New KP.3 sublineage with S:A435S and Orf8:E59* (68 sequences, 8 countries)

[FedeGueli]

As described in #1668 and #1673 S:A435S seems a mutation convergently appearing in multiple backbones recently:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_4d82c_8e8bc0.json?f_userOrOld=uploaded%20sample&label=id:node_6941555

Here i will propose aKP.3 sublineage with it and featuring also an Orf8:E59* truncation.
Moreover it has a silent nuc mutation at S:N343 the N Glycan thought to have a key role in Sars Cov 2 RBD (see: here)

KP.3 > S:N343N (C22591T), S:A435S (G22865T), A27540G, Orf8:E59* (G28068T)
Query: C22591T,G22865T
Samples: 6
First collected in Alberta on 2024-06-06
Countries: Canada, Wales, England

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_4d82c_8e8bb0.json?label=id:node_7038975

[xz-keg]

14 seqs now

[FedeGueli]

14 seqs now

Thx it started again to be collected after a hyathus in uploads

[FedeGueli]

+1 Canada

[FedeGueli]

20

[FedeGueli]

23, it seems slow.

[FedeGueli]

27 Netherlands

[FedeGueli]

33 Denmark, France, Norway

[FedeGueli]

39 +6 NY

[Over-There-Is]

A New York cluster got del28062_28067(Orf8:del57-58)

[FedeGueli]

A New York cluster got del28062_28067(Orf8:del57-58)

in frame deletion?

[FedeGueli]

A New York cluster got del28062_28067(Orf8:del57-58)

in frame deletion?

mm looking at all samples it seems there are three way to see Orf8:E59* one Orf8:E59* the other Orf8:57-58del + Orf8:59* and then Orf8:ins57X , maybe there is some single nuc inserted then creating the stop codon, just guessing. cc @corneliusroemer @ryhisner

[FedeGueli]

only two samples from September for a lineage that emerged in June closing it

[FedeGueli]

52 now with 10 seqs from September although a NY cluster in it better reopening it

[FedeGueli]

+1 NY it is circulating there.

[FedeGueli]

56

[FedeGueli]

67

[xz-keg]

designated KP.3.7 via cov-lineages/pango-designation@1620c06