Virus and Antibody Gene Sequencing Core

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PROJECT SUMMARY The development of broadly cross-reactive neutralizing antibodies (bNAbs) in HIV-1 infected humans and SHIV infected rhesus macaques (RMs) requires iterative rounds of envelope glycoprotein (Env)-mediated B cell receptor stimulation, neutralizing antibody (NAb) elicitation, and associated virus escape. In this virus/antibody “arms race”, particular Env escape mutants are generated which, among the myriads of other Env variants present in infected individuals, are able to prime and boost antibody lineages that are capable of developing neutralization breadth. Although the principle of virus/antibody co-evolution has been established, the number, identity, succession, and cooperation of the particular Env variants that initiate and sustain bNAb lineage maturation remain largely unknown. In this renewal application, this HIVRAD team proposes to use simian- human immunodeficiency virus (SHIV) infected rhesus macaques (RMs) as a molecular guide to develop HIV-1 Env immunogens that elicit V3 high mannose patch bNAbs. In collaboration with Projects 1 and 3, we will trace the patterns of Env-antibody coevolution in RMs that develop V3 glycan patch bNAbs and then use this information to identify specific Env variants that prime and affinity-mature these responses towards neutralization breadth. Recent work by the group provides strong support for these goals (1-6). First, the team identified heterologous neutralization breadth in 24 of 150 RMs infected with various HIV-1 Env bearing SHIVs, including nine animals with V3 high mannose patch bNabs (see Preliminary Data of Project 1). Second, Env-antibody coevolution in SHIV infected RMs was found to be strikingly similar to that observed in the corresponding humans, including similar immunogenetics, structural and chemical solutions to epitope recognition, and near- identical Env escape pathways in response to Nab pressures (1-5). Finally, the team devised a rational strategy for sequential immunogen design to circumvent difficult roadblocks in bNAb induction by vaccination (6). We thus hypothesize that characterization of Env-antibody coevolution in RMs infected by germline-targeted CH848 and BG505.N332 SHIVs will identify Env immunotypes that, when constructed as nanoparticles or SOSIP Env trimers and used to immunize RMs, will elicit V3 glycan bNAbs. The Virus and Antibody Sequencing Core (Core B) will continue to support this HIVRAD team by providing state-of-the-art virus and antibody sequencing services as well as unique virology expertise. Working closely with the Bioinformatics and Statistics Core (Core C) as well as Projects 1, 2 and 3, we will (i) characterize the evolving env quasispecies in SHIV infected macaques that develop V3 glycan bNAbs to map neutralization escape pathways (Aim 1), and (ii) sequence antibody heavy and light chain V(D)J variable regions from rhesus memory B cells before and after SHIV infection as well as knock-in mice after immunization to facilitate bNAb lineage tracing and define the role of antigen receptor affinity in B cell fates (Aim 2). The goal is to identify key steps in Env-antibody co-evolution required for V3 glycan bNAb development that can be rapidly translated into rational immunogen design.