Analysis by Dadonaite et al (2025)
See https://github.com/dms-vep/SARS-CoV-2_KP.3.1.1_spike_DMS for full code.
Barcode to codon-variant lookup table
Analysis notebooks
Data files
Count barcodes for variants
Analysis notebooks
Data files
Barcode count CSVs (click triangle to expand/collapse)
Functional effects of mutations
Final summary plots
Interactive plots of average mutation functional effects (click triangle to expand/collapse)
Interactive plots of average mutation functional effects from single-mutant variants only (click triangle to expand/collapse)
Interactive plots of average mutation latent-phenotype effects (click triangle to expand/collapse)
Analysis notebooks
- Analysis of functional scores
Notebooks with per-selection global epistasis fitting (click triangle to expand/collapse)
Notebooks averaging mutation functional effects (click triangle to expand/collapse)
Data files
Per-variant functional score CSVs (click triangle to expand/collapse)
Per-selection mutation functional effect CSVs (click triangle to expand/collapse)
Average mutation functional effects (CSV files) (click triangle to expand/collapse)
Average mutation functional effects from single-mutant variants only (CSV files) (click triangle to expand/collapse)
Average mutation latent-phenotype effects (CSV files) (click triangle to expand/collapse)
Antibody/serum escape
Final summary plots
antibody escape mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual antibody escape selections (click triangle to expand/collapse)
Average selections for antibody escape (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each antibody escape selection (CSVs) (click triangle to expand/collapse)
antibody escape CSVs (click triangle to expand/collapse)
ACE2 binding
Final summary plots
ACE2 binding mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual ACE2 binding selections (click triangle to expand/collapse)
Average selections for ACE2 binding (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each ACE2 binding selection (CSVs) (click triangle to expand/collapse)
ACE2 binding CSVs (click triangle to expand/collapse)
Integrated summary plots
all adult sera escape
pre vaccination infection
post vaccination infection
pre infection
pre vaccination
post infection
post vaccination
sera group averages
antibody escape
Additional files and charts
Comparison of escape pre and post vaccination
Analysis of ACE2 binding data and comparison to other experiments
Analysis of mutational effects on cell entry
Interactive entry data charts (click triangle to expand/collapse)