Active monitoring of long-term immunity to SARS-CoV-2 infection and vaccination

Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reminded us of the critical importance of monitoring immunity against infectious pathogens, providing essential insights for clinical practice. The transition of the coronavirus disease 2019 (COVID-19) pandemic to an endemic phase depends on the long-term dynamics of adaptive immunity against SARS-CoV-2 elicited by natural infection and/or vaccination as well as the impact of highly transmissible viral variants. However, immunocompromised individuals are particularly vulnerable to infections and characterized by an impaired ability to respond effectively to vaccination. Monitoring the durability of SARS-CoV-2-specific immunity in both immunocompetent and immunocompromised individuals may allow for improvements in global immunization strategies. Objectives: The aim of this PhD project is to investigate the immune response induced by SARS- CoV-2 infection and anti-SARS-CoV-2 vaccination, focusing on the profiling and long-term kinetics of virus-specific humoral and cell-mediated responses in both immunocompetent and immunocompromised individuals. Materials and Methods: A total of 209 individuals were enrolled from March 2020 to March 2022 at Careggi University Hospital and Meyer Children’s Hospital, Firenze, Italy, including 125 healthcare workers with or without history of SARS-CoV-2 infection who received the original BNT162b2 mRNA vaccine, 14 unvaccinated individuals hospitalized for COVID-19 in March- April 2020 followed up to one year post-hospital discharge, 41 patients with B-cell lymphoma either undergoing or previously treated with rituximab and 21 solid-organ transplant recipients on immunosuppressive therapy who received the original mRNA-1273 vaccine, and 8 people living with HIV who received a fourth original BNT162b2 mRNA vaccine dose. Main clinical data were collected. Humoral (serum levels of anti-Spike IgG and IgM, anti-RBD IgG, Spike-neutralizing antibodies, and anti-Nucleoprotein IgG) and cell-mediated (peripheral blood circulating Spike- specific T and B cells by multiparametric flow cytometry) responses were monitored. Results: In individuals who recovered from COVID-19, one mRNA vaccine dose was sufficient to reactivate immunological memory. However, naïve individuals, with no prior history of SARS- CoV-2 infection, required two mRNA vaccine doses to generate a robust immune response. SARS-CoV-2-Spike-specific CD4+ T and B cell-mediated immunity was still detectable 8 months after the second vaccine dose, while antibody levels significantly declined at 6 months, especially in naïve individuals. Immunological memory induced by vaccination showed similar decay kinetics to that observed following infection. Additionally, a booster dose was necessary for naïve individuals, as it not only restored but also enhanced anti-Spike immunity to levels similar to those observed in vaccinated COVID-19 recovered individuals. In patients with B-cell lymphoma receiving rituximab therapy, anti-SARS-CoV-2 mRNA vaccination induced a weak or absent humoral response, but a strong Spike-specific CD4+ T cell response. Bendamustine-containing chemotherapy further impaired the ability to mount a humoral response, even after prolonged discontinuation of treatment, and it was associated with the severity of breakthrough infections in vaccinated patients with B-cell lymphoma. Similarly, solid-organ transplant recipients on immunosuppressive regimens containing antimetabolites exhibited lower humoral and cell- mediated immune responses following vaccination compared to those on regimens without antimetabolites. Finally, in people living with HIV and lower CD4+ T cell counts, a fourth vaccine dose transiently boosted Spike-specific adaptive immunity, with cross-reactive CD4+ T cell and B cell responses against the Omicron variant. Conclusions: Active monitoring of long-term immunity against SARS-CoV-2, whether induced by infection and/or vaccination, provides essential information for optimizing immunization strategies. Anti-SARS-CoV-2 mRNA vaccines induce long-term adaptive immunity. Additional vaccine doses boost immunological memory, particularly in naïve and in immunocompromised individuals. Spike-specific cell-mediated immune responses induced by the original anti-SARS- CoV-2 mRNA vaccines are preserved against the Omicron variant.