Deep mutational scanning of HIV Envelope BF520 with anti-CD4 binding site sera and antibodies

This page documents the data analysis. For the actual code, see https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera

Study by Caelan Radford, Jesse Bloom, et al. See the pre-print here (https://www.biorxiv.org/content/10.1101/2023.03.23.533993v1).

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
• Functional scores of variants for viral entry
• Fit global epistasis models
• Functional effects of mutations across replicates
• Counts of variants
• Probabilities of escape and neutralization in antibody selections
• Fit polyclonal models
• Antibody-escape averaged across replicates
• Validation neutralization assays versus polyclonal fits
• Mutation effects compared to natural sequence variation

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

• PDB with 1-18 escape values as b factors

• PDB with 3BNC117 escape values as b factors

• PDB with PGT151 escape values as b factors

• PDB with IDC561 escape values as b factors

• PDB with IDC513 escape values as b factors

• PDB with IDC508 escape values as b factors

• PDB with IDF033 escape values as b factors

Interactive plots of mutation functional effects

• Observed phenotype effects

• Latent phenotype effects

Interactive plots of mutation antibody escape

• 1-18 escape plot

• 3BNC117 escape plot

• IDC508 escape plot

• IDC513 escape plot

• IDC561 escape plot

• IDF033 escape plot

• PGT151 escape plot