Genome overview of P-values for associations of SNPs with HIV-1-specific cross-reactive neutralizing activity.

<p>Genome overview (A) and Major Histocompatibility Complex region (B).</p

P-values for different endpoints in survival analysis and viral load at set-point of top ranking SNPs associated in GWA study with HIV-1-specific cross-reactive neutralizing activity.

<p>P-values for different endpoints in survival analysis and viral load at set-point of top ranking SNPs associated in GWA study with HIV-1-specific cross-reactive neutralizing activity.</p

Quantile-Quantile Plot (Q-Q Plot) of P-values distribution from the GWAS on HIV-1 specific cross-reactive neutralizing activity.

<p>The comparison of the distribution of observed Chi-Square values against the theoretical model distribution of expected Chi-Square values is shown.</p

Heatmap and clustering analysis of HIV-1 specific cross-reactive neutralizing activity in serum.

<p>IC₅₀ values of sera from 292 HIV-1 infected individuals at ∼35 months post (imputed) seroconversion (rows) against 6 viral isolates (columns) are shown. Darker colors represent more potent neutralization. Kmeans clustering was performed on the rows and the columns and the rows/columns that fall in the same cluster are represented by the same colors on the row/column side bar. Patients with cross-reactive neutralizing activity (CrNA) cluster together in the upper heatmap and patients with no CrNA cluster in the bottom of the heatmap.</p

P-values for top ranking associations of SNPs with HIV-1-specific cross-reactive neutralizing activity, as well as P-values after correction for viral load and CD4⁺ T-cell count at set-point as covariates.

<p>Chr; chromosome.</p

Survival Analysis for the −2G/C Genotype in Combination with the 136Q Genotype

<p>Kaplan Meier analysis for time in years from seroconversion to AIDS according to the CDC 1993 definition. Bold black lines indicate individuals with the −2GG genotype; dashed black lines indicate individuals with the −2GC genotype; thin black lines indicate individuals with the −2CC genotype.</p

Survival Analysis for the H43Y Genotype

<p>Kaplan Meier analysis for time in years from seroconversion to AIDS according to the CDC 1987 definition (A), to AIDS according to the CDC 1993 definition (B), to CD4 count below 200 cells/μl blood (C), to viral RNA load above 10^4.5 copies per ml plasma (D), and to first detection of X4-variants (E) based on the H43Y genotype. Bold lines indicate individuals with the wild type genotype (43HH); dashed black lines indicate individuals heterozygous for the 43Y genotype (43HY); thin black lines indicate individuals homozygous for the 43Y genotype (43YY).</p

Analysis of Trim5α mRNA Levels in Naïve and Memory CD4 T Cells

<div><p>(A) Trim5α mRNA levels in naïve CD4 T cells (CD45RO-CD27+) and memory CD4 T cells (CD45RO+) obtained from healthy controls.</p><p>(B) Average Trim5α mRNA levels in naïve and memory CD4 T cells during the course of infection from HIV-1 infected individuals. Trim5α mRNA levels are normalized for β-actin mRNA levels. Different symbols represent Trim5α mRNA levels of naïve and memory CD4 T cells from the different individuals.</p></div

MOESM5 of HIV-1 escapes from N332-directed antibody neutralization in an elite neutralizer by envelope glycoprotein elongation and introduction of unusual disulfide bonds

Additional file 5: Figure S5. Schematic representation of the V1V2 loop observed in D16916. Schematic of the V1V2 loops based on Bontjer et al. [125]. Cysteine residues and disulfide bridges are indicated in red. The variable loops are depicted in yellow and the conserved bridging sheet β-strands 2 and 3, are indicated in green. (A) V1V2 loop containing the normal number of cysteine residues. (B) V1V2 loop with 2 additional cysteine and adjacent residues, forming an “oven mitt” structure. (C) V1V2 loop with 2 additional cysteine and adjacent residues, resulting in a longer V1 compared to (A). (D-E) V1V2 with 4 additional cysteine and adjacent residues forming two “oven mitt” structures, (F) or an alternative structure

MOESM4 of HIV-1 escapes from N332-directed antibody neutralization in an elite neutralizer by envelope glycoprotein elongation and introduction of unusual disulfide bonds

Additional file 4: Figure S4. bNAb epitopes and the corresponding viral sequence alignment. Amino acid sequences of bNAb epitopes for isolates from 7 and 11 months post-SC. Contact residues (<5.0 Å distance from gp120 residues based on the crystal structures of gp120-bNAb co-complexes [60, 121, 122, 124] are indicated with black dots for (A) PGT135, (B) b12 (grey), 12A21 and (C) PG16