XBN | BA.2.75/XBB.3 - Githubissues

pango-designation issue: #1296
covSPECTRUM query: https://cov-spectrum.org/explore/World/AllSamples/AllTimes/variants?nucMutations=A2863G&nextcladePangoLineage=XBB*&

Parents

Clade: Omicron/BA.2.75/22D,Omicron/XBB/22F Lineage: BA.2.75*,BA.2* Lineage Confidence: 0.992,1.0

The second parental lineage (BA.2*) does not match the second parental clade (XBB). This is because the method for parental inference (covSPECTRUM LAPIS) does not have access to GISAID data. As a result, we don't yet have accurate allele frequencies for XBB. If I manually query cov-spectrum for the second parent's alleles, the second parent becomes unambiguously XBB*.

Lineage: BA.2.75*,XBB* Lineage Confidence: 0.992,0.9741

Parent 1 (BA.2.75*) | T670G,C2790T,C3037T,C3796T,C3927T,G4184A,C4321T,C4586T,C5183T
Parent 2 (XBB) | C12880T,C14408T,G15451A,C15714T,C15738T,T15939C,T16342C,C17410T,T17859C,A18163G,A19326G,C19955T,A20055G,C21618T,T21810C,G21987A,C22000A,C22109G,T22200A,G22577C,G22578A,G22599C,C22664A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,G22895C,T22896C,G22898A,T22942G,G22992A,C22995A,A23013C,T23019C,T23031C

Immunity

RBD Level: 7 RBD Substitutions S:R346T,S:V445P,S:G446S,S:N460K,S:F486S,S:F490S,S:R493Q Immune Escape: 0.9070 ACE2 Binding: 0.4069

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

proposed1296 = 0.9070
XBB = 0.9070
XBF = 0.8366

ACE2 Binding Ranking

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

XAK = 1.3244
XBF = 0.8366
XBC = 0.7927
XBE = 0.6697
XAY = 0.6144
XAV/XAS/XAZXAJ = 0.5583
XBD = 0.4677
proposed1296 = 0.4069
XBB = 0.4069

Alleles

proposed1296 is successfully detected with the sc2rf mode for VOC:

python3 sc2rf/sc2rf.py results/proposed1296/nextclade/alignment.fasta \
  --max-name-length 50 \
  --clades BA.2.10 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/proposed1296/sc2rf/stats.voc.csv

Breakpoints

Breakpoint #: 5184:12443

Nextclade calls this as XBB, while ncov-recombinant corrects this to XBB-like as the breakpoints and parents do not match the expected values for XBB.

breakpoints_clade

Tasks

[x] resources/breakpoints.tsv Updated

ktmeaton / ncov-recombinant

XBN | BA.2.75/XBB.3 #197