Q675H(32 seqs, 6 countries) with a further sublineage with S:F490P (13 seqs, mainly Japan) Jul 26, 2023
@FedeGueli
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@ryhisner i found this very close double synonymous mutation in the sublineage with S:F490P : A10132T, T10135A could be of any relevance?

@xz-keg xz-keg changed the title EG.2+S:Q675H(32 seqs, 6 countries) with a further sublineage with S:F490P (13 seqs, mainly Japan) EG.2+S:Q675H(37 seqs, 6 countries) with a further sublineage with S:F490P (13 seqs, mainly Japan) Jul 29, 2023
@xz-keg xz-keg changed the title EG.2+S:Q675H(37 seqs, 6 countries) with a further sublineage with S:F490P (13 seqs, mainly Japan) EG.2+S:Q675H(38 seqs, 6 countries) with a further sublineage with S:F490P (14 seqs, mainly Japan) Aug 5, 2023
@xz-keg xz-keg changed the title EG.2+S:Q675H(38 seqs, 6 countries) with a further sublineage with S:F490P (14 seqs, mainly Japan) EG.2+S:Q675H(39 seqs, 6 countries) with a further sublineage with S:F490P (16 seqs, mainly Japan) Aug 9, 2023
@xz-keg xz-keg changed the title EG.2+S:Q675H(39 seqs, 6 countries) with a further sublineage with S:F490P (16 seqs, mainly Japan) EG.2+S:Q675H(41 seqs, 7 countries) with a further sublineage with S:F490P (18 seqs, mainly Japan) Aug 16, 2023
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xz-keg commented Aug 16, 2023

41, UK

@xz-keg xz-keg changed the title EG.2+S:Q675H(41 seqs, 7 countries) with a further sublineage with S:F490P (18 seqs, mainly Japan) EG.2+S:Q675H(42 seqs, 7 countries) with a further sublineage with S:F490P (19 seqs, mainly Japan) Aug 21, 2023
@FedeGueli FedeGueli added designated and removed Convergent evolution Lineages with convergent mutations labels Aug 30, 2023
@FedeGueli FedeGueli added this to the EG.2.5 milestone Aug 30, 2023
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Designated EG.2.5 via cov-lineages/pango-designation@b375fca

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