Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus

Abstract

Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.

Figure 1. Development of neutralization breadth in donor CH505 and isolation of antibodies

a, Shown are HIV-1 viral RNA copies and reactivity of longitudinal plasmas samples with HIV1-1 YU2 core gp120, RSC3 and negative control RSC3Δ371I(ΔRSC3) proteins. b, PBMCs from week 136 was used for sorting CD19⁺, CD20+, IgG⁺, RSC3⁺ and ΔRSC3⁻ memory B cells (0.198%). Individual cells indicated as orange, blue and green dots yielded mAbs CH103, CH104 and CH106, respectively, as identified by index sorting. c, The neutralization potency and breadth of the CH103 antibody are displayed using a neighbor joining tree created with PHYLIP package. The individual tree branches for 196 HIV-1 Envs representing major circulating clades are colored according to the neutralization IC50 values as indicated. d, Cross competition of CH103 binding to YU2 gp120 by the indicated HIV-1 antibodies, and soluble CD4-Ig was determined by ELISA.

Figure 2. CH103-clonal family with time of appearance, V_HDJ_H mutations, and HIV-1 Env reactivity

Phylogenies of V_HDJ_H (a) and V_LJ_L (b) sequences from sorted single memory B cells and pyrosequencing. The ancestral reconstructions for each were done using the methods described in the Online Methods. The phylogenetic trees themselves were subsequently computed using neighbor joining on the complete set of DNA sequences (see Online Methods) to illustrate the correspondence of sampling date and read abundance in the context of the clonal history. Within time-point V_H monophyletic clades are collapsed to single branches; variant frequencies are indicated on the right. Isolated mature antibodies are red, pyrosequencing-derived sequences are black. The inferred evolutionary paths to observed matured antibodies are bold. c, Maximum-likelihood phylogram showing the CH103 lineage with the inferred intermediates (circles, I1–4, I7 and I8), and percentage mutated V_H sites and timing (blue), indicated. d, Binding affinity (Kd, nM) of antibodies to autologous CH505 (left box) and heterologous B.63521 were measured by surface plasmon reasonance (SPR) (right box).

Figure 3. Structure of antibody CH103 in complex with the outer domain of HIV-1 gp120 (OD)

a, Overall structure of complex with gp120 polypeptide depicted in red ribbon and CH103 shown as a molecular surface (heavy chain in green and light chain in blue). Major CH103-binding regions on gp120 are colored orange for Loop D, yellow for the CD4-binding site and purple for Loop V5. b, Superposition of OD bound by CH103 (red) and core gp120 bound by VRC01 (gray) with polypeptide shown in ribbon representation. c, CH103 epitope (green) on OD (red) with the initial CD4-binding site superposed (yellow boundaries) in surface representation. d, Sequence alignment of outer domains of the crystallized gp120 shown on the first line and diverse HIV-1 Envs recognized by CH103. Secondary structure elements are labeled above the alignment with gray dashed lines indicating disordered regions. Symbols in yellow or green denote gp120 OD contacts for CD4 and CH103, respectively, with open circles representing main-chain contacts, open circles with rays representing side-chain contact, and filled circles representing both main-chain and side-chain contacts.

Figure 4. Sequence Logo displaying variation in key regions of CH505 Envs

The frequency of each amino acid variant per site is indicated by its height, deletions are indicated by grey bars. The first recurring mutation, N279K, appears at week 4 (open arrow). The timing of BnAb activity development (from Supplementary Fig. 2 and Supplementary Table 1) is on the left. Viral diversification, which precedes acquisition of breadth, is highlighted by vertical arrows to the right of each region. CD4 and CH103 contact residues, and amino acid position numbers based on HIV-1 HXB2, are shown along the base of each Logo column.

Figure 5. Development of neutralization breadth in the CH103-clonal lineage

a, Phylogenetic CH103 clonal lineage tree showing the IC50 (μg/ml) of neutralization of either the autologous T/F (C.CH505), heterologous tier clades A (A.Q842) and B (B.BG1168) viruses as indicated. b, Interplay between evolving virus and developing clonal lineage mapped on to models of CH103-developmental variants and contemporaneous virus. The outer domain of HIV gp120 is depicted in worm representation, with worm thickness and color (white to red) mapping the degree of per-site sequence diversity at each time point. Models of antibody intermediates are shown in cartoon diagram with somatic mutations at each time point highlighted in spheres and colored red for mutations carried over from I8 to mature antibody, cyan for mutations carried over from I4 to mature antibody, green for mutations carried over from I3 to mature antibody, blue for mutations carried over from I2 to mature antibody, orange for mutations carried over from II to mature antibody, magenta for CH103 mutations from I1. Transient mutations that did not carry all the way to mature antibody are colored in deep olive. The antibody (paratope) residues are shown in surface representation and colored by their chemical types as indicated.