Deep mutational scanning of barcoded A/HongKong/45/2019

This page documents the data analysis. For the actual code, see https://github.com/dms-vep/flu_h3_hk19_dms

Study by Frances Welsh and Jesse Bloom.

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
• Process data from Perth/2009 HA
• Generate a file with all age cohort escape data from A/Hong Kong/45/2019 H3 HA

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

• escape for Perth2009 DMS

• escape for HongKong/2019 DMS

Interactive plots of mutation functional effects

• Observed phenotype effects

• Latent phenotype effects

Interactive plots of mutation antibody escape

• 150C escape plot

• 18C escape plot

• 197C escape plot

• 199C escape plot

• 210C escape plot

• 215C escape plot

• 2323 escape plot

• 2343 escape plot

• 2350 escape plot

• 2365 escape plot

• 2367 escape plot

• 2380 escape plot

• 2382 escape plot

• 2388 escape plot

• 2389 escape plot

• 2462 escape plot

• 2463 escape plot

• 33C escape plot

• 34C escape plot

• 3856 escape plot

• 3857 escape plot

• 3862 escape plot

• 3866 escape plot

• 3895 escape plot

• 3944 escape plot

• 3973 escape plot

• 4299 escape plot

• 4584 escape plot

• 68C escape plot

• 74C escape plot

• AUSAB-13 escape plot