XBJ | BA.2.3/BA.5.2

[ktmeaton]

• pango-designation issue: #1268
• covSPECTRUM query:

Parents

Clade: Omicron/BA.2/21L,Omicron/BA.5/22B Lineage: BA.2.3*,BA.5.2* Lineage Confidence: 0.996,0.979

Immunity

RBD Level: 5 RBD Substitutions: S:K444R,S:N450D,S:L452M,S:N460K,S:R493Q Immune Escape: 0.5925 ACE2 Binding: 1.0634

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

1. XBB = 0.9070
2. XBF = 0.8366
3. XBD = 0.6339
4. XBE = 0.6014
5. XBJ = 0.5925
6. XBC = 0.5283

ACE2 Binding Ranking

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

1. XAK = 1.3244
2. XBJ = 1.0634
3. XBF = 1.0428

Alleles

XBJ is successfully detected with the sc2rf mode for omicron_omicron:

python3 sc2rf/sc2rf.py results/proposed1268/nextclade/alignment.fasta \
  --max-name-length 50 \
  --clades BA.1 BA.2 BA.4 BA.5 \
  --ansi \
  --parents 2-4 \
  --breakpoints 0-10 \
  --unique 1 \
  --max-ambiguous 20 \
  --max-intermission-length 2 \
  --max-intermission-count 3 \
  --ignore-shared \
  --mutation-threshold 0.25 \
  --csvfile results/proposed1268/sc2rf/stats.omicron_omicron.csv

XBJ is also successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/proposed1268/nextclade/alignment.fasta \
  --max-name-length 50 \
  --clades BA.2.10 BA.2.3.17 BA.2.3.20 BA.2.75 BA.4.6 BA.5.2 BA.5.3 XBB \
  --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/proposed1268/sc2rf/stats.voc.csv

Breakpoints

This is an extraordinarily narrow breakpoint, almost suspiciously so. The alternative breakpoint 23019:25170 is reported by the sc2rf mode VOC between BA.2.3.20* and BA.5.2* and might be more reliable and specific.

Breakpoint 1: 23019:23039 Breakpoint 1 Alt: 23019:25170

Tasks

• [x] resources/breakpoints.tsv Updated

[ktmeaton]

This is upgraded from proposed1268 to XBJ.