KP.1.1.1 + S:F59S,T22N (10 seqs) with a S:K478T+M153I branch (5) and further S:H445R (2, India, GBW)

[Fearuncle]

This was spotted first by @aviczhl2 in the groups (edited)

Proposal edited by mod on November 17 KP.1.1.1 > S:F59S (T21738C) > S:T22N (C21627A) >> S:K478T (A22995C) > Orf1a:F2321L (T7226C) , T11974C ,G19677A>S:M153I (G22021A) > C4898T, T10084A, S:H445R (A22896G),Orf8:E106* (G28209T) Query for 22N - 59S branch: T21738C,C21627A,C20104T,-C6701T Samples: 9 Countries: India (GBW), NZL, Singapore Query for M153I branch: G22021A,T7226C, T11974C Samples: 5 Query for the new 445R branch : C4898T, G28209T ,T10084A Samples : 2 (India - GBW) found by @xz-keg

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_2968d_a20ca0.json?label=id:node_7409269

original proposal

 tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11c0e_ab6c20.json?c=gt-nuc_19677&gmax=20677&gmin=18677&label=id:node_7072051 Seq: 2024-08-07 Query: G19677A, G22021A PQ214096.1 PQ214174.1

[FedeGueli]

Thx great catch.

[FedeGueli]

Ah but this was spotted by @aviczhl2 a 10ish days ago, then i re found it so it is the third time it has been spotted. i have a query for it wait .. here:G19677A, G22021A ,T7226C,T3565C

[xz-keg]

No further seqs

[FedeGueli]

rearranging the proposal to just include 59S 22N

[xz-keg]

oh there is another traveler from india.

[FedeGueli]

The tree of this changed including a branch with a reversion at S:F59S>F:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_4b64b_a7ba80.json?c=gt-nuc_11704&gmax=12704&gmin=10704&label=id:node_7278672

Please @Fearuncle keep this checked broadly because i fear some surprise could come from this branch

[FedeGueli]

The tree of this changed including a branch with a reversion at S:F59S>F: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_4b64b_a7ba80.json?c=gt-nuc_11704&gmax=12704&gmin=10704&label=id:node_7278672

Please @Fearuncle keep this checked broadly because i fear some surprise could come from this branch

Now this has been proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/2120 Interestingly the 59S rev branch has a deletion from S:N30-31 S:F32I

[xz-keg]

Now this has been proposed in #2120 Interestingly the 59S rev branch has a deletion from S:N30-31 S:F32I

Nope it is an usher bug, there's no rev and it is a misplacement, only 5 of the seqs are actually in this branch, with 22N+59S.

The latest seq seem uploaded more than 3 weeks ago. GBW from India maybe we can wait for 1 more week or so.

[FedeGueli]

Now this has been proposed in #2120 Interestingly the 59S rev branch has a deletion from S:N30-31 S:F32I

Nope it is an usher bug, there's no rev and it is a misplacement, only 5 of the seqs are actually in this branch, with 22N+59S.

The latest seq seem uploaded more than 3 weeks ago. GBW from India maybe we can wait for 1 more week or so.

yeah for sure the branch was highlighted to be checked inside this issue because USher placed here and was only three at times. Anyway doesn't count what or who just to keep things together. One of the GBW sequence has 1086 reverted as we saw in another issue i dont recall now which one.

[xz-keg]

yeah for sure the branch was highlighted to be checked inside this issue because USher placed here and was only three at times. Anyway doesn't count what or who just to keep things together. One of the GBW sequence has 1086 reverted as we saw in another issue i dont recall now which one.

I mean they are separate branches and unrelated. Usher put together them just because some bugs. The proposed branch here has not appeared for a long time.

[Fearuncle]

updated

[xz-keg]

Only 6 seqs for this branch. Seqs on the A6124G sub-branch are unrelated. Please use query and don't include unrelated seqs

[FedeGueli]

+1 Singapore

[xz-keg]

+2 GBW from India, with additional S:M153I, K478T rev and H445R

[FedeGueli]

+2 GBW from India, with additional S:M153I, K478T rev and H445R Proposal edited