Diversification in the HIV-1 Envelope Hyper-variable Domains V2, V4, and V5 and Higher Probability of Transmitted/Founder Envelope Glycosylation Favor the Development of Heterologous Neutralization Breadth

Abstract

A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12). Single-genome analysis of full-length T/F Env sequences revealed that all 21 individuals were infected with a highly homogeneous population of viral variants, which were categorized as subtype C (n = 12), A1 (n = 7), or recombinant AC (n = 2). An extensive amino acid sequence-based analysis of variable loop lengths and glycosylation patterns in the T/F Envs revealed that a lower ratio of NXS to NXT-encoded glycan motifs correlated with neutralization breadth. Further analysis comparing amino acid sequence changes, insertions/deletions, and glycan motif alterations between the T/F Env and autologous early Env variants revealed that extensive diversification focused in the V2, V4, and V5 regions of gp120, accompanied by contemporaneous viral escape, significantly favored the development of breadth. These results suggest that more efficient glycosylation of subtype A and C T/F Envs through fewer NXS-encoded glycan sites is more likely to elicit antibodies that can transition from autologous to heterologous neutralizing activity following exposure to gp120 diversification. This initiates an Env-antibody co-evolution cycle that increases neutralization breadth, and is further augmented over time by additional viral and host factors. These findings suggest that understanding how variation in the efficiency of site-specific glycosylation influences neutralizing antibody elicitation and targeting could advance the design of immunogens aimed at inducing antibodies that can transition from autologous to heterologous neutralizing activity.

Viral Characteristics Associated with Maintenance of Elite Neutralizing Activity in Chronically HIV-1 Clade C-Infected Monozygotic Pediatric Twins

“…We observed two distinct evolutionary pathways of viral escape in response to increasing plasma potency and breadth in the twins. By generating chimeric pseudoviruses using the viruses sensitive and resistant to autologous plasma antibodies, we confirmed that the viruses of AIIMS_329 developed resistance to autologous plasma bnAbs by previously established mechanisms (26,27,(42)(43)(44) of V1V2 loop lengthening, an increased number of PNGS, and a loss of critical epitopes like N160. The AIIMS_330 viruses that were resistant to contemporaneous autologous plasma also had longer V2 loops but maintained all epitopes.…”

Clade C HIV-1 Envelope Vaccination Regimens Differ in Their Ability To Elicit Antibodies with Moderate Neutralization Breadth against Genetically Diverse Tier 2 HIV-1 Envelope Variants

“…three Envs, while classified as tier 2, are on the more neutralization-sensitive side of the spectrum (23,41). Less consistent neutralization of other, more resistant Envs in the panel was also observed at levels that were clearly distinguishable from those for the negative controls (MLV Env pseudovirus and naive monkey serum; also see Fig.…”

“…Neutralization assays. Neutralization against HIV-1 Envs 1086.C K160N and CNE8 was measured using serially diluted, heat-inactivated immunized rhesus macaque serum in the TZM-bl cell assays as previously described, using cells that had been plated 1 day prior to the assay (15,17,30,41,(71)(72)(73)(74)(75)(76)(77)(78)(79)(80). In brief, Env pseudoviruses were generated by transfecting the Env-expressing plasmid DNA alongside the HIV-1 SG3ΔEnv proviral backbone DNA into 293T cells, collecting the supernatant 48 to 72 h later, clarifying it by centrifugation, and storing it in small aliquots at Ϫ80°C.…”

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

“…However, there is one contradictory report which says that a longer V1V2 region is associated with resistance to neutralization (41). Of note, site-specific glycosylation can also influence neutralizing antibody elicitation in a subtype-specific manner (42,43). Although the HIV isolates had increased resistance to bNAbs at the population level, the newly identified bNAb PG16 displayed an extraordinary breadth and potency of neutralization with the chimeric viruses.…”