Characterization of Antiviral Antibody Repertoire Dynamics and Immune Correlates of Human Disease

Abstract

The human antiviral antibody repertoire is complex and dynamic. Profiling the antiviral antibody repertoire in high resolution and at scale has the power to enhance our understanding of individual infection histories, variability in immune responses, and disease mechanisms. This dissertation centers on the use of VirScan, a phage immunoprecipitation sequencing (PhIP-seq) technology that enables high-throughput mapping of antibody responses to the human virome. Through three distinct but interrelated studies, this work applies VirScan to: (1) investigate immune signatures associated with pediatric acute hepatitis of unknown etiology, (2) characterize agerelated diversity and temporal stability of antiviral antibody repertoires from infancy to adulthood, and (3) develop specialized peptide libraries to detect latent viral infections and explore potential viral drivers of chronic disease. In the first part of this dissertation, we applied VirScan to an emergent outbreak, severe acute hepatitis of unknown etiology (AHUE) in children. Antibody profiling of affected children revealed enriched responses to AAV-2 epitopes, with evidence of considerable epitope spreading and co-infection with multiple helper viruses capable of facilitating AAV-2 replication. This signature was absent in pediatric and adult controls. This work identified recent AAV-2 infection, facilitated by helper viruses, as a plausible cause of AHUE pathogenesis. These findings demonstrate the utility of VirScan in outbreak investigation and etiologic discovery. The second part of this dissertation characterized antiviral antibody repertoire dynamics across age groups using large cross-sectional and longitudinal cohorts. Children were found to produce broader antiviral responses than adults, with and target distinct patterns of viral epitopes. Repertoires were highly dynamic in early life, transitioning from maternally derived antibodies to endogenous responses, and gradually stabilizing with age. In contrast, adult repertoires were highly stable over decades and unique to individuals. We also observed that there was variation in stability of responses within and between viruses. The third study focused on the development of modular, targeted PhIP-seq libraries to investigate latent viral infections as potential drivers of chronic disease. New libraries enriched for public epitopes and complete proteomes of herpesviruses, adenoviruses, and parvoviruses were designed and validated. These tools were engineered for scalability in epidemiologic research and are ready to be applied to large case-control cohorts where they will enable detection of viral exposures and antibody responses relevant to chronic conditions such as multiple sclerosis and cardiovascular disease. Together, these studies illuminate how antibody repertoires reflect both individual immune experiences and broader epidemiological trends, and demonstrate VirScan’s power as a tool for immunological discovery, surveillance, and hypothesis generation.