XBB.1.5 sublineage with S:S494P and N:N77T/ORF9b:I74L (75 seqs as of 2023-05-12, mainly Singapore)

[c19850727]

Description

Sublineage of: XBB.1.5 Earliest sequence: 2023/03/06 (Singapore) Most recent sequence: 2023/04/11 (Singapore) Countries circulating: Singapore (51 local cases), Japan (1 local case)

Mutations on top of XBB.1.5: C18501T > C8092T, C10782T (ORF1a:T3506I), T23042C (S:S494P) > A28503C (N:N77T/ORF9b:I74L)

GISAID and Cov-spectrum query: C18501T , C8092T, C10782T ,T23042C

Evidence

Usher tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2de3_e681a0.json?c=gt-nuc_8092,28503&label=id:node_5884181

Also there are 5 more sequences on GISAID with S:S494P but without N:N77T/ORF9b:I74L, 2 of which are imported cases caught by US border surveillance with a travel history from Belgium in Feb 2023.

Cov-Spectrum growth rate: In recent 2 months in Singapore, this proposed sublineage has 60% growth advantage relative to XBB.1.5, 61% relative to XBB.1.9, and almost on par with XBB.1.16* (-5%).

Genomes:

EPI_ISL_17207348, EPI_ISL_17207361, EPI_ISL_17207368, EPI_ISL_17262381, EPI_ISL_17262435, EPI_ISL_17346958, EPI_ISL_17346963, EPI_ISL_17346990, EPI_ISL_17346994, EPI_ISL_17347001, EPI_ISL_17347027, EPI_ISL_17347035, EPI_ISL_17347205-17347206, EPI_ISL_17347211, EPI_ISL_17388028, EPI_ISL_17388412, EPI_ISL_17388474, EPI_ISL_17388499, EPI_ISL_17388515, EPI_ISL_17388528, EPI_ISL_17388539, EPI_ISL_17388584, EPI_ISL_17388595, EPI_ISL_17388624, EPI_ISL_17388647, EPI_ISL_17388662, EPI_ISL_17388692, EPI_ISL_17388790, EPI_ISL_17388814, EPI_ISL_17431911-17431912, EPI_ISL_17431914, EPI_ISL_17431929, EPI_ISL_17431997-17431998, EPI_ISL_17432034, EPI_ISL_17432125, EPI_ISL_17432176, EPI_ISL_17432212, EPI_ISL_17432246, EPI_ISL_17496122, EPI_ISL_17496124, EPI_ISL_17496126, EPI_ISL_17496129, EPI_ISL_17496132, EPI_ISL_17496137, EPI_ISL_17496144, EPI_ISL_17496149, EPI_ISL_17496154, EPI_ISL_17496333, EPI_ISL_17496406

[FedeGueli]

@c19850727 i think the correct query is : C18501T , C8092T, C10782T ,T23042C, yours doent seem to catch this lineage.

[c19850727]

Yes Fede thanks for pointing out! it must be a silly copy/paste error. let me edit the proposal now.

[FedeGueli]

one sample from Canada today

[corneliusroemer]

I'd rather not use growth advantages when there are so few samples. Now it's disappearing:

https://cov-spectrum.org/explore/Singapore/AllSamples/Past2M/variants?nextcladePangoLineage=XBB.1.5*&nucMutations1=C18501T%2CT23042C&nextcladePangoLineage1=XBB.1.5*&analysisMode=CompareToBaseline&

It's pretty clear that 478 is the most potent mutation. Other mutations have had time to happen and haven't shown much success comparatively so the prior for a single Spike mutation other than 478 to have big growth advantage is quite small now, that includes 494.

[corneliusroemer]

I've designated the parent branch as XBB.1.5.43

[c19850727]

65 seqs as of 2023-04-28.

[c19850727]

71 seqs as of 2023-05-05. Newly found in China-Shanghai and India-MH.

[c19850727]

75 seqs as of 2023-05-12. Newly found in Vietnam.

[DailyCovidCases]

This branch is dead, please close this issue