HIV-1 BG505 SOSIP immunization induced B cell expansion targeting the 465-glycan hole, with neutralizing antibodies exhibiting distinct binding modes and mechanisms of virus inhibition

High serum neutralization following BG505 SOSIP.664 envelope trimer immunization was associated with protection against BG505.SHIV challenge in rhesus macaques in a previous study. In an animal that developed high titer, durable neutralization against a glycan hole on envelope gp120, high throughput, longitudinal, antigen-specific B cell receptor sequencing was conducted. This analysis of more than 4,700 antigen-specific B cells revealed marked intra-clonal expansion and divergence from germline, including three abundant clonotypes that produced autologous neutralizing monoclonal antibodies. Monoclonal antibodies from the neutralizing clonotypes and two other expanded non-neutralizing clonotypes targeted epitopes in the same glycan hole, with neutralizers also demonstrating different capacities to obstruct CD4 binding. Cryo-electron microscopy structures of four neutralizing monoclonal antibodies revealed that they bound to glycan hole epitopes using distinct binding modes. One neutralizing antibody displaced a glycan in the loop V5 upon binding and its footprint includes the CD4 binding loop. The findings provide insight into how antibody recognition of a prominent glycan hole could facilitate different mechanisms of neutralization while underscoring how intra-clonal expansion and maturation with repeated BG505 SOSIP.664 immunization drove high serum neutralization.