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 been previously 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 (E(N)) 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 E(N). 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 E(N) 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.

Figure 1. Masking patterns for each virus across the four mAbs

Shown are the IC₅₀ values (concentration in ug/ml of the mAb required to achieve 50% viral neutralization) for four anti-V3 mAbs (3074, 2219, 2557, and 447-52D) against 98 HIV-1 pseudoviruses tested in an U87 cell infectivity experiment previously published by Hioe et al. (2010) [11]. For each virus, the cells colored green indicate the presence of the mAb’s signature motif, while red cells indicate their absence. These are the same data as shown in Figure 2, but here show more clearly the presence/absence of the range of neutralization activities for each virus across the different mAbs, as well providing the V3 sequence and more annotation concerning the origin of the envelope used to construct each pseudovirus.

Figure 2. Masking patterns of four anti-V3 mAb across a multi-subtype panel of pseudoviruses

Concentrations (ug/ml) at which 50% viral neutralization were achieved as performed by Monogram Biosciences’ cellular assay using monoclonal antibodies (mAbs) 3074, 2219, 2557, and 447-52-D [data derived from Hioe et al. (2010) [11]] plotted as bar heights (Y-axis) for four anti-V3 mAbs against 98 HIV-1 pseudoviruses (X-axis). For visualization purposes, IC₅₀ values of >50 were represented as 50 and values of <0.39 as 0.39. Virus names or identifying labels are indicated on the X-axis. For each plotted data point, green bars indicate that the virus contains the signature motif targeted by the tested mAb, while red bars denote the absence of the signature motif from that viral sequence. Viral masking can thus clearly be seen for each of the epitopes targeted by these antibodies: masked viruses are those that contain the antibody epitope (green bars) but were not neutralized by that mAb (IC₅₀ value = 50), while different degrees of the epitope’s exposure are denoted by shorter green bars. Note that for mAb 447-52D, neutralization data for only 65 viruses was collected; in this case only, an IC₅₀ value of “zero” for a particular virus actually means that the virus was not tested against the mAb. Results generated with mAb 2219 are shown in (A), with mAb 3074 in (B), with mAb 2557 in (C), and with mAb 447-52D in (D).