XDT : BA.2.86.4 + GK.1 recombinant (27 seqs, Ireland, UK, 8 with S:P174S)

[DeepakPhuyal]

Spotted first by @JosetteSchoenma (Edited)

EPI_ISL_18521215, EPI_ISL_18636413, EPI_ISL_18636423, EPI_ISL_18636425-18636426,
5 sequences from Ireland,
collected between Nov 13th and Dec 5th,
first one uploaded on Nov 20th and then 4 more on Dec 15th.

Breakpoint at Spike S2 between 23673 and 24378.

Private mutations: ORF1a:L446F, S:P174S

New Query by @aviczhl2 : A7842G, C1601T, A8633G, C897A (suggested one)
Previous Queries by @JosetteSchoenma :
T5767C, A7842G, C28005T
and
C1601T, T4654C, T7633C
(EDITED)_

Usher tree is a bit clueless at the moment: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_14949_db8910.json?label=id:node_5398024

[ryhisner]

Was looking at this one yesterday. ORF3a:I35T and ORF3a:T89I, both taken from the GK* part of this recombinant, have positive fitness values in the Bloom Lab fitness calculator.

[aviczhl2]

EPI_ISL_18521215 was previously registered on #991 by @JosetteSchoenma .This again highlights the importance of #991.

[FedeGueli]

S:P174S was in HK.3.5 quite good.

[JosetteSchoenma]

I have been using these 2 queries since I saw that first one.

T5767C, A7842G, C28005T
and
C1601T, T4654C, T7633C

[aviczhl2]

10 seqs now, new seqs don't have S:S50L so only @JosetteSchoenma 's query work now.

[aviczhl2]

13 seqs now

[FedeGueli]

13 seqs now

I think now S:P174S could be removed from the defining mutations, cause 4 of the samples belonging to this lineage have not it:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2f005_fb05a0.json?label=id:node_6819599

The query finds all 13 sequences tough.

[aviczhl2]

+1 UK

[aviczhl2]

17 seqs now

[aviczhl2]

25 seqs now.

[FedeGueli]

Please propose it

[aviczhl2]

Suggest to change query to A7842G,C1601T,A8633G,C897A, which finds 27.

[FedeGueli]

Suggest to change query to A7842G,C1601T,A8633G,C897A, which finds 27.

Thank you! added to the issue,

[FedeGueli]

Now designated XDT via cov-lineages/pango-designation@48ee76d

[Over-There-Is]

BA.2.86.4> A8633G> T5767C(UK 5, Luxembourg 2)
GK.1> C5173T, C5724T, C7858T, T25496C, G29778A> T23633C> G27014A (Belgium 2, France 1)
C1601T, T4654C, T7633C, C9661T, A19326G are private.

Interestingly, A19326G is also the only private mutation of XBB. But due to the breakpoint, it could not be inherited from GK.1.

[JosetteSchoenma]

BA.2.86.4> A8633G> T5767C(UK 5, Luxembourg 2)
GK.1> C5173T, C5724T, C7858T, T25496C, G29778A> T23633C> G27014A (Belgium 2, France 1)
C1601T, T4654C, T7633C, C9661T, A19326G are private.

Interestingly, A19326G is also the only private mutation of XBB. But due to the breakpoint, it could not be inherited from GK.1.

@Over-There-Is I named the private mutation in the pango-designation issue.
cov-lineages/pango-designation#2485

And indeed, you're right about the A19326G. I didn't notice that one!