XBF | BA.5.2.1*,BA.2.75*

[ktmeaton]

• pango-designation issue: #1259
• covSPECTRUM query: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=T3339C%2CC8692T&

Parents

Clade: Omicron/BA.5/22B,Omicron/BA.2.75/22D Lineage: BA.5.2.1*,BA.2.75* Lineage Confidence: 0.627,1.0

The first parent's confidence (BA.5.2.1* = 0.627) is low because of how specific it is to a sublineage. After BA.5.2.1*, the next likely parent would be (BA.5.2* = 0.924). So we can be extremely confident that the first parent is BA.5.2*. That degree of confidence is quite surprising, given that the BA.5.2* parent only contributed 5 alleles that distinguish it from BA.2.75* before recombination. I suspect this is due to the specificity of 1627T to BA.5.2*.

• 1627T, 2790T, 3037T, 4184A, 4321T | BA.5.2.1*

Immunity

RBD Level: 6 RBD Substitutions: S:R346T,S:G446S,S:N460K,S:F486P,S:F490S,S:R493Q Immune Escape: 0.8366 ACE2 Binding: 1.0428

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

1. XBB = 0.9070
2. XBF = 0.8366
3. XBD = 0.6338

ACE2 Binding Ranking

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

1. XAK = 1.3244
2. XBF = 0.8366
3. XBC.1 = 0.7927

Alleles

XBF is successfully detected with the sc2rf mode for XBB:

python3 sc2rf/sc2rf.py results/XBF/nextclade/alignment.fasta \
  --max-name-length 50 \
  --clades BA.2.10 BA.2.75 BA.4 BA.5 \
  --ansi \
  --parents 2 \
  --breakpoints 1-3 \
  --unique 1 \
  --max-ambiguous 20 \
  --max-intermission-length 2 \
  --max-intermission-count 3 \
  --ignore-shared \
  --mutation-threshold 0.25 \
  --csvfile results/XBF/sc2rf/stats.XBB.csv

Breakpoints

Breakpoint 1: 5184:9865

Tasks

• [x] resources/breakpoints.tsv Updated