ktmeaton / ncov-recombinant

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
MIT License
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XBH | BA.2.3.17/BA.2.75 #198

Closed ktmeaton closed 1 year ago

ktmeaton commented 1 year ago

Parents

Clade: BA.2.3.17,Omicron/BA.2.75/22D Lineage: BA.2*,BA.2.75* Lineage Confidence: 0.999,0.998

The first parental lineage (BA.2*) does not match the first parental clade (BA.2.3.17). This is because the mutation 13730C is considered a private mutation rather. When 13730C is included in the first parent's subs, the second parent becomes most likely to be BA.2.3.17.

Lineage: BA.2.3.17,BA.2.75* Lineage Confidence: 0.5223,0.998

Immunity

RBD Level: 5 RBD Substitutions: S:R346T,S:G446S,S:N460K,S:F486S,S:R493Q Immune Escape: 0.6339 ACE2 Binding: 0.4603

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

  1. XBB = 0.9070
  2. XBF = 0.8366
  3. XBH = 0.6339
  4. XBD = 0.6014

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. XBD = 0.4677
  8. XBH = 0.4603
  9. XBB = 0.4069

Alleles

XBH is successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/proposed1229/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 \
  --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/proposed1229/sc2rf/stats.voc.csv

image

Breakpoints

Breakpoint 1: 20236:22000

breakpoints_clade

Tasks

ktmeaton commented 1 year ago

Now designated as XBH.