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XCZ: GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (18 seqs, 6 countries) #839

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xz-keg opened this issue Sep 20, 2023 · 9 comments
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XCZ: GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (18 seqs, 6 countries) #839

xz-keg opened this issue Sep 20, 2023 · 9 comments
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designated FLip = S:L455F / S:F456L ORF9b recombinant XCZ
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XCZ

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@xz-keg
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xz-keg commented Sep 20, 2023 •
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XBB.1.5+
C2334T, G5720A, C6541T,C9693T, C12789T, G13627A, A15436G, A16878T, A18492G,T22609G,C22624T, G22927T, T22928C, C23280T, C23673T,A25045G, C26735T,C25658T,C27059T,C28005T,C28519T, C28657T

image

Plus Orf9b:T79I which is not shown on the figure.

C2334T,G5720A,C6541T,C9693T,C12789T,G13627A,A15436G,A16878T,A18492G from EG.5.1.1
C22624T, G22927T, T22928C, C23280T, C23673T,A25045G, C26735T,C25658T,C27059T,C28005T,C28657T from GK.1.1
T22609G,C28519T from a GK.1.1 branch

A15436G is private mutation, I don't find it in any EG.5.1.1 branches.

Spike is GK.1.1-spike(Flip+573+704)
EG.5.1.1--GK.1.1
Breakpoint between 18493 and 22623

GISAID query: A15436G,T22609G,C28519T
No. of seqs: 5(USA 2(1 from UK, 1 imported), Italy 2 France 1)

6 on GISAID, 1 GBW-H10/20 duplicate

First: EPI_ISL_18222077, USA imported 2023-8-22
Latest:EPI_ISL_18275613, Italy, 2023-9-5

One of the seqs EPI_ISL_18222077 seems different from the other 4, lack of some mutations and having T29625C indicating a second breakpoint between 28658 and 29624, but it also has A15436G.

An undetected A15436G branch on EG.5.1.1 recombs 2 times with GK.1.1, or just artefact?

usher
image

usher for GK.1.1 donor
image
@xz-keg
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xz-keg commented Sep 20, 2023

By the way, @AngieHinrichs, is EPI_ISL_18222077 removed due to reversions?

@FedeGueli FedeGueli added recombinant FLip = S:L455F / S:F456L labels Sep 20, 2023
@AngieHinrichs
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Yes, it has 8 reversions relative to its nextclade placement and I filter out anything with more than 5 (because the Omicron wave brought a wave of dropout-riddled sequences). That is two more reversions than EPI_ISL_18275613 which has 6. I added exceptions for the sequences in your usher subtree.

@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1 recombinant(5 seqs, 4 countries) GK.1.1/EG.5.1.1 recombinant(6 seqs, 4 countries) Sep 26, 2023
@xz-keg xz-keg mentioned this issue Sep 30, 2023
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@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1 recombinant(6 seqs, 4 countries) GK.1.1/EG.5.1.1 recombinant(9 seqs, 4 countries) Oct 3, 2023
@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1 recombinant(9 seqs, 4 countries) GK.1.1/EG.5.1.1 recombinant(10 seqs, 4 countries) Oct 4, 2023
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xz-keg commented Oct 5, 2023

+1 Slovenia

@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1 recombinant(10 seqs, 4 countries) GK.1.1/EG.5.1.1 recombinant(11 seqs, 5 countries) Oct 5, 2023
@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1 recombinant(11 seqs, 5 countries) GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant(11 seqs, 5 countries) Oct 5, 2023
@FedeGueli
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12 now

@xz-keg
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xz-keg commented Oct 5, 2023

A15436G,T22609G,C28519T

One pair of GBW-H10/20 duplicate.

@FedeGueli
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A15436G,T22609G,C28519T

One pair of GBW-H10/20 duplicate.

yes please count them so i have not to chekc everytime. Gisiad count is what counts. then we know already that.

@FedeGueli FedeGueli changed the title GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant(11 seqs, 5 countries) GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (12 seqs, 5 countries) Oct 5, 2023
@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (12 seqs, 5 countries) GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (13 seqs, 5 countries) Oct 9, 2023
@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (13 seqs, 5 countries) GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (14 seqs, 5 countries) Oct 13, 2023
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xz-keg commented Oct 14, 2023

18, one American seq from Switzerland

@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (14 seqs, 5 countries) GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (18 seqs, 6 countries) Oct 14, 2023
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xz-keg commented Oct 16, 2023

Designated XCZ @FedeGueli

@xz-keg xz-keg closed this as completed Oct 16, 2023
@xz-keg xz-keg changed the title GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (18 seqs, 6 countries) XCZ: GK.1.1/EG.5.1.1(Flip+573+704+Orf9b:79) recombinant (18 seqs, 6 countries) Oct 16, 2023
@FedeGueli FedeGueli added the XCZ label Oct 16, 2023
@FedeGueli FedeGueli added this to the XCZ milestone Oct 16, 2023
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Designated XCZ via cov-lineages/pango-designation@b36a0f3

FedeGueli referenced this issue in cov-lineages/pango-designation Oct 16, 2023
@corneliusroemer
Designate XCZ (Recombinant lineage of EG.5.1.1, GK.1.1 (breakpoint 18…
b36a0f3 
…492-21718), France/Italy/England) with 17 seqs
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