XBB.1.5 sublineage with S:K462R and 2 ORF mutation (21 seqs- Peru, Japan and USA)

[HynnSpylor]

• Transfer from XBB.1.5 sublineage with S:K462R and 2 ORF mutation (21 seqs- Peru, Japan and USA) sars-cov-2-variants/lineage-proposals#45

Defining mutations: XBB.1.5>G15649A (ORF1b:V728I), G22947A (S:K462R), C27925T (ORF8:T11I, but with the ORF8:G8* ahead), C835T, C4391A
GISAID query: A22947G, C835T, C4391A
Earliest seq: 2023-03-18 (Peru, EPI_ISL_17616713)
Most recent seq: 2023-04-24 (USA, EPI_ISL_17650996)
Countries detected: Peru (17), USA (3), Japan (1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a787_5272b0.json

The S:K462R is quite rare (even all S:K462 mutations), with only about 110 high quality seqs before. It emerged in some small branches of BA.1*, BA.2.38 and BA.2.76. Although the new escape calculator no longer shows the maximum potential in RBD for site S:462, it still deserves tracking.

Genomes:
EPI_ISL_17351703, EPI_ISL_17521421, EPI_ISL_17616713, EPI_ISL_17631142, EPI_ISL_17634855, EPI_ISL_17634870, EPI_ISL_17634978, EPI_ISL_17634987, EPI_ISL_17635028, EPI_ISL_17635059-17635060, EPI_ISL_17635066, EPI_ISL_17639854, EPI_ISL_17639868, EPI_ISL_17646085, EPI_ISL_17646128, EPI_ISL_17646130, EPI_ISL_17646151, EPI_ISL_17650996, EPI_ISL_17654865, EPI_ISL_17669371

[oobb45729]

K462 interacts with the NTD, which may be the reason we haven't seen more cases of K462X. (I468 is also near the NTD, which is another residue that is not in play yet despite the prediction).