Deep mutational scanning of SARS-CoV-2 Omicron BA.1 spike using a barcoded lentiviral platform

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

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.

• Analyze PacBio CCSs
• Build PacBio consensus sequences
• Build the codon variants
• Counts of variants
• Functional scores of variants for viral entry
• Fit global epistasis models
• Functional effects of mutations averaged across replicates
• Probabilities of escape and neutralization in antibody selections
• Fit polyclonal models
• Antibody-escape averaged across replicates
• Validation neutralization assays versus polyclonal fits
• Compare functional effects of mutations to other data

Data files

• parental gene sequence

• parental protein sequence

• sequential-to-reference site numbers

• codon-variant table

• processed barcode sequencing runs

• variant counts

• functional selection experiments

• mutation effects for each functional selection

• mutation functional effects replicate average (observed phenotype)

• mutation functional effects replicate average (latent phenotype)

• antibody selection experiments

• antibody escape values

• sequential to reference site numbering

• natural evolution enrichment vs DMS

Interactive plots of mutation functional effects

• Observed phenotype effects

• Latent phenotype effects

Interactive plots of mutation antibody escape

• 268C.59A escape plot

• CC25.103 escape plot

• CC25.43 escape plot

• CC67.105 escape plot

• CC9.104 escape plot

• CC95.102 escape plot

• LyCoV-1404 escape plot

• NTD 5-7 escape plot

• SD1 12-19 escape plot

Additional plots

• natural enrichment versus DMS