Deep mutational scanning of SARS-CoV-2 XBB.1.5 spike using a barcoded lentiviral platform

Analysis by Dadonaite et al, Nature (2024) (2023)

See https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS for full code.

Contents

Barcode to codon-variant lookup table

Analysis notebooks

Data files

Count barcodes for variants

Analysis notebooks

Data files

Functional effects of mutations

Final summary plots

Analysis notebooks

Data files

Antibody/serum escape

Final summary plots

Analysis notebooks

Data files

ACE2 binding

Final summary plots

Analysis notebooks

Data files

Summary of results across assays

Final summary plots

Data files

Additional files and charts

Analysis of escape and other properties at key sites

Analysis of ACE2 binding data and comparison to other experiments

Comparison of escape in medium and high ACE2 cells

Comparison of escape in full-spike and RBD deep mutational scans

DMS measurements versus clade growth (XBB clades)

DMS measurements versus clade growth (BA.2, BA.5, and XBB clades)

Comparison of growth rates estimated by Murrell and Bedford groups

Comparison to BA.2.86 evolution

Escape stratified by one or multiple prior infections

Analysis of mutational effects on cell entry

ACE2 binding effects of non-RBD mutations in natural sequences

Spike site numbering