Contribution to the Understanding of Chronic Infections and Immune Responses to Vaccines in Immunocompromised Individuals, Including People with HIV

Emerging infectious diseases continue to pose a profound global challenge. Over the past
century, humanity faced successive waves of viral threats: from the influenza pandemic and the persistent burden of seasonal flu to the enduring HIV/AIDS pandemic and recurrent Ebola
outbreaks, and, more recently, the worldwide spread of SARS-CoV-2 and the resurgence of
monkeypox. These events have highlighted both the vulnerabilities of our interconnected world and the remarkable adaptive capacity of viruses, driven by rapid evolution enabling cross- species transmission, immune evasion, and global dissemination. In immunocompromised individuals, including people with HIV, the impact of these viral
threats is amplified by the increased risk of suboptimal vaccine-induced immunity, delayed
viral clearance, and severe clinical outcomes. This thesis investigates the interplay between
chronic infection, immune dysfunction, and vaccine-induced immunity in
immunocompromised hosts, integrating clinical immunology, viral genomics, and translational research. To address this, we conducted a series of immunological and virological investigations in immunocompromised individuals, focusing on SARS-CoV-2 and monkeypox virus as models of emerging viral threats. By late 2021, COVID-19 case numbers surged globally, first with widespread circulation of the SARS-CoV-2 Delta variant and then with the rapid emergence of Omicron, which was associated with reduced neutralising antibody activity and subsequently led to the recommendation of additional mRNA vaccine doses. Yet, evidence on vaccine immunogenicity in people with HIV was limited, raising concerns about their level of protection. To address this gap, we assessed the impact of a third SARS-CoV-2 mRNA vaccine
dose in this population. This additional dose significantly enhanced humoral immune responses in people with HIV, restoring levels comparable to those of HIV-negative controls. However, infection-naïve individuals within the HIV group mounted weaker T-cell immune responses after boosting, suggesting that T-cell immunity in this subgroup remains suboptimal. In contrast, prior SARS-CoV-2 infection largely mitigated this gap, resulting in comparable T-cell immunity across groups. To further dissect the heterogeneity of vaccine responses, we applied unsupervised K-means clustering, which revealed substantial variation in baseline immunological status, partly shaped by prior antigenic exposure, and delineated divergent immunological trajectories after the third vaccine dose, ranging from robust T-cell–dominated profiles to antibody-driven responses and globally weak responders. These findings underscore that serological measures alone cannot
capture the full complexity of antiviral immune responses. Beyond immunogenicity, we investigated how immune dysfunction shapes intra-host viral evolution in immunocompromised patients with persistent SARS-CoV-2 infection. In one case, infection appeared to extend beyond a year, marked by the progressive accumulation of mutations and the emergence of genetically distinct viral lineages across anatomical compartments. Divergent evolutionary trajectories between the upper and lower respiratory
tracts indicated that nasopharyngeal sampling alone does not fully capture viral dynamics
within the lower airways. These findings illustrate how immunosuppressed hosts can act as
reservoirs for the generation of novel variants, with intra-host evolutionary processes far
exceeding those observed in acute infections. Finally, extending these investigations to monkeypox, we evaluated immune responses to third-generation smallpox vaccination in people with HIV and HIV-negative individuals at high risk of Mpox. Although vaccination elicited a transient increase in antibody responses to 12 immunodominant orthopoxvirus antigens, levels declined to near-baseline within one year in both groups, underscoring the limited durability of vaccine-induced humoral immunity. Prior mpox disease emerged as the strongest determinant of more robust and sustained responses, while the number of vaccine doses and a history of childhood smallpox vaccination further shaped antibody levels. These findings indicate that current vaccination elicits only a transient humoral response, highlighting the urgent need to define immunological correlates of protection against monkeypox and to develop long-term immunisation strategies. Altogether, this work provides an integrated perspective on how chronic infection and immune dysregulation shape vaccine responses and viral evolution in immunocompromised hosts, underscoring the urgent need for tailored vaccination strategies, long-term immune monitoring, and proactive genomic surveillance to protect the most vulnerable populations against evolving viral threats.