XBB.1.5 sublineage with S:E281D and further gets S:P445S (67seqs)

[HynnSpylor]

Defining mutations: XBB.1.5>C29095T>A22405T (S:E281D), then one branch further gets C22895T (S:P445S)
GISAID query: Spike_E281D, C29095T, T17124C
Earliest seq: 2023-01-13 (USA, EPI_ISL_16668636)
Most recent seq: 2023-04-12 (Vietnam, EPI_ISL_17481620)
Countries detected: South Korea (33), USA (13), Vietnam (9), Japan (3), Singapore (2), Canada (2), China (1), Germany (1), France (1), Austria (1), Sweden (1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_36286_220110.json
The early seqs mainly appear in USA. When the branch further got S:P445S (probably in South Korea) the growth increased again.

https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-01-16%26to%3D2023-04-10/variants?nextcladePangoLineage=XBB.1.5*&aaMutations1=S%3AE281D&nextcladePangoLineage1=XBB.1.5*&analysisMode=CompareToBaseline&

Genomes:
EPI_ISL_16668636, EPI_ISL_16780469, EPI_ISL_16889111, EPI_ISL_16906974, EPI_ISL_17014591, EPI_ISL_17090120, EPI_ISL_17193753, EPI_ISL_17249397, EPI_ISL_17262150-17262151, EPI_ISL_17278656, EPI_ISL_17281565, EPI_ISL_17343756, EPI_ISL_17348604, EPI_ISL_17364938, EPI_ISL_17373874, EPI_ISL_17373960, EPI_ISL_17374219, EPI_ISL_17374430, EPI_ISL_17375024, EPI_ISL_17375273, EPI_ISL_17375278, EPI_ISL_17388520, EPI_ISL_17414702, EPI_ISL_17414840, EPI_ISL_17414854, EPI_ISL_17414884, EPI_ISL_17414889,
EPI_ISL_17415006, EPI_ISL_17415147, EPI_ISL_17415185, EPI_ISL_17415187, EPI_ISL_17415810, EPI_ISL_17415866, EPI_ISL_17415868, EPI_ISL_17415945, EPI_ISL_17416174, EPI_ISL_17416195, EPI_ISL_17428356, EPI_ISL_17431915, EPI_ISL_17433114, EPI_ISL_17445002, EPI_ISL_17445008, EPI_ISL_17472090, EPI_ISL_17473525, EPI_ISL_17474196, EPI_ISL_17474423, EPI_ISL_17474541-17474544, EPI_ISL_17481608-17481609, EPI_ISL_17481613-17481616, EPI_ISL_17481618-17481620, EPI_ISL_17489973, EPI_ISL_17490046, EPI_ISL_17491136, EPI_ISL_17491832, EPI_ISL_17493945, EPI_ISL_17511419, EPI_ISL_17511614,

[FedeGueli]

Interestingly a S in 445 if 444 changes further to N as we saw a lot of times in BA.5s could lead to a potential new N Glycan due to 446S .
@thomaspeacock

[corneliusroemer]

Designated broadly, requiring S:E281D but not S:P445S

[FedeGueli]

@HynnSpylor @corneliusroemer One of this showed up today in Yunnan very recent sample with S:69/70del beyond 445S and 281D : EPI_ISL_17547638.

i suggest to opne up an issue for the sublineage with 445S so the variant seeking community can keep it checked, this could give us some surprise. It is a change in one defining mut of XBB better to keep it under the spotlight (thinking of also vaccine makers community)

[FedeGueli]

I am seeing that it is the lineage with Orf1a:K1655N to be growing faster and being the most represented in the recent samples.
It is partially found by A22405T,G5230T query (17 out of 21)
Usher has 21 on its tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_be2d_8f9670.json?c=userOrOld&label=id:node_5962882

Interestingly it has been sampled fro travellers from S Korea, Thailand, Vietnam, and in two chinese samples (Shangai, Yunnan)

[FedeGueli]

I was looking at Vietnam( or from Vietnam ) samples uploaded after 20th of March 2023 to search which variant is causing a super steep increase in cases and i noticed that out of 83 samples worlwide labelled as Vietnam related on Gisaid an impressive 9 are XBB.1.5.42 . Interestingly most of them has no coverage at 445 so likely they all have 445S and likely this lineage has emerged there. A 10% of prevalence is very much, i m not able to say if this is pushing up cases or they are the many XBB.1.16 sampled from Vietnam ( or Vietnam related).

But this makes me think that is correct to restrict this lineage starting with S:P445S cause most of the samples without it likely have it instead (except the american ones which are likely the ancestors of this sublineages). @corneliusroemer @thomasppeacock @HynnSpylor @AngieHinrichs @InfrPopGen

Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_aea2_bb3800.json?c=country&label=id:node_5968793