XBB.1 Sublineage with S:Y453F, ORF7a:A50S, ORF1a:E148D, ORF1a:L642F, ORF1a:T2121I, ORF1b:L2497I (8 seq, Mar 30)

[ryhisner]

Description

Sub-lineage of: XBB.1
Earliest sequence: 2023-2-23, Philippines, Davao — EPI_ISL_17343863
Most recent sequence: 2023-3-6, Philippines, Davao — EPI_ISL_17343910 + 5 others
Countries circulating: Philippines (Davao)
Number of Sequences: 8
GISAID AA Query: Spike_Y453F, NSP1_E148D, NSP3_T1303I
GISAID Nucleotide Query: G709T, C6627T, A22920T
CovSpectrum Query: Nextcladepangolineage:XBB.1* & A22920T & [3-of: G709T, C2189T, C6627T, T3676C, T14865C, C20956A, G27541T]
Substitutions on top of XBB.1:
Spike: Y453F
ORF7a: A50S
ORF1a: E148D, L642F, T2121I (NSP1_E148D, NSP2_L462F, NSP3_T1303I)
ORF1b: L2497I (NSP16_L100I)
Nucleotide: G709T, C2189T, C6627T, T3676C, T13704C, T14865C, C20956A, A22920T, G27541T

USHER Tree
Note: As is typical for sequences from the Philippines, coverage is spotty, so there are several artifactual reversions on the tree, especially in the S:360-417 area.
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1_Y453F_ORF7aA50S_subtreeAuspice1_genome_43047_572970.json

Evidence
The Philippines recently uploaded 147 sequences collected between Feb 13 and Mar 7. A majority (75) were still BA.2.3.20*, which remarkably continues to maintain dominance there, despite being driven to negligible levels elsewhere in the world. But 8/147 sequences (5.4%) were from this XBB.1 sublineage. Furthermore, six of the eight sequences were collected on March 6, which puts them among the 20 most recently collected sequences from this upload.

Six of the eight sequences also have ORF1a:A2123V. One sequence has S:N450D and another has S:E281Q, S:A845S, and ORF1a:D2296E. Two have ORF1a:C3301G (NSP5_C38G).

In addition to being a mutation associated with mink outbreaks, S:Y453F increases ACE2 binding strength by more than any other known mutation on a BA.2 background according to the Bloom Lab RBD Heat Map.

Genomes

Genomes

EPI_ISL_17343831, EPI_ISL_17343863, EPI_ISL_17343901, EPI_ISL_17343903, EPI_ISL_17343904, EPI_IDL_17343905, EPI_ISL_17343907, EPI_ISL_17343910

[Sinickle]

Edit: It looks like this has been handled in issue #1908

Yesterday Thailand uploaded 5 sequences, collected April 19 and April 21, that cluster with the S:N450D sequence here.

spike_y453f,spike_n450d,spike_v445p

On Jbloom's calculator, the 2 spike mutations give between 4-15% immune escape for XBB, depending on the prior infections (largest escape for BA.1, lowest for Pre-Omicron only.)

[FedeGueli]

Sorry i didnt see it was already proposed!