Fig. 5: Deep mutational scanning analyses reveal distinct viral escape from 007.
a, Logo plots showing effects of mutations on neutralization escape in HIV EnvTRO.11 for antibodies 007, 10-1074, BG18, PGT121 and PGT128. The height of each letter represents the effect of that amino acid mutation on antibody neutralization, with positive heights (letters above the zero line) indicating mutations that cause escape, and negative heights (letters below the zero line) indicating mutations that increase neutralization. Letters are colored by the effect of that mutation on Env-mediated cell entry function, with yellow corresponding to reduced cell entry and brown corresponding to neutral effects on cell entry. Only key sites are shown. See https://dms-vep.org/HIV_Envelope_TRO11_DMS_007/htmls/all_antibodies_and_cell_entry_overlaid.html for interactive versions of the escape maps that show all mutations. Escape maps against HIV-1 EnvBF520 are shown in Extended Data Fig. 8c. b, Scatter plots of EnvTRO.11 mutant fold-change IC50s measured by deep mutational scanning versus those measured in traditional neutralization assays. Each scatter plot shows log fold change IC50s for neutralization assays using the antibody labeling the logo plot in the same row. Each point represents the mean of two replicate neutralization curve measurements of one EnvTRO.11 mutant. EnvTRO.11 mutants are colored by Env region or site. Vertical dotted lines represent the limit of detection of the neutralization assays. See Methods, “Deep mutational scanning data analysis”, for details on how deep mutational scanning measured escape values are converted to deep mutational scanning measured IC50 values. The deep mutational scanning measured effects of mutations on escape from antibody 10-1074 shown in this figure were previously published41.
