Closed ktmeaton closed 1 year ago
Clade: Omicron/BA.2/21L,Omicron/BA.5/22B Lineage: BA.2.3*,BA.5.2* Lineage Confidence: 0.996,0.979
Omicron/BA.2/21L
Omicron/BA.5/22B
BA.2.3*
BA.5.2*
0.996
0.979
RBD Level: 5 RBD Substitutions: S:K444R,S:N450D,S:L452M,S:N460K,S:R493Q Immune Escape: 0.5925 ACE2 Binding: 1.0634
S:K444R
S:N450D
S:L452M
S:N460K
S:R493Q
0.5925
1.0634
Higher values indicate an increased capacity to evade antibodies.
0.9070
0.8366
0.6339
0.6014
0.5283
Higher values indicate an increased capacity for viral entry into the host cell.
XBJ is successfully detected with the sc2rf mode for omicron_omicron:
XBJ
sc2rf
omicron_omicron
python3 sc2rf/sc2rf.py results/proposed1268/nextclade/alignment.fasta \ --max-name-length 50 \ --clades BA.1 BA.2 BA.4 BA.5 \ --ansi \ --parents 2-4 \ --breakpoints 0-10 \ --unique 1 \ --max-ambiguous 20 \ --max-intermission-length 2 \ --max-intermission-count 3 \ --ignore-shared \ --mutation-threshold 0.25 \ --csvfile results/proposed1268/sc2rf/stats.omicron_omicron.csv
XBJ is also successfully detected with the sc2rf mode for VOC:
VOC
python3 sc2rf/sc2rf.py results/proposed1268/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/proposed1268/sc2rf/stats.voc.csv
This is an extraordinarily narrow breakpoint, almost suspiciously so. The alternative breakpoint 23019:25170 is reported by the sc2rf mode VOC between BA.2.3.20* and BA.5.2* and might be more reliable and specific.
23019:25170
BA.2.3.20*
Breakpoint 1: 23019:23039 Breakpoint 1 Alt: 23019:25170
23019:23039
resources/breakpoints.tsv
This is upgraded from proposed1268 to XBJ.
Parents
Clade:
Omicron/BA.2/21L
,Omicron/BA.5/22B
Lineage:BA.2.3*
,BA.5.2*
Lineage Confidence:0.996
,0.979
Immunity
RBD Level: 5 RBD Substitutions:
S:K444R
,S:N450D
,S:L452M
,S:N460K
,S:R493Q
Immune Escape:0.5925
ACE2 Binding:1.0634
Immune Escape Ranking
0.9070
0.8366
0.6339
0.6014
0.5925
0.5283
ACE2 Binding Ranking
1.0634
Alleles
XBJ
is successfully detected with thesc2rf
mode foromicron_omicron
:XBJ
is also successfully detected with thesc2rf
mode forVOC
:Breakpoints
This is an extraordinarily narrow breakpoint, almost suspiciously so. The alternative breakpoint
23019:25170
is reported by thesc2rf
modeVOC
betweenBA.2.3.20*
andBA.5.2*
and might be more reliable and specific.Breakpoint 1:
23019:23039
Breakpoint 1 Alt:23019:25170
Tasks
resources/breakpoints.tsv
Updated