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. 2021 Jan 11;10:e63444. doi: 10.7554/eLife.63444

Figure 9. Lineage 105 epitope largely remains stable over time.

(A–B) Heatmaps depict scaled differential selection: the relative effect of each possible substitution within the V3 region of Env (HXB2 numbering), compared to wild type BG505.W6M.C2 Env, on binding by (A) 105 inferred naïve mAb and (B) 105 mature mAb. Wild-type residues are indicated by black dots. Mutations enriched above the wild-type residue are colored blue while those depleted are colored red; color intensity reflects the relative amount of differential selection as indicated by the key. Data are the average of two biological replicates. See also Figure 9—figure supplement 1 for peptide enrichment plots and Figure 9—figure supplement 2 for scaled differential selection in C.ZA.1197MB Env. Figure 9—source code 1 and Figure 9—source datas 1–3 contain fold enrichment and scaled differential selection data and calculations. (C) Logo plots of the residues comprising the 105 lineage epitope amongst 28 total longitudinal QA255 Env sequences (GenBank MW383929-MW383956) using HXB2 numbering.

Figure 9—source code 1. R markdown file detailing and performing the analysis of Phage-DMS deep sequencing data in order to map antibody-targeted Env epitopes.
Figure 9—source data 1. CSV file required for R analysis: gp41V3_PhageDMS_library_key.
This file maps the numbering between each Env strain and the HXB2 reference strain.
Figure 9—source data 2. CSV file required for R analysis: Phage-DMS-105epitope-Rep1annotatedCounts.
This file contains raw counts of each sequence for each sample, with annotated information for each sequence and peptide (replicate 1).
Figure 9—source data 3. CSV file required for R analysis: Phage-DMS-105epitope-Rep2annotatedCounts.
This file contains raw counts of each sequence for each sample, with annotated information for each sequence and peptide (replicate 2).

Figure 9.

Figure 9—figure supplement 1. Phage-DMS peptide enrichment for 105 inferred naive and 105 mature mAbs.

Figure 9—figure supplement 1.

(A–B) Line plot showing fold enrichment of wild-type peptides in the background of each indicated HIV Env strain (see key) for (A) 105 inferred naive mAb and (B) 105 mature mAb. Data are the average of two biological replicates. Amino acid positions within HIV Env are numbered based on HXB2 reference sequence. Figure 9—source code 1 and Figure 9—source datas 1–3 contain fold enrichment and scaled differential selection data and calculations.
Figure 9—figure supplement 2. Lineage 105 epitope and predicted escape routes within C.ZA.1197MB Env.

Figure 9—figure supplement 2.

(A–B) Heatmaps depict scaled differential selection: the relative effect of each possible substitution within the V3 region of Env (HXB2 numbering), compared to wild-type C.ZA.1197MB Env, on binding by (A) 105 inferred naive mAb and (B) 105 mature mAb. Wild-type residues are indicated by black dots. Mutations enriched above the wild-type residue are colored blue while those depleted are colored red; color intensity reflects the relative amount of differential selection as indicated by the key. Data are the average of two biological replicates. Figure 9—source code 1 and Figure 9—source datas 1–3 contain fold enrichment and scaled differential selection data and calculations.