Quantitative assessment of masking of neutralization epitopes in HIV-1

Abstract

Despite the frequent observation of masking of HIV-1 neutralization epitopes, its extent has not previously been systematically assessed either for multiple epitopes presented by individual viruses or for individual epitopes across multiple viral strains. Using a recently developed method to identify amino acid sequence motifs required for recognition by HIV-1-neutralizing monoclonal antibodies (mAbs), we visualized the patterns of masking of specific epitopes targeted by mAbs in a diverse panel of HIV-1 isolates. We also calculated a specific masking intensity score for each virus based on the observed neutralization activity of mAbs against the epitopes in the virus. Finally, we combined these data with estimates of the conservation of each mAb-targeted epitope in circulating HIV-1 strains to estimate the effective neutralization potential (EN) for each mAb. Focusing on the V3 loop of gp120 as a prototype neutralization domain, we found that the V3 loop epitope targeted by mAb 2219 is one of the least masked mAbs and it has the highest EN. Interestingly, although the V3 loop epitope targeted by mAb 3074 is present in over 87% of all viruses, it is 82.2% masked, so its EN is lower than that for mAb 2219. Notably, 50% of the viruses that mAb 3074 is able to neutralize are classified as subtype C viruses, while 70% or more of the viruses neutralized by mAbs 2219, 2557 or 447-52D are classified as subtype B. Thus, neutralization epitopes (in this case, in the V3 loop) have differential patterns of masking and also display distinct patterns of distribution among circulating HIV-1 viruses. Both factors combine to contribute to the practical vaccine value of any single epitope/mAb. Here we have developed a quantitative score for this value. These results have important implications for rational design of vaccines designed to induce neutralizing Abs by revealing epitopes that are minimally masked and maximally reactive with neutralizing Abs.

Cross-Clade HIV-1 Neutralizing Antibodies Induced with V3-Scaffold Protein Immunogens following Priming with gp120 DNA

“…While the field currently understands neither the physicochemistry nor the biology underlying the relative sensitivity or resistance of a given HIV strain to Abmediated neutralization, in the case of V3, we know that Abs may fail to neutralize a virus even if the cognate epitope is present, a phenomenon attributable to conformational masking (1,39); this precludes a clear correlation between the boosting immunogen and the V3 sequence of the viruses neutralized. Nonetheless, there is an indication that the V3 2219 -and V3 3074 -CTB boosting immunogens induced polyclonal Abs with specificities and activities similar to those of the MAbs that gave rise to the epitope-scaffold immunogen designs (T. Cardozo et al, submitted for publication).…”

The presence of glutamine at position 315 but not epitope masking predominantly hinders HIV subtype C neutralization by the anti-V3 antibody B4e8

“…The third variable (V3) region is one of the first neutralizing antibody (nAb) targets during infection with HIV subtype B but, strikingly, not other subtypes (reviewed in (Overbaugh and Morris, 2012)), suggesting relative differences in V3 exposure in the context of subtype B versus non-subtype B viruses. There has been much skepticism towards targeting V3 in a vaccine formulation because of the general inability of V3-specific monoclonal antibodies (mAbs) to neutralize viral isolates across many different subtypes (Agarwal et al, 2011; Binley et al, 2004; Cardozo et al, 2009; Eda et al, 2006; Zolla-Pazner et al, 2004). …”

“…The limited neutralization breadth of V3 mAbs is often attributed to masking of the V3 region by other variable loops, particularly V1V2 (Agarwal et al, 2011; Hatada et al, 2010; Krachmarov et al, 2006; Liu et al, 2011; Rusert et al, 2011; Sagar et al, 2006; Saunders et al, 2005; van Gils et al, 2011). Because the V3 region is more conserved in non-subtype B viruses than subtype B viruses, there has been a tendency to assume that V3 is masked to a greater extent in non-subtype B viruses (Hartley et al, 2005).…”

“…Because the V3 region is more conserved in non-subtype B viruses than subtype B viruses, there has been a tendency to assume that V3 is masked to a greater extent in non-subtype B viruses (Hartley et al, 2005). Indeed, many well-characterized V3 mAbs preferentially neutralize subtype B viruses or chimeric viruses containing subtype B-derived V3 sequences (Agarwal et al, 2011; Almond et al, 2012; Corti et al, 2010; Krachmarov et al, 2006; Pantophlet et al, 2007; Salomon et al, 2014). However, the V3 region, along with the V1V2 variable regions, has re-gained interest over the last few years as a possible target for vaccine design.…”

Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL

“…However, these V3-specific MAbs neutralize mainly the relatively sensitive tier 1 viruses and are ineffective against tier 2 and tier 3 isolates (2,26,32). The failure of anti-V3 MAbs to neutralize tier 2 and tier 3 viruses in the face of recognition of their corresponding soluble gp120 proteins indicates that V3 epitopes are present but inaccessible on the functional Env spikes on the virions (33,34). Nonetheless, there are distinct epitopes on the V3 loop (17,35).…”