proposed1440 | CJ.1/BA.5.2

[ktmeaton]

Very similar to XBK, may also need to be an auto-pass lineage.

• pango-designation issue: #1440
• covSPECTRUM query: TBD

Parents

Clade: Omicron/BA.5.2,Omicron/CJ.1 Lineage: BA.5.2.1*,CJ.1* Lineage Confidence: 0.612,0.56

Immunity

RBD Level: 6 RBD Substitutions: S:R346T,S:G446S,S:N460K,S:F486P,S:F490S,S:R493Q Immune Escape: 0.837 ACE2 Binding: 1.0428

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

proposed1440 is successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/proposed1440/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/proposed1440/sc2rf/stats.voc.csv

Breakpoints

Breakpoint 1: 1628:3795

Tasks

• [x] resources/breakpoints.tsv Updated