Individuals with primary and secondary immunodeficiencies, being more susceptible to infections, are a priority for vaccination. Here, we determined and compared in a longitudinal study the immune response elicited by SARS-CoV-2 vaccination across different groups of individuals who are immunocompromised. In the PatoVac_COV longitudinal prospective single-centre study, the spike-specific B cell and antibody responses to SARS-CoV-2 mRNA vaccination were compared across 5 different groups of individuals with haematological malignancies, hematopoietic stem cell (HCT) or solid organ transplantation (SOT), undergoing haemodialysis, and people living with HIV (PLWH), for a total of 585 participants. Data from participants who were immunocompromised were compared to a group of 123 participants who were immunocompetent. Blood samples were collected before and after each vaccine administration, up to 2 years. A different immune responsiveness was observed after the first two vaccine doses, with haematological, haemodialysis, and SOT participants showing reduced responsiveness compared to HCT and PLWH, and relative to the comparison group. Spike-specific B cell response was both slower and lower in all groups except in PLWH when compared to participants who were immunocompetent. However, the first booster dose enhanced both the B and the antibody responses in all groups, that persisted up to 2 years after the first vaccine administration. The administration of Omicron-adapted booster vaccines promoted a primary BA.2 RBD-specific B cell response, especially in participants who were immunocompromised. Despite repeated vaccinations, a subset of persistent low-responders, especially among SOT, was identified. Our study highlights the heterogeneous immune response across individuals with different pathologies, the pivotal role of the first booster dose, the primary activation of Omicron-specific B cells elicited by updated variant-adapted vaccines and the persistence of low-responders despite multiple vaccine administrations. These aspects have a clinical relevance for planning vaccination schedules tailored for individuals with different immunocompromising conditions. This work was supported by funds from the Department of Medical Biotechnologies of the University of Siena, and from EU within the NextGenerationEU-MUR PNRR Tuscany Health Ecosystem (Project no ECS00000017-THE).

The mRNA vaccines for SARS-CoV-2 have demonstrated efficacy and immunogenicity in the real-world setting. However, most of the research on vaccine immunogenicity has been centered on characterizing the antibody response, with limited exploration into the persistence of spike-specific memory B cells. Here we monitored the durability of the memory B cell response up to 9 months post-vaccination, and characterized the trajectory of spike-specific B cell phenotypes in healthy individuals who received two doses of the BNT162b2 vaccine. To profile the spike-specific B cell response, we applied the tSNE and Cytotree automated approaches. Spike-specific IgA⁺ and IgG⁺ plasmablasts and IgA⁺ activated cells were observed 7 days after the second dose and disappeared 3 months later, while subsets of spike-specific IgG⁺ resting memory B cells became predominant 9 months after vaccination, and they were capable of differentiating into spike-specific IgG secreting cells when restimulated in vitro. Other subsets of spike-specific B cells, such as IgM⁺ or unswitched IgM⁺IgD⁺ or IgG⁺ double negative/atypical cells, were also elicited by the BNT162b2 vaccine and persisted up to month 9. The analysis of circulating spike-specific IgG, IgA, and IgM was in line with the plasmablasts observed. The longitudinal analysis of the antigen-specific B cell response elicited by mRNA-based vaccines provides valuable insights into our understanding of the immunogenicity of this novel vaccine platform destined for future widespread use, and it can help in guiding future decisions and vaccination schedules.

Background The spread of SARS-CoV-2 Omicron variant and its subvariants, highly transmissible but responsible of milder disease, has increased unreported infection cases. Identifying unaware infected individuals is crucial for estimating the true prevalence of infection and evaluating the breadth of hybrid immunity. In this study, this challenge was addressed by applying several Machine Learning approaches. Methods A group of 116 participants, vaccinated against SARS-CoV-2, was enrolled in the IMMUNO_COV study at Siena University Hospital, Italy. Blood samples were collected before and six months after third vaccine dose. Machine Learning analysis, involving dimensionality reduction techniques, unsupervised clustering methods and classification models, were applied to serological data including antibody responses specific for wild type SARS-CoV-2 strain as well as Delta, Omicron BA.1 and Omicron BA.2 variants. Spike- and nucleocapsid-specific B cells were also assessed in each participant. Results Using dimensionality reduction and unsupervised clustering, participants are grouped into high- and low-responders, with infected participants mainly distributed within the high-responders. Implementation of a consensus-based approach, including k-NN, RF, and SVM models, identifies 14 participants unaware of previous infection. Their immunological profile, characterized by strong spike- and nucleocapsid-specific humoral and B cell responses, significantly differs from that of non-infected participants. Conclusions Machine Learning approaches are applied to identify participants unaware of prior infection and to dissect their hybrid immunity profiles. Based on serological data, this cost-effective method can be a valuable tool for estimating the true prevalence of infection, improving comprehension of immune responses elicited by vaccination alone or combined with infection, and tailoring public health interventions.

The mRNA vaccines for SARS-CoV-2 have demonstrated efficacy and immunogenicity in the re-al-world setting. However, most of the research on vaccine immunogenicity has been centered on characterizing the antibody response, with limited exploration into the persistence of spike-specific memory B cell response. Here we monitored the durability of the memory B cell response and characterize the trajectory of spike-specific B cell phenotypes in healthy individuals who have received two doses of the BNT162b2 vaccine up to 9 months post-vaccination. To profile the spike-specific B cell response we applied the tSNE and Cytotree automated approaches. Our data showed the induction of spike-specific IgA+ and IgG+ plasmablasts and IgA+ activated cells 7 days after the second dose which disappeared 3 months later, while subsets of spike-specific IgG+ resting memory B cells became predominant 9 months after vaccination, and they were capable to differentiate into spike-specific IgG secreting cells when in vitro restimulated. Other subsets of spike-specific B cells, such as IgM+ or unswitched IgM+IgD+ or IgG+ double negative/atypical cells, were also elicited by the BNT162b2 vaccine and persisted up to month 9. The analysis of circulating spike-specific IgG, IgA and IgM was in line with the plasmablasts observed. The longitudinal analysis of the antigen-specific B cell response elicited by mRNA-based vaccines provides valuable insights into our understanding of the immunogenicity of this novel vaccine platform destined to a future widespread use, and it is crucial in guiding future decisions and vaccination schedules.

Indigenous Saccharomyces cerevisiae strains persist within individual cellars and contribute to the character of spontaneously fermented wines, yet the molecular basis of their oenological differences remains largely unknown. In this work, eight predominant strains isolated from spontaneous fermentations in four Tuscan wineries were characterized by technological traits of oenological relevance and laboratory-scale fermentations of both a synthetic must and Sangiovese grape must. In each must, the strains reached similar final ethanol concentrations, although lag phase and maximum fermentation rate differed significantly, whereas the resulting wines differed significantly in glycerol, acetic acid and phenolic alcohol content and in the scores assigned by a trained sensory panel. Four strains spanning the observed range of behaviors were hence analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-ToF MS) at an early and a mid-fermentation stage, yielding 30–46 differentially abundant proteins identified per strain. Strain-specific abundance of proteins involved in glycerol formation, acetaldehyde oxidation and sulfur amino acid metabolism paralleled the corresponding differences in glycerol, acetic acid and hydrogen sulfide production, whereas glycolytic enzyme abundance varied without any corresponding variation in ethanol. Proteomic analysis thus identified candidate molecular correlates of the traits that distinguish strains, suggesting that it could complement traditional screening in the selection of indigenous starter cultures.