The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility

Abstract

Purpose of review: Designing an HIV vaccine capable of eliciting broadly cross-reactive neutralizing antibodies is an extraordinarily difficult challenge. Here we focus on the implications of HIV diversity for vaccine design, detailing the impact of levels of variation in epitopes of known potent neutralizing antibodies, and summarizing patterns of overall variation in regional domains within gp120. Strategies for rational vaccine design, to enhance coverage of HIV's natural diversity, are considered.

Recent findings: Each amino acid in an envelope gp120 three-dimensional structure was grouped with its 10 nearest neighbors and classified by their natural sequence variability. Within-subtype variation is superimposed on patterns of subtype-specific variation. Regions under selection with moderate diversity are realistic vaccine targets; their variation reflects the value of escape in these regions, whereas the level of diversity is potentially approachable with a vaccine.

Summary: HIV diversity is so extensive that vaccine design strategies may benefit by factoring in diversity from the earliest stages, even for vaccines that target relatively conserved regions.

Figure 1.. Phylogenetic relationships and epitope diversity.

This show a maximum likelihood tree of patient consensus sequences based on single genome amplified sequence sets from B or C subtype infections from subjects sampled very early in infection (Fiebig stages 1–4)^, . These sequences were selected because early within-patient consensus sequences are an excellent approximation of the transmitted virus, which are the most relevant vaccine targets. Adjacent to each terminal branch on the tree are alignments of the core epitopes of the 4 most studied monoclonal neutralizing antibodies, illustrating patterns of within-clade and between-clade diversity. 4E10 is the most broadly reactive Nab. The direct contact residues for this antibody have been mapped to 4 amino acids on a helical face of its core binding peptide NWFDIT: W672, F673, I675, and T676 and these amino acids are nearly perfectly preserved within the M group. The antibody tolerates Thr/Ser variation at position 676, and the 4E10 binding motif xWFxI[S/T] is highly conserved. Positions 671 and 673, designated “x” are quite variable, but that variation does appear to impact 4E10s cross-neutralizing prowess. There are rare exceptions to 4E10 susceptibility; for example in a virus from a subtype C infected patient, 4E10 resistance was observed due to a change in F673L, whereas 2F5 epitope was maintained. Neutralization by 2F5 antibody correlates with the presence of the LDKW motif at positions 663–666; a K to S change is very common in the C clade. 2G12 requires a set of non-contiguous N-linked glycosylation motifs (of the pattern Nx[ST]), and three critical motifs are shown here^, (the glycosylation sites at positions 295, 332, 392). One or both of the critical glycosylation motifs are lost in the majority of the C clade sequences. Discontinuous positions from the IgG1b12 binding site, the set listed in Table 1, are included here, with the exception of the sites T257, Y384 and P386 as these sites were invariant. There are scattered IgG1b12 epitope substitutions throughout the B and C clades, with distinctive patterns of variants populating subsets of the C clade.

Figure 2.. Variation in of epitope-like domains.

A local domain of 10 proximal amino acids was calculated centered on every position in the 395 amino acid stretch of gp120 included in the structure (which lacks the N- and C-terminal regions) described in the legend to Fig. 3. For part A, 395 mini-alignments, including only the positions included in each of the 395 10 amino acid local domains, were created from the B and C clade transmitted virus sequence alignment described in Fig. 1. The B consensus sequence was compared separately to B and C clade transmitted sequence sets, and the frequency of identities, 90% matches, and 80% matches was calculated for each of 395 local regions. The most to least conserved regions were plotted left to right. Local regions that are highly conserved are relatively rare, and the frequency of well-matched sequences rapidly drops off. Part B shows the overall fraction of perfectly conserved, 90% conserved, and 80% conserved local domains for either the B and C clade transmitted sequence sets when compared to the B or C consensus, a natural B clade strain (HXB2). Inter-clade coverage drops off dramatically, as seen in both part A and B, and HXB2 coverage of local regions is substantially reduced relative to consensus coverage.

Figure 3.. Lack of sequence conservation in immunogenic regions of Env.

The fraction of sequences that exhibit less or equal to a 420% mismatch within an epitope-like spatial cluster are shown when (i) the B consensus is compared to B acute sequences, (ii) B consensus was compared to C acute sequences, (iii) C consensus compared to C acutes, and (iv) C consensus compared to B acutes. The fractions are graphically mapped on a gp120 core backbone that corresponds CD4-liganded HIV-1 YU-2 gp120 structure with modeled V1V2 and V3 loops added as described previously.The loops are shown only to illustrate the regional sequence variation and they do not represent the actual dominant conformation. The color gradient is used to capture the sequence invariance with blue indicating conservation, with most sequences having less than a 20% mismatch, and red indicating high diversity, with most sequences having a 20% mismatch or more within the spatial cluster. The spatial clusters were gathered from the contact matrix obtained from the long timescale molecular dynamics simulations of gp120 of YU2 strain with modeled loops in explicit aqueous solvent^, . For each residue in the simulated structure a spatial cluster was generated such that it contained the top ten closest contact amino acids that fall within the average C-alpha distance cutoff of 10Å. A total of 395 such spatial clusters were generated corresponding to the total number of residues in the simulated gp120 structure.