ORCID
0000-0002-5805-4461
Date of Award
3-26-2025
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
The primary series of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines greatly reduced the burden of the coronavirus disease 2019 (COVID-19) pandemic and saved millions of lives. However, waning levels of circulating neutralizing antibodies and the continuous emergence of SARS-CoV-2 variants with increasing numbers of mutations in the spike (S) protein have decreased vaccine effectiveness and led to a recommendation for booster immunizations. In addition, new vaccines based on circulating variants have been developed to enhance the ability of induced antibodies to combat such variants. However, a critical unanswered question was how prior exposure to the ancestral SARS-CoV-2 strain impacts the subsequent immune response following exposure to variant viruses. Specifically, do variant-based booster immunizations induce de novo B cell responses to that variant, or do they primarily recall preexisting B cells targeted against shared epitopes? Understanding this distinction is essential for the rational design of vaccine strategies that can induce broadly neutralizing antibodies against mutating viruses. Herein, we evaluated antigen-specific B cell responses following SARS-CoV-2 mRNA-based booster immunizations in humans. Using ultrasound-guided fine needle aspiration to serially sample draining axillary lymph nodes, we showed that boosting with either the ancestral SARS-CoV-2 mRNA vaccine or the bivalent B.1.351/B.1.617.2 (Beta/Delta) mRNA vaccine elicited robust S-specific germinal center (GC) B cell responses in all sampled participants. These GC responses persisted for at least eight weeks post-booster immunization, leading to significantly more mutated antigen-specific bone marrow plasma cell (BMPC) and memory B cell (MBC) compartments. We also showed that S-specific plasmablast and GC responses predominantly originated from preexisting clonal lineages, which is consistent with our observation that most MBC-derived monoclonal antibodies (mAbs) recognized the original SARS-CoV-2 S protein. Nonetheless, using a more targeted sorting approach, we isolated mAbs that recognized the BA.1 S protein but not the original SARS-CoV-2 S protein from individuals who received the mRNA-1273.529 booster, suggesting that immunization with the monovalent B.1.1.529 BA.1-matched vaccine could induce rare de novo B cell responses against novel epitopes in the B.1.1.529 BA.1 S protein. Therefore, SARS-CoV-2 booster immunizations in humans induce robust GC B cell responses, and immunization with a distinct antigen can generate de novo B cell responses targeting variant-specific epitopes. Over the course of the COVID-19 pandemic, a dozen mAbs that target the virus S protein have been approved for clinical use in treating those infected by, or exposed to, SARS-CoV-2. These antibodies, which largely target the receptor-binding domain (RBD) of the S protein, were all raised against and efficiently neutralize the original SARS-CoV-2 strain (WA1/2020). While WA1/2020-targeting antibodies can provide a degree of protection against emerging variants, including those with minor mutations, they may lose efficacy against variants with significant changes in their S proteins. In fact, all clinically authorized mAbs are now rendered inactive by the latest Omicron subvariants, raising the question of whether antibodies that are specifically tailored to the unique features of Omicron can maintain efficacy against newer, more divergent Omicron subvariants. Herein, we assessed the ability of Omicron BA.1-specific mAbs to recognize and neutralize recently emerged SARS-CoV-2 Omicron subvariants. Out of six mAbs tested, only one mAb, 1A05, demonstrated broad binding and neutralization capacity against multiple SARS-CoV-2 Omicron subvariants, from BA.1 through HV.1. Prophylactic administration of 1A05 significantly reduced infectious virus titers for Omicron BA.5 in the lungs, nasal turbinate, and nasal wash of infected animals. Structural analysis of 1A05 Fab fragment in complex with Omicron BA.1 RBD using cryo-electron microscopy (cryo-EM) showed that the bulk of the 1A05 footprint overlapped with the receptor-binding motif (RBM), allowing 1A05 to achieve neutralization by blocking ACE2 binding. However, with the continuous evolution of Omicron subvariants and the emergence of antibody-evading JN.1, 1A05 lost efficacy, indicating that Omicron BA.1-specific B cell responses may lose efficacy against newer, more divergent Omicron subvariants, which emphasizes the need for mAbs with enhanced breadth and resilience against the continuously evolving SARS-CoV-2. Overall, the studies I describe here provide crucial insights into how prior exposure to SARS-CoV-2 shapes subsequent immune responses, particularly in the context of variant-adapted vaccines. This knowledge not only informs strategies for combating the ongoing evolution of SARS-CoV-2 but also helps us prepare against future emerging viruses.
Language
English (en)
Chair and Committee
Ali Ellebedy
Committee Members
Brian Edelson; Jacco Boon; Jennifer Phillips; Michael Vahey
Recommended Citation
Al Soussi, Wafaa, "Defining B cell responses to emerging viral pathogens" (2025). Arts & Sciences Electronic Theses and Dissertations. 3456.
https://openscholarship.wustl.edu/art_sci_etds/3456