Deep mutational scanning of how mutations to the influenza HA from A/American Wigeon/South Carolina/USDA-000345-001/2021 (H5N1) affect its interaction with tufted duck MHC-II
Analysis by Dadonaite et al (2026)
See https://github.com/dms-vep/Flu-H5N1-American-Wigeon-2021-HA-tufted-duck-MHCII-DMS for full code.
Documentation of results rendered as of Wed Jul 22 14:42:11 2026
Barcode to codon-variant lookup table
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 functional effects from single-mutant variants only (click triangle to expand/collapse)
Interactive plots of differences in functional effects between conditions (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 taking differences in functional effects between conditions (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 functional effects from single-mutant variants only (CSV files) (click triangle to expand/collapse)
Average mutation latent-phenotype effects (CSV files) (click triangle to expand/collapse)
Differences in functional effects (CSV files) (click triangle to expand/collapse)
MHCII binding
Final summary plots
MHCII binding mutation effect plots (click triangle to expand/collapse)
Analysis notebooks
Fits of polyclonal models to individual MHCII binding selections (click triangle to expand/collapse)
Average selections for MHCII binding (click triangle to expand/collapse)
Data files
Probability (fraction) escape for each variant in each MHCII binding selection (CSVs) (click triangle to expand/collapse)
MHCII binding CSVs (click triangle to expand/collapse)
Integrated summary plots
entry all cells
tufted duck MHCII binding
Compare entry among cells
Final plots
Analysis notebooks
Data files
Row-wrapped heatmaps
Heatmap HTMLs
dms-viz visualizations
dms-viz JSON files
Notebooks prepping dms-viz JSONs
Additional files
HA site numbering
Additional plots
Entry titers measured for pseudoviruses with specific HAs from natural strains
Interactive charts
- H5 HAs, titers normalized to noSA cells (horizontal)
- H5 HAs, titers normalized to noSA cells (vertical)
- H5 HAs, raw titers (horizontal)
- H5 HAs, raw titers (vertical)
- H1 HAs, titers normalized to noSA cells (horizontal)
- H1 HAs, titers normalized to noSA cells (vertical)
- H1 HAs, raw titers (horizontal)
- H1 HAs, raw titers (vertical)
- H2 HAs, titers normalized to noSA cells (horizontal)
- H2 HAs, titers normalized to noSA cells (vertical)
- H2 HAs, raw titers (horizontal)
- H2 HAs, raw titers (vertical)
- H3 HAs, titers normalized to noSA cells (horizontal)
- H3 HAs, titers normalized to noSA cells (vertical)
- H3 HAs, raw titers (horizontal)
- H3 HAs, raw titers (vertical)
Numerical titers