Abstract
Viruses are infectious agents that depend on host cells for replication and can cause diseases ranging from mild illness to severe outcomes, including cancer and death. In the 21st century, several major viral outbreaks have occurred, including the 2002 severe acute respiratory syndrome coronavirus (SARS), the 2009 H1N1 influenza pandemic, the 2012 Middle East respiratory syndrome (MERS), the 2014 Ebola virus outbreak, and most recently, the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019. SARS-CoV-2 is a positive-sense, single-stranded RNA virus of the Betacoronavirus genus in the Coronaviridae family. First identified in Wuhan, China, the virus quickly spread worldwide and was announced as a pandemic by the World Health Organization (WHO) in 2020. Coronavirus disease 2019 (COVID-19) manifests with signs and symptoms ranging from mild, flu-like illness to acute respiratory distress, severe pneumonia, and death. The development of mRNA vaccines targeting the viral spike protein, a crucial mediator for viral entry, contributed to early pandemic control. However, as SARS-CoV-2 evolved, mutations in the spike protein reduced the neutralizing capacity of antibodies elicited by the initial vaccines, leading to the design and deployment of variant-matched vaccines including Wuhan-1/Omicron bivalent formulations and more recent monovalent Omicron XBB.1.5 and KP.2 vaccines. Although the goal of variant-matched vaccines is to enhance immunogenicity and protection against the variant strain, it is not clear whether variant-specific immunity is induced, or if such responses are limited by immune imprinting, in which prior exposure to ancestral antigens biases subsequent immune responses. During an initial encounter with SARS-CoV-2, naïve B cells recognizing spike proteins are activated and differentiate into antibody-secreting cells (ASCs) for rapid production of antibodies or differentiate into germinal center (GC) B cells that ultimately give rise to memory B cells (MBCs) and long-lived plasma cells (LLPCs). Upon secondary antigen exposures, MBCs are rapidly activated and initiate a recall response. In imprinted individuals, cross-reactive MBCs that recognize epitopes shared between the original and the secondary antigen are thought to outcompete and limit the activation of naïve B cells targeting epitopes unique to the secondary antigen. Multiple studies have suggested that SARS-CoV-2 infections and vaccinations result in imprinting effects on subsequent responses to variant strains. However, as these studies examined either the serum response as a whole or the specificity of MBCs, a key question remains as to whether variant-matched booster vaccines induce serum antibody responses that are cross-reactive or variant-specific, and how much each of these contribute to neutralization of the variant strain. In this study, we designed an antibody-depletion assay to isolate type-specific from cross-reactive antibodies. Using the assay, we characterized immune responses in mice and humans primed with the Wuhan-1-based mRNA-1273 vaccine and subsequently boosted with variant-matched vaccines. In mice, two priming doses of mRNA-1273 imprinted serum responses such that Omicron BA.1 boosters induced minimal variant-specific antibodies. However, imprinting was alleviated by a second dose of BA.1 booster. In humans who received two Omicron-matched boosters following two or more doses of mRNA-1273, strong imprinting was observed, with antibody responses largely cross-reactive to the Wuhan-1 strain. These cross-reactive antibodies neutralized Omicron variants and even distantly related sarbecoviruses, suggesting a potentially beneficial effect of imprinting in increasing the breadth of protection. Given the continued emergence of variant strains that evade neutralization provided by Wuhan-1-based vaccines, the induction of variant-specific immunity may be increasingly important. Thus, we also evaluated strategies to enhance variant-specific responses in mice imprinted by Wuhan-1-based vaccines and then boosted with variant-matched vaccines targeting XBB.1.5. Whereas extending the boosting interval or altering the intramuscular injection site did not noticeably improve variant-specific serum antibody responses, increasing booster antigen doses, administering repeated variant boosters, and delivering variant booster vaccines intranasally enhanced XBB.1.5-specific responses. Intranasal boosting with a chimpanzee adenoviral-vectored vaccine encoding the XBB.1.5 spike protein (ChAd-XBB.1.5) elicited stronger XBB.1.5-specific responses in serum, bronchoalveolar lavage fluid, and draining lymph nodes than intramuscular boosting with the same vaccine. Notably, and in contrast to earlier SARS-CoV-2 variants, neutralization of XBB.1.5 was mediated predominantly by XBB.1.5 spike-specific antibodies rather than those cross-reactive to Wuhan-1. These findings highlight the potential of intranasal or repeated variant-matched boosting to mitigate imprinting and improve protective immunity. Overall, this work provides new insights into how immune imprinting shapes humoral responses to variant vaccines and identifies strategies to enhance variant-specific immunity. These findings have important implications for the design of future vaccination regimens capable of achieving protection against current and emerging viral variants.
Committee Chair
Michael Diamond
Committee Members
Adrianus Boon; Ali Ellebedy; Deborah Lenschow; Megan Baldridge
Degree
Doctor of Philosophy (PhD)
Author's Department
Biology & Biomedical Sciences (Immunology)
Document Type
Dissertation
Date of Award
11-6-2025
Language
English (en)
DOI
https://doi.org/10.7936/tcsy-dr58
Author's ORCID
0009-0007-0964-7424
Recommended Citation
Liang, Chieh-Yu, "Humoral Immune Responses following Immunization with SARS-CoV-2 Variant Vaccines" (2025). Arts & Sciences Theses and Dissertations. 3680.
The definitive version is available at https://doi.org/10.7936/tcsy-dr58