In this study, the authors describe a system that uses pseudovirus to perform deep mutational scanning on viral glycoproteins. They used this system to map escape from monocolonal antibodies against the full SARS-CoV-2 Spike protein.
The visualization above shows the total mutation-escape for each antibody on the Omicron BA1 Spike structure.
The configure-dms-viz command used to generate this visualization is:
configure-dms-viz format
--input tests/SARS2-Omicron-BA1-DMS/input/LyCoV-1404_avg.csv
--sitemap tests/SARS2-Omicron-BA1-DMS/sitemap/sitemap.csv
--output tests/SARS2-Omicron-BA1-DMS/output/LyCoV-1404_avg.json
--name "LyCoV-1404"
--metric "escape_mean"
--metric-name "Escape"
--structure "6xr8"
--included-chains "polymer"
--join-data tests/SARS2-Omicron-BA1-DMS/join-data/muteffects_observed.csv
--tooltip-cols "{'times_seen': '# Obsv', 'effect': 'Func Eff.'}"
--filter-cols "{'effect': 'Functional Effect', 'times_seen': 'Times Seen'}"
--title "LyCoV-1404"For more information about the study, check out the manuscript:
A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike
Bernadeta Dadonaite, Katharine H D Crawford, Caelan E Radford, Ariana G Farrell, Timothy C Yu, William W Hannon, Panpan Zhou, Raiees Andrabi, Dennis R Burton, Lihong Liu, David D. Ho, Richard A. Neher, Jesse D Bloom
To view the analysis pipeline and raw data, checkout the GitHub repository.