Mapping Neutralizing Antibody Epitope Specificities to an HIV Env Trimer in Immunized and in Infected Rhesus Macaques

Abstract

Summary BG505 SOSIP is a well-characterized near-native recombinant HIV Envelope (Env) trimer that holds promise as part of a sequential HIV immunogen regimen to induce broadly neutralizing antibodies (bnAbs). Rhesus macaques are considered the most appropriate pre-clinical animal model for monitoring antibody (Ab) responses. Accordingly, we report here the isolation of 45 BG505 autologous neutralizing antibodies (nAbs) with multiple specificities from SOSIP-immunized and BG505 SHIV-infected rhesus macaques. We associate the most potent neutralization with two epitopes: the C3/V5 and V1/V3 regions. We show that all of the nAbs bind in close proximity to known bnAb epitopes and might therefore sterically hinder elicitation of bnAbs. We also identify a “public clonotype” that targets the immunodominant C3/V5 nAb epitope, which suggests that common antibody rearrangements might help determine humoral responses to Env immunogens. The results highlight important considerations for vaccine design in anticipation of results of the BG505 SOSIP trimer in clinical trials.

The C3/465 glycan hole cluster in BG505 HIV-1 envelope is the major neutralizing target involved in preventing mucosal SHIV infection

“…To gain further insight into the specificities of serum nAbs targeting the 465 glycan hole, we performed additional mapping experiments using three mutants that have been used to define recognition of sites within the BG505 C3/465 epitope cluster [ 12 , 19 ]. These mutants shift (TI357KT) or remove (T357A to remove N355; N398A knock out) glycans in this region ( S2 Fig ) [ 12 ].…”

“…Neutralization against HIV-1 Env BG505.T332N (derived from BG505.W6M.Env.C2, Genbank accession #DQ208458), BG505.W6M.C2 containing T332, and ten HIV-1 BG505.T332N mutants described in [ 5 , 12 , 19 ] were measured using serially diluted, heat-inactivated immunized RM serum or mAbs in the TZM-bl assay as previously described, using cells plated one day prior to the assay [ 28 , 32 , 34 – 46 ]. In brief, Env PV was generated by transfecting the Env-expressing plasmid DNA alongside the HIV-1 SG3ΔEnv proviral backbone DNA into 293T cells, using the Fugene HD reagent as recommended (E2312, Promega).…”

“…Here we expand on nAb-mediated protection against intra-vaginal challenge by defining the targets recognized in 12 immunized RM. A panel of BG505 Env mutants [ 12 , 19 ] was used to map nAb on the day of challenge and at preceding time points in a subset of animals. This approach, combined with negative stain electron microscopy polyclonal epitope mapping (nsEMPEM), revealed that BG505 SOSIP-elicited nAb targeted one or more sites in the 465 glycan hole cluster in all RM, often in combination with an array of other neutralizing and non-neutralizing specificities.…”

Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM

“…The neutralization potential of the C3/V5 epitope in BG505 has been reported previously (Lei et al, 2019, Nogal et al, 2020a, Zhao et al, 2020, Cirelli et al, 2019. Antibodies bound to this site can sterically block CD4 binding, which represents a potential mechanism of virus neutralization.…”

“…This antibody class can interact with the BG505 SOSIP.v3 antigen (Figure S1C; depicted in light green) and is likely responsible for the serum neutralization observed for animal Rh.33172 at the week 38 time point. Previous studies have shown that V1-targeting antibodies in BG505 can be moderately neutralizing (Klasse et al, 2018, Zhao et al, 2020, Nogal et al, 2020a).…”