Analysis by Dadonaite et al, bioRxiv, DOI 10.1101/2023.11.13.566961 (2023)
See https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_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 latent-phenotype effects (click triangle to expand/collapse)
Interactive plots of average shifts in functional 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)
Notebooks fitting shifts in functional effects (click triangle to expand/collapse)
Notebooks averaging shifts in 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 latent-phenotype effects (CSV files) (click triangle to expand/collapse)
Per-condition functional effect shifts CSVs (click triangle to expand/collapse)
Average shifts in functional 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)
Summary of results across assays
Final summary plots
Data files
Additional files and charts
Analysis of escape and other properties at key sites
Analysis of ACE2 binding data and comparison to other experiments
Comparison of escape in medium and high ACE2 cells
Comparison of escape in full-spike and RBD deep mutational scans
DMS measurements versus clade growth (XBB clades)
Comparison for current_dms (XBB clades) (click triangle to expand/collapse)
Comparison for yeast_RBD_DMS (XBB clades) (click triangle to expand/collapse)
Comparison for muts_from_Wuhan-Hu-1 (XBB clades) (click triangle to expand/collapse)
Comparison for EVEscape (XBB clades) (click triangle to expand/collapse)
Comparison for EVEscape_components (XBB clades) (click triangle to expand/collapse)
DMS measurements versus clade growth (BA.2, BA.5, and XBB clades)
Comparison for current_dms (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)
Comparison for yeast_RBD_DMS (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)
Comparison for muts_from_Wuhan-Hu-1 (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)
Comparison for EVEscape (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)
Comparison for EVEscape_components (BA.2, BA.5, and XBB clades) (click triangle to expand/collapse)
Comparison of growth rates estimated by Murrell and Bedford groups
Comparison to BA.2.86 evolution
Escape stratified by one or multiple prior infections
Analysis of mutational effects on cell entry
ACE2 binding effects of non-RBD mutations in natural sequences
Spike site numbering