Deep mutational scanning of SARS-CoV-2 Omicron BA.1 spike and mapping of escape mutations for COV2-2130 and its derivative antibody

This page documents the data analysis. For the actual code, see https://github.com/dms-vep/SARS-CoV-2_Omicron_BA.1_spike_DMS_COV2-2130

Study by Bernadeta Dadonaite and Jesse Bloom.

Workflow

Below is the rulegraph for the snakemake workflow. Click here for the more detailed filegraph.

Analysis notebooks

Many of the plots in these notebooks are interactive, so try mousing over points for details, using dropdowns, etc.

• Counts of variants
• Probabilities of escape and neutralization in antibody selections
• Fit polyclonal models
• Antibody-escape averaged across replicates
• Compare antibody neutralization values

Data files

• parental gene sequence

• parental protein sequence

• sequential-to-reference site numbers

• codon-variant table

• processed barcode sequencing runs

• variant counts

• antibody selection experiments

• antibody escape values

• sequential to reference site numbering

Interactive plots of mutation antibody escape

• 2130-1-0114-112 escape plot

• COV2-2130 escape plot

Additional plots

• COV2-2130_vs_2130-1-0114-112_escape