Deep mutational scanning of Junin virus Romero strain glycoprotein using a barcoded lentiviral platform

Analysis by Caleb Carr and Jesse Bloom (2026)

See https://github.com/dms-vep/JUNV-Romero-GPC-DMS for full code.

Documentation of results rendered as of Thu Oct 8 14:23:16 2026

Barcode to codon-variant lookup table

Analysis notebooks

• Analysis of PacBio CCSs
• Building barcoded variant consensus sequences
• Building of codon-variant table

Data files

• parental codon sequence
• parental protein sequence
• barcode to codon-variant lookup table

Count barcodes for variants

Analysis notebooks

• Analysis of variant counts

Data files

• Barcode count CSVs (click triangle to expand/collapse)

  • LibA-260430-VSVG-1
  • LibB-260430-VSVG-1
  • LibA-260506-pH-4.9-1
  • LibA-260506-pH-5.1-1
  • LibA-260506-pH-5.3-1
  • LibA-260506-pH-5.7-1
  • LibA-260506-pH-6.1-1
  • LibA-260506-pH-pbs-1
  • LibB-260506-pH-4.9-1
  • LibB-260506-pH-5.1-1
  • LibB-260506-pH-5.3-1
  • LibB-260506-pH-5.7-1
  • LibB-260506-pH-6.1-1
  • LibB-260506-pH-pbs-1
  • LibA-260516-293T-TFRC-KO-C_callosus-1
  • LibA-260516-293T-TFRC-KO-C_musculinus_EU164541-1
  • LibB-260516-293T-TFRC-KO-C_callosus-1
  • LibB-260516-293T-TFRC-KO-C_musculinus_EU164541-1

Functional effects of mutations

Final summary plots

• Interactive plots of average mutation functional effects (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Interactive plots of average mutation functional effects from single-mutant variants only (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Interactive plots of differences in functional effects between conditions (click triangle to expand/collapse)

  • C_musculinus_vs_C_callosus
  • C_musculinus_vs_C_callosus correlation chart
• Interactive plots of average shifts in functional effects (click triangle to expand/collapse)

  • TfR1_comparison

Analysis notebooks

• Analysis of functional scores
• Notebooks with per-selection global epistasis fitting (click triangle to expand/collapse)

  • LibA-260516-293T-TFRC-KO-C_musculinus-1
  • LibB-260516-293T-TFRC-KO-C_musculinus-1
  • LibA-260516-293T-TFRC-KO-C_callosus-1
  • LibB-260516-293T-TFRC-KO-C_callosus-1
• Notebooks averaging mutation functional effects (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Notebooks taking differences in functional effects between conditions (click triangle to expand/collapse)

  • C_musculinus_vs_C_callosus
• Notebooks fitting shifts in functional effects (click triangle to expand/collapse)

  • LibA
  • LibB
• Notebooks averaging shifts in functional effects (click triangle to expand/collapse)

  • TfR1_comparison

Data files

• Per-variant functional score CSVs (click triangle to expand/collapse)

  • LibA-260516-293T-TFRC-KO-C_musculinus-1
  • LibB-260516-293T-TFRC-KO-C_musculinus-1
  • LibA-260516-293T-TFRC-KO-C_callosus-1
  • LibB-260516-293T-TFRC-KO-C_callosus-1
• Per-selection mutation functional effect CSVs (click triangle to expand/collapse)

  • LibA-260516-293T-TFRC-KO-C_musculinus-1
  • LibB-260516-293T-TFRC-KO-C_musculinus-1
  • LibA-260516-293T-TFRC-KO-C_callosus-1
  • LibB-260516-293T-TFRC-KO-C_callosus-1
• Average mutation functional effects (CSV files) (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Average mutation functional effects from single-mutant variants only (CSV files) (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Average mutation latent-phenotype effects (CSV files) (click triangle to expand/collapse)

  • 293T-TFRC-KO-C-callosus-TfR1
  • 293T-TFRC-KO-C-musculinus-TfR1
• Differences in functional effects (CSV files) (click triangle to expand/collapse)

  • C_musculinus_vs_C_callosus
• Per-condition functional effect shifts CSVs (click triangle to expand/collapse)

  • LibA
  • LibB
• Average shifts in functional effects (CSV files) (click triangle to expand/collapse)

  • TfR1_comparison

Stability

Final summary plots

• stability mutation effect plots (click triangle to expand/collapse)

  • stability

Analysis notebooks

• Fits of polyclonal models to individual stability selections (click triangle to expand/collapse)

  • LibA-260506-pH-1
  • LibB-260506-pH-1
• Average selections for stability (click triangle to expand/collapse)

  • stability

Data files

• Probability (fraction) escape for each variant in each stability selection (CSVs) (click triangle to expand/collapse)

  • LibA-260506-pH-1 LibA-260506-pH-6.1-1
  • LibA-260506-pH-1 LibA-260506-pH-5.7-1
  • LibA-260506-pH-1 LibA-260506-pH-5.3-1
  • LibA-260506-pH-1 LibA-260506-pH-5.1-1
  • LibA-260506-pH-1 LibA-260506-pH-4.9-1
  • LibB-260506-pH-1 LibB-260506-pH-6.1-1
  • LibB-260506-pH-1 LibB-260506-pH-5.7-1
  • LibB-260506-pH-1 LibB-260506-pH-5.3-1
  • LibB-260506-pH-1 LibB-260506-pH-5.1-1
  • LibB-260506-pH-1 LibB-260506-pH-4.9-1
• stability CSVs (click triangle to expand/collapse)

  • stability

Integrated summary plots

entry 293T-various-TfR1s

• Summary plot
• CSV summarizing results

cell entry and pH stability

• Summary plot
• CSV summarizing results

dms-viz visualizations

dms-viz JSON files

• func_effects
• pH_stability

Notebooks prepping dms-viz JSONs

• func_effects
• pH_stability

Additional analyses and data files

Variant mutation analysis

• Notebook creating altair version of mutation distribution

Compare cell entry

• Scatter plots of mutation effects in different cells
• Zoomable site chart of differences

Row-wrapped heatmaps

• entry_in_C_musculinus_TfR1
• entry_in_C_callosus_TfR1
• pH_stability
• pH_core
• pH_intersubunits
• pH_transmembrane_domain
• pH_stabilizing_candidates

Map DMS scores onto PDB structure

• Notebook mapping scores onto pdb structure

Analyze DMS scores for specific GPC regions

• Notebook analyzing specific GPC regions and DMS scores

Compare DMS scores to natural GPC sequences

• Notebook analyzing DMS scores of natural GPC mutations