For most viruses, neutralizing antibodies (NAbs) are the single clearest correlate of protection, and passively administered NAbs confer protection in many SIV and SHIV models. Further, about half of HIV-infected individuals develop NAb responses that are broad enough to neutralize isolates distinct from their own infecting strain. Despite this, currently tested immunogens cannot elicit any useful degree of breadth. Therefore, this proposal is designed to answer the critical open question in HIV-1 vaccine research: What happens in natural HIV infections that leads to the development of antibody breadth? While a number of factors (viral or host) likely contribute to the development of breadth, this proposal places a strong bet that the primary contribution is from the composition and dynamics of the protein antigen, HIV-1 Env, and that by looking at the right env populations in the right way, we can figure out how to elicit breadth. The proposed project stands on two key pillars: 1) our novel approach to deep sequencing and analyzing full- length env from HIV RNA populations, and 2) access to an astounding longitudinal primary infection cohort.
Specific Aim 1 : Refine full-length env deep sequencing and analysis protocols, including barcoded multiplexing for high-throughput sequencing of longitudinal samples.
Specific Aim 2 : Longitudinally deep sequence full-length env in 16 donors who develop a broadly neutralizing antibody response against the N332 glycan-dependent epitope, and in 32 donors that do not. The data generated with this novel sequencing approach will, for the first time, allow us to systematically study the role of env in eliciting anti-N332 breadth, drawing robust conclusions from the largest collection of N332 targeting donors (and controls) ever studied.
Antibodies that neutralize a broad variety of HIV-1 strains occur in natural infections, but we do not know how to elicit these through vaccination. With a new approach to full-length deep sequencing of HIV-1 env, we will discover how these antibodies arise in a large cohort of individuals.
