Long-term and low-level envelope C2V3 stimulation from highly diverse virus isolates leads to frequent development of broad and elite antibody neutralization in HIV-1 infected individuals

Elicitation of potent neutralizing antibodies against genetically diverse HIV-1 isolates is important for an effective HIV-1 vaccine. Some HIV-1 infected patients produce such broadly neutralizing antibodies (bNAbs). Identification of host and viral correlates of bNAb production may help develop the next generation of HIV-1 vaccines. We carried out the first detailed characterization of the neutralizing antibody response and identify viral and host factors associated with the development of bNAbs in HIV-1 infected patients from Angola, one of the oldest, more dynamic, and diverse HIV-1 epidemics in the world. Plasma samples from 322 HIV-1 infected patients were collected in 2001, 2009 and 2014. Phylogenetic analysis of C2V3C3 envelope sequences identified a diverse array of subtypes including A1, A2, B, C, D, F1, G, H, J, untypable strains, and recombinant forms which prevailed over pure subtypes. Notably, 56% of the patients developed cross, broad, or elite neutralizing responses against a reference panel of tier 2 Env-pseudoviruses far exceeding results obtained elsewhere in the world. The frequency of elite neutralizers was higher in 2014, when patients were on ART and had low viremia, than in 2009 when patients were drug naive. In drug naive patients, broad neutralization was associated with subtype C infection, lower CD4+ T cell counts, higher age, or higher titer of C2V3C3-specific antibodies relative to patients that did not develop bNAbs. Neutralizing antibodies targeted the V3-glycan supersite in most patients but antibodies specific for the V2 apex, the CD4 binding site, the gp41 membrane-proximal external region (MPER) and unknown epitopes were also found in some patients. V3 and C3 regions were significantly less variable and less subject to positive selection in elite neutralizers compared to weak or no neutralizers suggesting an active role of bNabs directed against these regions in controlling HIV-1 replication and diversification. Hence, development of broad and elite antibody neutralization against HIV-1 requires long-term and low-level envelope V3C3 stimulation from highly diverse subtype C isolates. These results have direct implications for the design of a new generation of HIV-1 vaccines.