XBK | BA.5.2/CJ.1

[ktmeaton]

This will probably need to be an auto-pass based on how close the breakpoint is to the 5' termini.

• pango-designation issue: #1418
• covSPECTRUM query: TBD

Parents

Clade: BA.5.2,CJ.1 Lineage: BA.5.2.1*,CJ.1* Lineage Confidence: 0.611,0.579

Immunity

RBD Level: 6 RBD Substitutions: S:R346T,S:G446S,S:N460K,S:F486P,S:F490S,S:R493Q Immune Escape: 0.837 ACE2 Binding: 1.042

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

TBD

ACE2 Binding Ranking

Higher values indicate an increased capacity for viral entry into the host cell.

TBD

Alleles

XBK is successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/XBK/nextclade/alignment.fasta --max-name-length 50 --clades BA.2.10 BA.2.3.17 BA.2.3.20 BA.2.75 BA.2.76 BA.4.6 BA.5.2 BA.5.3 XBB CJ.1 --ansi --parents 2-4 --breakpoints 1-5 --unique 1 --max-ambiguous 20 --max-intermission-length 2 --max-intermission-count 3 --ignore-shared --mutation-threshold 0.25 --csvfile results/XBK/sc2rf/stats.voc.csv

Breakpoints

Breakpoint 1: 1628:3795

Tasks

• [x] resources/breakpoints.tsv Updated

[ktmeaton]

CJ.1 seems to interfere with other BA.2.75 recombinants. I'm going to try removing CJ.1 from the VOC mode, and just rely on the auto-pass. The sc2rf output contributes little information for XBK currently.

[ktmeaton]

I'm going to leave CJ.1 in the VOC mode until XBK is released in a nextclade dataset.

[ktmeaton]

I might make two different voc modes, one with CJ and one without?