XBH | BA.2.3.17/BA.2.75

pango-designation issue: #1229
covSPECTRUM query: TBD

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

Parent 1 (BA.2.3.17) | G4184A,C4321T,C9344T,A9424G,C9534T,C9866T,C10029T,C10198T,G10447A,C10449A,C12880T,C13730T,C14408T
Parent 2(BA.2.75*) | A22001G,T22016C,C22033A,A22190G,T22200G,G22331A,G22577C,G22578A,G22599C,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,G22898A,T22942G,G22992A,C22995A,A23013C,T23019C,A23055G,A23063T,T23075C,A23403G,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A,C25000T,C25416T,C25584T,C26060T,C26270T,A26275G

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.

XBB = 0.9070
XBF = 0.8366
XBH = 0.6339
XBD = 0.6014

ACE2 Binding Ranking

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

XAK = 1.3244
XBF = 1.0428
XBC = 0.7927
XBE = 0.6697
XAY = 0.6144
XAV/XAS/XAZXAJ = 0.5583
XBD = 0.4677
XBH = 0.4603
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

Breakpoints

Breakpoint 1: 20236:22000

breakpoints_clade

Tasks

[x] resources/breakpoints.tsv Updated

ktmeaton / ncov-recombinant

XBH | BA.2.3.17/BA.2.75 #198