BA.5.2.24 with S:N460K (T22942A) and Orf7a:T39I - 100 sequences (Austria, Greece, England, Singapore,Germany,Australia,Spain, Usa, Switzerland , Canada)

[FedeGueli]

From #1089 here i want to propose the second of apparent sublineages of BA.5.2.24 which have acquired S:N460K

This potential sublineage has been already sampled in three different countries: Austria (EPI_ISL_15109578), England (PHEC-YYG56SA/2022) Greece (EPI_ISL_15110912)

it is defined by an Orf7a:T39I mutation that comes just before the S:N460K ( interestingly this AA substitution comes from T22942A as BQ.1) covspectrum query : BA.5.2 (Nextclade) + T22942A + S:K444N, ORF7a:T39I catches zero sequences being all very recent ones https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A444N%2COrf7a%3AT39I&nucMutations=T22942A&nextcladePangoLineage=BA.5.2*&aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

Edited

Gisaid query -NSP2_Q376K,NS7a_T39I,Spike_N460K,Spike_K444N finds all the three sequences

Here the tree as requested by @corneliusroemer :

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_14417_1ac6e0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C27509T

Note that it is very close to the other BA.5.2.24 + S:460K that there is instead T22942G

[corneliusroemer]

Do you have an Usher link for this one?

Is BA.5.2.24 defined as having S:K444N already?

[FedeGueli]

yes BA.5.2.24 has S:444N as defining.

the tree is ready @corneliusroemer :edited in the main post.

[FedeGueli]

one more sample of this one, a local case in Singapore.EPI_ISL_15209081

[FedeGueli]

6 sequences as today one more from England and one from Germany (query : -NSP2_Q376K,NS7a_T39I,Spike_N460K,Spike_K444N)

[corneliusroemer]

Bit slow growth, wouldn't designate at this point

[FedeGueli]

7 viruses as today last one from Singapore - local case

[corneliusroemer]

Very slow growth if it's still only 7 sequences up from 3 19 days ago, i'll close for now

[FedeGueli]

This grew to 16 with 3 from Australia. I suggest @corneliusroemer not to close this S:460K + 444N too early, consider they ususally come from very undersampled area so first sequences are slow to accumulate.

New tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3a08d_d4b170.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C27509T

[FedeGueli]

-NSP2_Q376K,NS7a_T39I,Spike_N460K,Spike_K444N finds now 16 sequences the last uploaded is from Canada.

@corneliusroemer my suggestion is to designate this one too so we have every BA.5.2.24 + 460K designated.

Remember this one has T22942A and not T22942G as CK.1 /CK.2.1* https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1092_1a67d0.json?branchLabel=aa%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C27509T

[corneliusroemer]

There isn't much evidence that this is not a CK.1 - with extra ORF7a:T39I

This one USA/TX sequence could well be dropout. So I've added this to CK.1

We can split it out if we get strong evidence that there are in fact ORF7a:T39I without S:N460K circulating.

But unless we have that I think we should just consider this a CK.1 and be happy :)

[FedeGueli]

There isn't much evidence that this is not a CK.1 - with extra ORF7a:T39I

This one USA/TX sequence could well be dropout. So I've added this to CK.1

We can split it out if we get strong evidence that there are in fact ORF7a:T39I without S:N460K circulating.

But unless we have that I think we should just consider this a CK.1 and be happy :)

No Cornelius this has T22942A for S:N460K (as BQ.1 and XAW) while Ck.1 and Ck.2.1.1s have T22942G as XBB and BA.2.75s. So they are unrelated .

@corneliusroemer

[FedeGueli]

24 Viruses as today , last sequences span from Spain to Singapore, from Israel to Usa. i push for a designation of this one it could be as fitter as the other already designasted as CK.1 CK.2.1 and others @corneliusroemer

[FedeGueli]

As today i find 54 viruses on Gisaid with -NSP2_Q376K,NS7a_T39I,Spike_N460K,Spike_K444N

Nextclading them i can confirm they are all from this lineage.

here the Usher tree that confirms this is monophyletic:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_7513_6a9f20.json?c=pango_lineage_usher&label=nuc%20mutations:C27509T

And this is distinct from every other BA.5.2.24 cause it has T22942A for S:N460K while the others have T22942G:

(on the top part of the tree is the CK.2 lineage while in the bootom part of the tree we can see CK.1, in the middle the lineage proposed here).

CC @InfrPopGen @corneliusroemer @AngieHinrichs @thomaspeacock i ask you to designate this for its relevance

and also for its widespread distribution although in low numbers:

[FedeGueli]

77 sequences growing very fast @AngieHinrichs @thomaspeacock @corneliusroemer @InfrPopGen please reopen and designate this one

[corneliusroemer]

~This is probably just CK.1 where one sample has dropout. There's not enough evidence that this is homoplasic.~

Thanks @FedeGueli I missed the different mutation

[FedeGueli]

100 seqsas today newly found in Switzerland and Canada doubling time for date of submission is around 7-10days.

@corneliusroemer @InfrPopGen by the fact it is growing and reaching more and more countries i think it deserves a designation

[InfrPopGen]

Thanks for submitting. We've added lineage CK.3 with 76 newly designated sequences, and 15 updated designations from CK.1. Defining mutations T22942A (S:N460K) (following C27509T (ORF7a:T39I)).

[FedeGueli]

Thx @InfrPopGen and @corneliusroemer for taking your time to listen to my thoughts on this one.