Beneficial and harmful long-term consequences of COVID-19

Beneficial and harmful long-term consequences of COVID-19Background. There is considerable interindividual heterogeneity in human T and B cell effector responses, which can result in pathogen clearance and immunological memory or in immunopathology. The role of infection history in shaping different immune cell compartments is increasingly appreciated, although many aspects are still unclear in humans. Moreover, the effects of infections that generate strong systemic inflammation - such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - on T and B cells specific to other pathogens, autoantigens, and allergens is even less well understood.Hypothesis. We surmise SARS-CoV-2 infection generates immunological memory across different compartments, with compartment-specific phenotypical and functional features. Furthermore, we hypothesize acute infection will also impose an expansion-contraction dynamic on previously established memory populations, albeit to a lower extent than in SARS-CoV-2-specific T and B cells, thus resulting in shifts of T cell receptor (TCR) and B cell receptor (BCR) repertoires. We suspect that similar changes affect autoreactive and allergen-specific T and B cells and that such changes might be prominent in a subset of individuals with post-acute coronavirus disease 2019 (COVID-19) syndrome ('long-Covid').Aim 1: Characterization of SARS-CoV-2-specific T and B cells across different tissues. We have recently investigated SARS-CoV-2-specific T cell immunity in our COVID-19 cohort, which comprises 175 individuals followed up until one year after acute infection (Adamo et al. Nature 2022). In this proposal, we will assess SARS-CoV-2-specific T and B cell responses in blood, tonsils, and skin biopsies by using spectral flow cytometry, single-cell RNA sequencing (scRNAseq), and imaging mass cytometry. This comprehensive characterization will address important outstanding issues of long-lived memory cell distribution and phenotypes across lymphoid and non-lymphoid tissues.Aim 2: Effect of SARS-CoV-2 infection on pre-existing memory T and B cells. In our well-characterized COVID-19 cohort, we will assess the impact of SARS-CoV-2 infection on pre-existing memory T and B cell populations. To this end, we will perform spectral flow cytometry analysis and scRNAseq along with TCR and BCR sequencing, probing epitopes derived from common human pathogens such as cytomegalovirus (CMV), Epstein-Barr virus (EBV), and influenza A virus (IAV). Combining these approaches, we will estimate the dynamics and sizes of CMV+, EBV+, and IAV+ memory T and B cells during and after COVID-19 and observe changes in phenotype and transcriptome of memory cells, including bystander T and B cell activation and shifts in TCR and BCR repertoires.Aim 3: Effect of SARS-CoV-2 infection on autoreactive and allergen-specific T and B cells. We will investigate the effect of COVID-19 infection on autoreactive and allergen-specific memory T and B cells. Thus, we will adopt a similar experimental strategy to that described in Aim 2. Moreover, we will analyze these T and B cells in subjects recovering from COVID-19 compared to those with long-Covid.Expected results and impact. We will study the effects of acute infection on newly-formed and pre-existing memory cells, thus gaining insight into the dynamics of longevity, expansion and attrition of immunological memory. Furthermore, we will assess the impact of acute infection on autoreactive and allergen-specific T and B cell repertoires. Together, these findings will inform on the long-term beneficial and potentially harmful consequences of a natural acute infection in humans.