Delineating HIV-1 Evolutionary Pathways in an Individual With a Broadly Neutralizing Antibody Response

Abstract

Despite the identification of potent broadly neutralizing antibodies (bNAbs) against HIV-1, such as VRC01 and VRC13, the induction of bNAbs through vaccination remains hindered due to an incomplete understanding of the complex pathways invoking these responses. Specifically, we lack detailed information regarding the evolutionary HIV-1 env pathways required for lineage-based vaccines to guide the development of bNAbs. In this thesis, we trace plasma epitope specificity and env evolution within an HIV-1-infected individual known to develop neutralization breadth, delineating a unique cross-neutralizing CD4-binding site (CD4bs) response within this individual. Complementary longitudinal sequence analysis and functional assays indicate viral evolution in response to a VRC13-like immune pressure, suggesting the presence of a CD4bs response distinct from the well-characterized VRC01-class. Utilizing autologous env chimeras we identify previously undescribed VRC13 escape mutations likely important to the development of this response. We further isolate autologous single B-cells expressing CD4bs-targeted antibodies where functional screening assays suggest the presence of non-VH1-2-derived cross-neutralizing antibodies. The germline-inferred B-cell receptor sequences for these cross-neutralizing monoclonal antibodies represent previously identified CDRH3-dominated CD4bs bNAbs, further supporting the potential contribution of a VRC13-like response to breadth. Additionally, we demonstrate how env mutations in this individual result in a viral fitness defect, which is uniquely rescued by the host immune response. We identify a rare substitution in env gp41 that reduces viral infectivity by disrupting six-helix bundle formation and membrane fusion. We demonstrate that both HIV-1-positive polyclonal sera, as well as gp41-specific human antibodies restore viral infectivity, likely by stabilization of the six-helix bundle to compensate for the disruptive effect of this substitution. Our results indicate that structural changes mediated by this substitution improve binding of MPER-targeted bNAbs, providing insight into the design of Env-based HIV-1 immunogens. Thus, we identify potential env escape mutations from a VRC13-like response in natural infection and CD4bs monoclonal antibodies that exhibit cross-neutralization, enabling us to study virus-antibody coevolution. We also demonstrate a novel mechanism whereby a viral defect can be mitigated by the host immune response. Future studies aim to identify critical coevolutionary patterns within the viral env and the developing bNAb lineage to aid VRC13-targeted immunogen design.