Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors

The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures –8 determined here– of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

<div><p>The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or “signatures” and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.</p></div

Vaccine protein signature sites AA distributions.

<p>For the vaccine protein signature sites shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003973#pcbi.1003973.g002" target="_blank">Fig. 2</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003973#pcbi.1003973.g003" target="_blank">Fig. 3</a> shows distributions of amino acids relative to the vaccine sequences for vaccine versus placebo recipient sequences: Each subject is represented by a bar. Bars all have equal height. The vaccine sequence AA residue, in black, is shown above the midline. Within a bar, colors depict the fraction of the subject’s sequences with that AA residue (or insertion or deletion, indicated by a “−“). The widths of the bars are scaled so that the total width of the vaccine-recipient part of the plot is the same as for the placebo-recipient part.</p

Signature sites in vaccine proteins: 2-sided unadjusted p-values calculated by five methods.

<p>Signature sites in vaccine proteins: 2-sided unadjusted p-values calculated by five methods.</p

Vaccine efficacy at the signature sites in the vaccine proteins.

<p>¹HXB2 numbering</p><p>²The sieve effect was detected for the indicated vaccine sequence; for Env positions, these are 92TH023, CM244, both of the CRF01_AE sequences, the subtype B sequence MN, or all three. The corresponding vaccine amino acids are given after the colon. They are in parentheses if the effect was “vMismatch” (with greater divergence from vaccine AA among placebo recipients).</p><p>³Symmetrized estimated vaccine efficacies (for hazard ratio (HR) above 1, symmetrized VE = [1 − hazard ratio (HR)]×100%; for HR below 1, symmetrized VE = − [1 − (1/(HR))]×100%) to prevent infection with specific HIV-1 genotypes.</p><p>⁴The p-value for Env 379 was not calculable for the DVE method because one of the treatment groups (the vaccine-recipient group) exhibited no variation at the site.</p><p>Vaccine efficacy at the signature sites in the vaccine proteins.</p

Non-vaccine protein signature sites AA distributions: First half.

<p>For the first half of the non-vaccine protein signature sites shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003973#pcbi.1003973.g002" target="_blank">Fig. 2</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003973#pcbi.1003973.g004" target="_blank">Fig. 4</a> shows distributions of amino acids relative to the vaccine sequences for vaccine versus placebo recipient sequences: Each subject is represented by a bar. Bars all have equal height. The vaccine sequence AA residue, in black, is shown above the midline. Within a bar, colors depict the fraction of the subject’s sequences with that AA residue (or insertion or deletion, indicated by a “−“). The widths of the bars are scaled so that the total width of the vaccine-recipient part of the plot is the same as for the placebo-recipient part.</p

Analysis methods.

<p>Methods evaluate (1) differential deviation (vaccine versus placebo) from the immunogen sequences at specific loci or in peptide regions that are relevant to antibody binding; (2) differential codon selection, and differences in physico-chemical properties across vaccine and placebo; (3) differential vaccine efficacy versus HIV-1 sequences that do not match immunogen sequences at individual sites and in each of several pre-specified antibody-relevant protein regions; (4) greater or more rapid viral escape (vaccine versus placebo) at predicted class I and class II HLA-restricted T cell epitopes; and (5) differences in phylogenetic diversity of the breakthrough amino acid sequences (vaccine versus placebo) or differential evolutionary divergence from the vaccine immunogen sequences. T cell and tree images are from <a href="http://openclipart.org" target="_blank">openclipart.org</a>.</p

Vaccine efficacy at the signature sites in the non-vaccine proteins.

<p>¹HXB2 numbering</p><p>²The sieve effect was detected for the CRF01_AE consensus sequence. The corresponding vaccine amino acids are given after the colon. They are in parentheses if the effect was “vMismatch” (with greater divergence from the vaccine AA among placebo recipients).</p><p>³Symmetrized estimated vaccine efficacies (for hazard ratio (HR) above 1, symmetrized VE = [1 − hazard ratio (HR)]×100%; for HR below 1, symmetrized VE = − [1 − (1/(HR))]×100%) to prevent infection with specific HIV-1 genotypes.</p><p>⁴The p-values for Env 777 and Pol 497 were not calculable for the DVE method because one of the treatment groups (the vaccine-recipient group) exhibited no variation at these sites.</p><p>Vaccine efficacy at the signature sites in the non-vaccine proteins.</p