Polyvalent vaccine approaches to combat HIV-1 diversity

Abstract

A key unresolved challenge for developing an effective HIV-1 vaccine is the discovery of strategies to elicit immune responses that are able to cross-protect against a significant fraction of the diverse viruses that are circulating worldwide. Here, we summarize some of the immunological implications of HIV-1 diversity, and outline the rationale behind several polyvalent vaccine design strategies that are currently under evaluation. Vaccine-elicited T-cell responses, which contribute to the control of HIV-1 in natural infections, are currently being considered in both prevention and treatment settings. Approaches now in preclinical and human trials include full proteins in novel vectors, concatenated conserved protein regions, and polyvalent strategies that improve coverage of epitope diversity and enhance the cross-reactivity of responses. While many barriers to vaccine induction of broadly neutralizing antibody (bNAb) responses remain, epitope diversification has emerged as both a challenge and an opportunity. Recent longitudinal studies have traced the emergence of bNAbs in HIV-1 infection, inspiring novel approaches to recapitulate and accelerate the events that give rise to potent bNAb in vivo. In this review, we have selected two such lineage-based design strategies to illustrate how such in-depth analysis can offer conceptual improvements that may bring us closer to an effective vaccine.

Keywords: AIDS; B cells; antibodies; antigens/peptides/epitopes; vaccination; viral.

Figure 1

The diversity of HIV‐1 Env and Gag considered in terms of epitope‐length fragments (9‐mers). The left‐hand panels (A and C) summarize the frequency of each unique 9‐mer in the global 2015 HIV M group alignments curated at the Los Alamos database (http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html, 08/31/2015). Note the log scale on the y‐axis. While the overall distribution is captured here, the very high numbers of completely unique epitopes that was brought out in the main text are difficult to discern, as the green line corresponding to number of distinct 9‐mers that are only repeated once is very thin and on the extreme left. There are, precisely, 89 957 9‐mers only found once of 136 828 unique 9‐mers found in 4500 Gag sequences, and 556 401 9‐mers found only once out of 719 578 unique 9‐mers among 4600 Env sequences. The right‐hand panels (B and D) show the coverage, as number of perfect 9‐mer matches, that can be obtained with a 3‐valent antigen vaccine. The coverage distribution shown in grey is based on 1000 trials, each a random selection of three natural strains from the data set, as a putative polyvalent immunogen. The best 9‐mer coverage possible is indicated by a red line, and the median value for the set is noted. The coverage achieved by a 3‐valent Epigraph vaccine is indicated by the blue line, and is expected to be comparable to a Mosaic design. The new epigraph tool suite was used to create this figure20

Figure 2

(A) Contact regions of representative bNAbs that bind four regions commonly targeted by bNAbs isolated from different individuals. The contact regions are shown on the crystal structure of a subtype G Env SOSIP trimer60 (PDB: 5FYJ), colored according to the bNAb epitope, with different colors for overlapping contact sites of multiple bNAbs. For calculations of bNAb contact regions, crystal structures for antibodies CH235.1268 (PDB:5F96), PGT12889 (PDB: 5C7K) and 10E890 (PDB:4G6F), and a structural model for CAP256‐VRC26.0962 were used. A generous cutoff of 8.5 Å between heavy atoms of antibody and Env was used to define contacts, so as to capture the full region where Env amino acid substitutions might directly impact binding. For 10E8, the core epitope is an alpha helix between positions 671‐683 in HIV‐1; this region is not part of the trimer structure used here. HXB2 positions 656‐665 are highlighted here, however, as 10E8 contacts sites, since they are in the structure and within 8.5 Å of the bound 10E8 surface. (B) Sequence entropy of bNAb contact sites. Env sequences from a often‐used 207 M‐group virus neutralization panel were used to calculate sequence entropy, and deletions were included in the entropy calculation. Entropy scores are mapped on the crystal structure for a subtype G Env SOSIP trimer60 (PDB:5FYJ) and the MPER peptide90 (PDB:4G6F) using the color scheme indicated, which uses blue for low entropy (high sequence conservation), yellow for intermediate entropy and red for high entropy (high sequence variation). The view of CAP256‐VRC26.09 contacts is from the top as in right panel in (A). Hyp = hypervariable

Figure 3

Env diversity in subject CH505 accompanies development and expansion of heterologous neutralization breadth. (Left) Frequency of mutations among sites in CH505 sequences with at least 80% TF loss in any time point sampled through week 160; these are the sites we consider candidates for being under the greatest selective pressure from the immune response. (Right) Breadth develops over longitudinal plasma neutralization ID50s against Tier 1 (autologous CH0505.TF, then B|SF162 through B|BG1168) and Tier 2 (A|Q842.d12 through B|AC10.0.29) Env‐pseudotyped viruses. Heatmaps summarize neutralization ID ₅₀ values

Figure 4

Env mutations, antibody binding phenotypes, and the phylogeny representing CH505 sequences selected for immunological testing. (A) Accruing mutations among a subset of 32 LASSIE selected gp120 sites are indicated as colored boxes. Blanks match the TF, red and blue depict negative and positive charge change, black shows insertions/deletions, cyan a gain of an asparagine in a potential N‐linked glycosylation motif, and gray shows other mutations. (B) Log AUCs of ELISA binding are displayed as heatmaps to show the relative affinities for the CH235 and CH103 bNAb lineage members, one column per antibody and one row per Env. Deeper reds indicate higher affinity, gray undetected. Each row in this figure follows the ordering of leaves in the tree on the right (C), which was made by maximum likelihood (in phyML, with HIVw+g4+I) from gp120 sequences. The CH505 TF sequence was used to root the tree. Note that these sequences were selected for experimental evaluation prior to the availability of LASSIE. The six lineage‐based Envs [ref. 68] are outlined

Figure 5

(A) Sequence logos summarize variant amino acid frequency in 35 sites selected for having high TF loss in CH505. The CH505 TF is shown at the top. The letter O represents an asparagine in a potential N‐linked glycosylation motif. A grey box is a gap. Red indicates a positively charged amino acid; blue, negative; and black, all other amino acids. The sites shown are the 35 sites selected by LASSIE for evidence of positive selection over time in CH505. In the sequence logo plots, white space stands in for the TF amino acids at the top; these are left out of the logo to emphasize differences. The height of the letter in the sequence logo indicates the frequency in the population. (B) Sequential and cumulative diversity increase for swarm immunization illustrated using a CH505 example. A priming immunization for a lineage‐based vaccine modeled on CH505 includes 3 Envs, the TF Env, plus two addition Envs with single mutations introduced that increase binding susceptibility in the Loop D of the CD4 binding site.68 In subsequent boosts, the 54 swarm immunogens selected using LASSIE would be divided into three sets of 18 each, the first set (a) the least diverse and favoring earlier time, with the subsequent two sets (b and c) to represent increasing divergence sampled over time in the subject

Figure 6

Structural mapping of global sequence coverage at V3 glycan bNAb contact sites by candidate vaccine immunogens. Position‐wise sequence coverage is calculated as the percentage of sequences in a commonly used 207 M‐group virus neutralization panel that have the same amino acid as at least one of the sequences for a given vaccine strategy. Vaccine strategies considered are: Con‐S, an M group consensus; the CH848 is a 5‐valent CH848/DH270 lineage‐based design, and a 3 valent Env mosaic.36 Con S and the mosaic Envs are currently being evaluated in the HVTN106 Phase I human trial. Color‐coding for sequence coverage is indicated by the color bar, with red shades indicating low, yellow indicating intermediate and blue indicating high sequence coverage. Crystal structure for a subtype G Env SOSIP trimer60 (PDB:5FYJ) was used, and PGT128 contacts from Figure 2 are used. This figure shows a close‐up view of the PGT128 contacts as in Figure 1B