Long-term immune profiling of COVID-19 recovered patients: effects of disease severity and vaccination

Introduction: The COVID-19 pandemic caused varied disease outcomes globally, with individuals experiencing severe, non-severe, or no disease. Immune responses generated post-exposure to SARS-CoV-2 play a critical role in protecting against severe COVID-19 upon re-infection. This study aimed to analyze immune-cell phenotypes and functions in COVID-19 Recovered Patients (C-19RPs) from varying disease severities. Objective: To compare the immune-cell phenotypes and functions in C-19RPs from different forms of the disease, more than six months post-infection. Methods: Between September 2021 and July 2023, 101 C-19RPs with hospital data (median age 31) were recruited from Mbeya Zonal Referral Hospital, Tanzania. In addition, seven uninfected and 19 Actively Infected Patients (AIPs) (median age 34 and 58. 5, respectively) were included as controls. Blood samples were collected for SARS-CoV-2 serology, immune and genomic analysis, whereas demographic and vaccination data were gathered through a questionnaire. Results: Serum anti-SARS-CoV-2 levels were similar between severe and non-severe C-19RPs but significantly higher in vaccinated non-severe cases than in unvaccinated ones. Severe C-19RPs and AIPs showed a trend towards decreased switched memory B cells. Frequencies of T-cell subsets were broadly similar across groups, but AIPs had increased central memory and decreased effector memory and effector CD4 T cells. T-cell responses to SARS-CoV-2 nucleocapsid peptides were not affected, but severe C-19RPs had increased CD8 cytokine responses and degranulation upon stimulation with Staphylococcus enterotoxin B (SEB). The frequency of CD56DimCD16Bright NK subsets was high in C-19RPs, while CD56DimCD16Neg subsets were reduced only in severe C-19RPs. DNA sequence analysis of the HLA from 18 C-19RPs and five uninfected participants revealed 11 and 20 alleles, which were exclusively found in severe and non-severe C-19RPs, respectively. Conclusion: COVID-19 vaccination was particularly beneficial for non-severe C-19RPs, highlighting the benefits of vaccination in this group. Frequencies of B and NK cell subsets were long-term altered in the C-19RPs, while CD4 T-cell subset alterations were only in the AIPs. The enhanced T-cell response to SEB in the severe C-19RPs suggests potential long-term T-cell hyperresponsiveness, warranting further research. The unique HLA alleles exclusively found in either severe or non-severe C-19RPs may require additional exploration to confirm their association with disease severity.