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ktmeaton / ncov-recombinant

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
MIT License
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proposed1658 | BQ.1.8, XBF(?) or CJ.1(?) #233

Open ktmeaton opened 1 year ago

ktmeaton commented 1 year ago

Parents

Clade: BA.5.3,CJ.1 Lineage: BQ.1.8*,BA.2* Lineage Confidence: 0.993,0.977

Immunity

RBD Level: 6 RBD Substitutions: S:K444T,S:L452R,S:N460K,S:F486P,S:F490S,S:R493Q Immune Escape: 0.7621 ACE2 Binding: 0.8882

Immune Escape Ranking

Higher values indicate an increased capacity to evade antibodies.

TBD

ACE2 Binding Ranking

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

TBD

Alleles

proposed1658 is successfully detected with the sc2rf mode for voc-2022 and voc-2023:

The second parent could be CJ.1 (BA.2.75.3*):

image

Or the second parent could be XBF :

image

And is less likely to be XBB:

image

Breakpoints

Breakpoint 1: 22918:23018

breakpoints_clade

Tasks

ktmeaton commented 1 year ago

The genetic similarities between XBB, XBF, and CJ.1 are going to cause problems for identifying diagnostic mutations when I next update the sc2rf mutation frequencies. This will also impact #234.