XBB.1.9.1 saltation with 6 spike mutations (S:76I, 190S, 356T, 572I, 899S, 1070T) UK, US, Den(12)

[FedeGueli]

Spotted using Dave McNally tool

Defining mutations:
XBB.1.9.1 > > Orf1a: V3925I ( G12038A = NSP7_V66I) > S:R190S (G22132T), S:K356T (A22629C), S:T572I (C23277T), S:A899S (G24257T)> Orf1a:N1076D (A3491G = NSP3_N258D), C9532T, T16776C, C21054T, S:T76I (C21789T), C23707T, S:A1070T (G24770A)

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_130c_19a650.json?label=id:node_7002353

Gisaid query : C23277T, G24257T,G22132T, A22629C

Actually it finds 5 samples on Gisaid ,
one of them (EPI_ISL_18239057) lacks S:T76I,S:A1070T and was sampled from a traveller entering US from Netherlands but it has no coverage at 1070

Samples:
EPI_ISL_18244522, EPI_ISL_18244529 (Firs collected in England on 26/08/2023) , EPI_ISL_18248577,
EPI_ISL_18248583

[oobb45729]

3 N-glycan changes on this one, gaining N354 and N188 but losing N74.

[FedeGueli]

3 N-glycan changes on this one, gaining N354 and N188 but losing N74.

Tgank you! I didnt notice this

[krosa1910]

3 N-glycan changes on this one, gaining N354 and N188 but losing N74.

Is that from the the N-X(not P)-S/T/C rule? Just wonder how credible it is.

[krosa1910]

Also that is another one with K356T, T572I. I still miss those from my first designated lineage of XBB.1.5.44*
I think we have the most information on K356T. According to Cao that seems a very risky trade, pumping up great escape at E1-E3 sites ( have no ideas what they are exactly though), but at the risk of losing so much infectivity (Maybe that is why BN* are being comparatively unsuccessful up to now).
Maybe 356T flip is what we are afraid of?

[olias120676]

There is a new one in the UK data, not on GISAID yet, sample date of 2023-09-06

The previous 4 from the UK could be in some way linked but this one looks fairly distinct.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_805a_2f5090.json?c=userOrOld&label=id:node_10870200

[oobb45729]

3 N-glycan changes on this one, gaining N354 and N188 but losing N74.

Is that from the the N-X(not P)-S/T/C rule? Just wonder how credible it is.

S:R190S is also in Gamma, and we know that Gamma has the N188-glycan.

[FedeGueli]

I have double counted the climb seqs so with the sequence spotted by @olias120676 we are at 6.

[FedeGueli]

Now found also in Us and Denmark.

[FedeGueli]

ping @corneliusroemer this seems going.

[FedeGueli]

12 now both from England

[corneliusroemer]

Yeah just found this independently. I did a deep dive to see if this might be a recombinant, but couldn't find anything. Sure, the Spike could be from HC.2 but there's not much evidence this isn't just convergence.

[FedeGueli]

Yeah just found this independently. I did a deep dive to see if this might be a recombinant, but couldn't find anything. Sure, the Spike could be from HC.2 but there's not much evidence this isn't just convergence.

Thx.. yeah me too searched without results