proposed1305

[ktmeaton]

• pango-designation issue: #1305
• covSPECTRUM query: A9533T, G11743A, T22693C, G25157A, C28087A, A28154G

  Parents

Clade: Omicron/BA.2.75/22D,Omicron/BA.5.2 Lineage: BA.2.75*,BA.5.2.1* Lineage Confidence: 1.0,0.988

Immunity

RBD Level: 5 RBD Substitutions: S:R346T,S:G446S,S:N460K,S:F486S,S:R493Q Immune Escape: 0.6339 ACE2 Binding: 0.4677

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

1. XBB = 0.9070
2. XBF = 0.8366
3. proposed1305 = 0.6339
4. XBD = 0.6339

ACE2 Binding Ranking

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

1. XAK = 1.3244
2. XBF = 1.0428
3. XBC = 0.7927
4. XBE = 0.6697
5. XAY = 0.6144
6. XAV/XAS/XAZXAJ = 0.5583
7. proposed1305 = 0.4677
8. XBD = 0.4677

Alleles

proposed1305 is successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/S521941/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/S521941/sc2rf/stats.voc.csv

Breakpoints

Breakpoint 1: 27013:27037

Tasks

• [x] resources/breakpoints.tsv Updated