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XBB.1.5 sublineage with S:K462R and 2 ORF mutation (21 seqs- Peru, Japan and USA) #45

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HynnSpylor opened this issue May 12, 2023 · 3 comments
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designated New mutations Lineage with an unusual/new/interesting mutation To be proposed Green light for proposal
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@HynnSpylor
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HynnSpylor commented May 12, 2023

Defining mutations: XBB.1.5>G15649A (ORF1b:V728I), G22947A (S:K462R), C27925T (ORF8:T11I, but with the ORF8:G8* ahead), C835T, C4391A
GISAID query: Spike_K462R, C835T, C4391A ( Edited :or A22947G,C835T, C4391A)
Earliest seq: 2023-03-18 (Peru, EPI_ISL_17616713)
Most recent seq: 2023-04-18 (Japan, EPI_ISL_17631142)
Countries detected: Peru (11), USA (2), Japan (1)

Ushe Tree:
QQ截图20230512094903

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20296_d99d10.json
The S:K462R is quite rare (even all S:K462 mutations), with only about 110 high quality seqs. It emerged in some small branches of BA.1*, BA.2.38 and BA.2.76. Escape calculator shows the maximum potential in RBD region for XBB in site 462.
QQ截图20230512094509

https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/
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

@HynnSpylor HynnSpylor changed the title XBB.1.5 sublineage with S:K462R and 2 ORF mutation (14 seqs- Peru, Japan and USA) XBB.1.5 sublineage with S:K462R and 2 ORF mutation (18 seqs- Peru, Japan and USA) May 12, 2023
@FedeGueli FedeGueli added the New mutations Lineage with an unusual/new/interesting mutation label May 12, 2023
@FedeGueli
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I would propose it in the main page. New potentisl interesting rbd mutation and geographical spread.

@FedeGueli FedeGueli added the To be proposed Green light for proposal label May 12, 2023
@HynnSpylor
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@FedeGueli I'm waiting for reaching 20 seqs (now 18seqs)

@FedeGueli
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@HynnSpylor now 21!! Lets go with a proposal!

@FedeGueli FedeGueli changed the title XBB.1.5 sublineage with S:K462R and 2 ORF mutation (18 seqs- Peru, Japan and USA) XBB.1.5 sublineage with S:K462R and 2 ORF mutation (21 seqs- Peru, Japan and USA) May 17, 2023
@aviczhl2 aviczhl2 added this to the XBB.1.5.74 milestone Dec 17, 2023
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