Broadly neutralizing plasma antibodies effective against autologous circulating viruses in infants with multivariant HIV-1 infection

Abstract

Broadly neutralizing antibodies (bnAbs) develop in a subset of HIV-1 infected individuals over 2-3 years of infection. Infected infants develop plasma bnAbs frequently and as early as 1-year post-infection suggesting factors governing bnAb induction in infants are distinct from adults. Understanding viral characteristics in infected infants with early bnAb responses will provide key information about antigenic triggers driving B cell maturation pathways towards induction of bnAbs. Herein, we evaluate the presence of plasma bnAbs in a cohort of 51 HIV-1 clade-C infected infants and identify viral factors associated with early bnAb responses. Plasma bnAbs targeting V2-apex on the env are predominant in infant elite and broad neutralizers. Circulating viral variants in infant elite neutralizers are susceptible to V2-apex bnAbs. In infant elite neutralizers, multivariant infection is associated with plasma bnAbs targeting diverse autologous viruses. Our data provides information supportive of polyvalent vaccination approaches capable of inducing V2-apex bnAbs against HIV-1.

Fig. 1. Identification of plasma bnAb-inducing infants.

a Heatmap representing HIV-1 specific neutralization titres (inverse plasma dilution) of plasma nAbs from 47 infant samples against the 12-virus global panel. ID₅₀ values are color-coded per the key given, with darker colors implying higher ID₅₀ titres. b, c Comparison of breadth (pseudoviruses showing >50% neutralization at 1/50 plasma dilution) and geometric mean titres of infants (n = 47) with previously established cohorts of chronically infected children (labeled ‘adolescents’) (n = 27) and adults (n = 15). Statistical difference between infant versus adolescents and adults was computed with two-tailed Mann–Whitney U test. ***Represents a p-value less than 0.001. d Modified neutralization scores predict geometric mean titres.

Fig. 2. V2-apex targeting plasma nAbs predominate in HIV-1 infected infants.

a Epitope mapping done by mutant viruses in HIV-25710_2_43 backbone for V2-apex (N160A), V3-glycan (N332A), CD4bs (R456W), Interface (A512W-G514W) and MPER (W672L-F673L-T676A). PG9 (V2-apex), 10-1074 (V3-glycan), 3BNC117 (CD4bs), PGT151 (Interface) and 10E8 (MPER) bnAbs were used as positive controls. b V2-apex (N160A) dependence of infants with diverse pseudoviral backbones. PG9 (V2-apex targeting bnAb) was used as positive control. c V3-glycan (N332A) dependence of AIIMS706 plasma nAbs against diverse pseudoviral backbone. 10-1074 (V3-glycan targeting bnAb) was used as negative control. d Comparison of ID₅₀ titres of AIIMS704 plasma (undepleted) and MPER-peptide depleted plasma against the 12-virus global panel. Neutralization assays were performed in triplicates and repeated thrice. Average Ic50 values are shown and used for defining epitope dependence.

Fig. 3. Multivariant infection in infants with elite plasma neutralizing activity.

a Maximum-likelihood tree of env SGA amplicons (V2C5 region, HXB2 position 6690–7757) of circulating viral variants from infants with elite and broad plasma neutralizing activity. BG505.W6M.C2 (Clade A, labeled BG5, yellow) and HXB2 (Clade B, labeled HXB, brown) were used as outgroups. Distinct multiple branches for AIIMS704 (red), AIIMS706 (green) AIIMS709 (blue), and AIIMS743 (deep pink) were observed. b Maximum-likelihood tree of full-length env sequences (HXB2 position 6225–8795) from the four elite neutralizers (AIIMS704, red; AIIMS706, green; AIIMS709, blue; and AIIMS743, deep pink). BG505.W6M.C2 (Clade A, labeled BG5, light pink) and HXB2 (Clade B, labeled HXB, purple) were used as outgroups. The numerals at the node represent bootstrap value. The horizontal scale bar represents genetic distance. nt, nucleotide.

Fig. 4. Distinct circulating viral variants in infant elite neutralizers.

a–d Highlighter plots with maximum-likelihood trees of 40 SGA env sequences from each infant suggests productive infection with more than two distinct viruses. Maximum-likelihood trees are color coded (AIIMS704—red, AIIMS706—green, AIIMS709—blue and AIIMS743—deep pink). Colored hash marks on each highlighter plot represent nucleotide difference (A—green; T—red, C—blue, and G—orange) compared to the sequence at the top of the plot. The horizontal scale bar represents genetic distance. nt, nucleotide.

Fig. 5. Neutralization profile and antigenic characteristics of pseudoviruses from infant elite neutralizers.

a Neutralization susceptibility of circulating viruses from elite neutralizers to autologous plasma nAbs and known bnAbs was assessed using TZM-bl cells. The potency of plasma and bnAbs is color coded per the key given. Most potent neutralization was seen with V2-apex targeting bnAbs. b–e Surface binding assay with varying concentration of trimer-specific V2-apex targeting bnAbs (PGDM1400, CAP256.25), V3-glycan targeting bnAb 10-1074, gp120–gp41 interface targeting bnAb PGT151, CD4-induced nnAbs (17b and A32, in presence and absence of sCD4), and gp120 outer domain targeting bnAb (2G12, in presence and absence of sCD4). Neutralization assays were performed in triplicates and repeated thrice. Average IC50 values were used for drawing heatmaps. All binding experiments were repeated thrice, and shown are the average MFI values. MFI, median fluorescence intensity.