New XBB.1 sublineage with S:F486P orf1a:K120R , - likely emerged from Malaysia -25 sequences - Singapore, Japan,

[FedeGueli]

_EDITED ON 09-03-23
Now the tree has competely changed so i am editing the proposal to start this lineage with:
Orf1:K120R (A624G)> S:F486P, C27297A

justified by the following tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d48_a49000.json?c=userOrOld&label=id:node_7760413

15 sequences

Gisaid query:
A624G,C27297A,T23018C

has to be noticed that all the three "branches of this sublineage have additional spike mutations we have seen in variant soup at S:255 and s:256 but also at S:158 as Delta (but different AA)_

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ORIGINAL proposal:

Put here to simplify the work in monitoring XBB.1 * 486P sublineages.

This is totally independent from the others already designated.

it carries two additional defining mutations: Orf1a:K120R , Orf1a:k261N beyond S:F486P

Tree:


https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_430f4_a60ea0.json?c=userOrOld&label=id:node_9610401

Gisaid query:NSP1_K120R,NSP2_K81N, Spike_F486P

it has to be highlighted that one sample (with travel history from Malaysia) has also S:255F,S:T678P and N:E136Q

Sequences:
EPI_ISL_16847528, EPI_ISL_16899415, EPI_ISL_16899433 all of them have been sampled in Singapore and in February 2023
( 2 imported into Singapore from Malaysia, one local case in an elderly man)

Defining mutations:
Orf1:K120R (A624G) then Orf1a:K261N G1048T), C27297A, S:F486P (T23018C)

[FedeGueli]

two new samples from Japan and Singapore.

[FedeGueli]

2 new sequences uploaded from Malaysia (the first directly sampled there) confirming initial.hypothesis this arose in Malaysia

[FedeGueli]

10 sequences as today. Last samples from elderly people in Singapore (local cases)

[FedeGueli]

Now the tree has competely changed so i am editing the proposal to start this lineage with:
Orf1:K120R (A624G)> S:F486P, C27297A

justified by the following tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d48_a49000.json?c=userOrOld&label=id:node_7760413

15 sequences

Gisaid query:
A624G,C27297A,T23018C

@corneliusroemer @InfrPopGen @AngieHinrichs @thomasppeacock i ve broaden this proposal . Although low numbers they deserve a check, the area is dense of XBB.1*486P variants they should be designated to be distinguished btw slow and fast ones

[FedeGueli]

20 samples of this one, two new samples from two different district of Japan

[FedeGueli]

25 sequences as today . Last samples from Japan and Singapore, one of them with travel history from Philippines.

[alurqu]

Lineage notes and the git commit log say this is XBB.1.5.27, which makes sense as the next-available designation, but this has been added to the XBB.1.27 milestone instead of the XBB.1.5.27 milestone.

[Mydtlwn]

This is indeed a mistake, the latest specified branch in the subbranch of XBB.1 is currently XBB.1.23, while the latest specified branch in the subbranch of XBB.1.5 is XBB.1.5.27

[HynnSpylor]

It should be XBB.1.24 (without T17124C)

[FedeGueli]

It hs been designated XBB.1.5.27 , just the milestone is uncorrect. About the fact to be a broader xbb.1.5 descendant or XBB.1 independent 486P acquisition i tend to think the second is more likely cause its geographical origin from Malaysia is quite well documented , but too few evidence to state it is not a broader xbb.1.5 descendant for certain t

[corneliusroemer]

Sorry - I made a mistake here.

It should indeed be XBB.1.24 and not XBB.1.5.27 - I messed up somewhere along the way.

I'm fixing.

[FedeGueli]

Please remove XBB.1.27 milestone makes a bit mess when searching for it!