Characterizing the cellular and molecular variabilities of peripheral immune cells in healthy recipients of BBIBP-CorV inactivated SARS-CoV-2 vaccine by single-cell RNA sequencing

Longitudinal assessment of immunogenicity of inactivated COVID-19 booster immunization and breakthrough infection in blood donors: A multicenter study from 2021 to 2023

Assessing immune responses across diverse populations is essential for refining public health strategies. Blood donors offer valuable insights into community-level immunity. This study aims to investigate immune responses associated with inactivated COVID-19 booster immunization and breakthrough infections in blood donors. This study was conducted in a cohort of blood donors from six centers across five of China's seven major geographical regions, spanning from December 2021 to February 2023. Blood samples were collected before booster vaccination, at 1, 3, and 6 months post-vaccination, as well as 1 month post-infection. SARS-CoV-2-specific antibodies, T cell specific IFNγ levels, and neutralizing antibodies against wild-type and Omicron strains were measured. Platelet count, anti-PF4 antibody, and D-dimer levels were assessed. Demographic characteristics were analyzed to determine their impact on immunogenicity. SARS-CoV-2-specific antibodies and IFNγ levels significantly increased post-booster, peaking one month after immunization. Antibodies continued to decrease at six months, while IFNγ levels remained stable at this point. Pseudovirus neutralization assays revealed elevated neutralizing antibodies following the booster dose, with minimal response to the XBB.1.5 variant. Following Omicron infection, antibody and IFNγ levels surpassed that observed post-booster. Participants aged 36-49 and those over 50 exhibited weaker immune responses post-booster than those ages 18-35, while those with BMI above 28 showed lower IFNγ levels. This study demonstrates the utility of blood donor samples for tracking immunization effectiveness against emerging pathogens, and highlights enhanced immune responses after booster immunization and breakthrough infections, underscoring the need for tailored vaccination strategies for different groups.

Impact of CD4+ T cell and TCR repertoires on SARS-CoV-2-Specific antibody responses in PLWH following COVID-19 vaccination

In people living with human immunodeficiency virus (HIV, PLWH), the coronavirus disease 2019 (COVID-19) vaccine often results in a limited humoral immune response. While a reduced absolute CD4+ T cell count is a known factor, other determinants remain unclear. To investigate variables influencing the differential antibody response to the COVID-19 vaccine in PLWH, 43 HIV-1/AIDS patients receiving antiretroviral therapy (ART) and 2 doses of the COVID-19 vaccine were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G (IgG) levels and neutralizing antibody (NAb) titers. A retrospective analysis was also performed, examining immune reconstitution and epidemiological history, including annual CD4+ T-cell counts and the duration of HIV-1 infection. To further elucidate the role of CD4+ T cells in the antibody response to the COVID-19 vaccine, next-generation sequencing was used to analyze the T cell receptor (TCR) profiles of CD4+ T cells from twelve representative individuals. The results showed that the SARS-CoV-2-specific antibody response in PLWH was not solely determined by the current CD4+ T cell count, the progression of immune reconstitution and the TCR profile of CD4+ T cells also played significant roles. These findings provide critical insights into the multifaceted roles of CD4+ T cells in SARS-CoV-2-specific antibody responses in PLWH following COVID-19 vaccination.

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age

A comprehensive understanding of the evolution of the immune landscape in humans across the entire lifespan at single-cell transcriptional and protein levels, during development, maturation and senescence is currently lacking. We recruited a total of 220 healthy volunteers from the Shanghai Pudong Cohort (NCT05206643), spanning 13 age groups from 0 to over 90 years, and profiled their peripheral immune cells through single-cell RNA-sequencing coupled with single T cell and B cell receptor sequencing, high-throughput mass cytometry, bulk RNA-sequencing and flow cytometry validation experiments. We revealed that T cells were the most strongly affected by age and experienced the most intensive rewiring in cell-cell interactions during specific age. Different T cell subsets displayed different aging patterns in both transcriptomes and immune repertoires; examples included GNLY+CD8+ effector memory T cells, which exhibited the highest clonal expansion among all T cell subsets and displayed distinct functional signatures in children and the elderly; and CD8+ MAIT cells, which reached their peaks of relative abundance, clonal diversity and antibacterial capability in adolescents and then gradually tapered off. Interestingly, we identified and experimentally verified a previously unrecognized 'cytotoxic' B cell subset that was enriched in children. Finally, an immune age prediction model was developed based on lifecycle-wide single-cell data that can evaluate the immune status of healthy individuals and identify those with disturbed immune functions. Our work provides both valuable insights and resources for further understanding the aging of the immune system across the whole human lifespan.

Single-cell transcriptome atlas of peripheral immune features to Omicron breakthrough infection under booster vaccination strategies

Introduction

The high percentage of Omicron breakthrough infection in vaccinees is an emerging problem, of which we have a limited understanding of the phenomenon.

Methods

We performed single-cell transcriptome coupled with T-cell/B-cell receptor (TCR/BCR) sequencing in 15 peripheral blood mononuclear cell (PBMC) samples from Omicron infection and naïve with booster vaccination.

Results

We found that after breakthrough infection, multiple cell clusters showed activation of the type I IFN pathway and widespread expression of Interferon-stimulated genes (ISGs); T and B lymphocytes exhibited antiviral and proinflammatory-related differentiation features with pseudo-time trajectories; and large TCR clonal expansions were concentrated in effector CD8 T cells, and clonal expansions of BCRs showed a preference for IGHV3. In addition, myeloid cells in the BA.5.2 breakthrough infection with the fourth dose of aerosolized Ad5-nCoV were characterized by enhanced proliferation, chemotactic migration, and antigen presentation.

Discussion

Collectively, our study informs the comprehensive understandings of immune characterization for Omicron breakthrough infection, revealing the positive antiviral potential induced by booster doses of vaccine and the possible "trained immunity" phenomenon in the fourth dose of aerosolized Ad5-nCoV, providing a basis for the selection of vaccination strategies.

An insight into COVID-19 host immunity at single-cell resolution

Host immunity helps the body to fight against COVID-19. Single-cell transcriptomics has provided the scope of investigating cellular and molecular underpinnings of host immune response against SARS-CoV-2 infection at high resolution. In this review, we have systematically described the virus-induced dysregulation of relative abundance as well as molecular behavior of each innate and adaptive immune cell type and cell state during COVID-19 infection and for different vaccinations, based on single-cell studies published in last three-four years. Identification and characterization of these disease-associated specific cell populations might help to design better, efficient, and targeted therapeutic avenues.

The characteristics of TCR CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccine recipients

The COVID-19 pandemic and large-scale administration of multiple SARS-CoV-2 vaccines have attracted global attention to the short-term and long-term effects on the human immune system. An analysis of the "traces" left by the body's T-cell immune response is needed, especially for the prevention and treatment of breakthrough infections and long COVID-19 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infections. T-cell receptor complementarity determining region 3 (TCR CDR3) repertoire serves as a target molecule for monitoring the effects, mechanisms, and memory of the T-cell response. Furthermore, it has been extensively applied in the elucidation of the infectious mechanism and vaccine refinement of hepatitis B virus (HBV), influenza virus, human immunodeficiency virus (HIV), and SARS-CoV. Laboratories worldwide have utilized high-throughput sequencing (HTS) and scTCR-seq to characterize, share, and apply the TCR CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccine recipients. This article focuses on the comparative analysis of the diversity, clonality, V&J gene usage and pairing, CDR3 length, shared CDR3 sequences or motifs, and other characteristics of TCR CDR3 repertoire. These findings provide molecular targets for evaluating T-cell response effects and short-term and long-term impacts on the adaptive immune system following SARS-CoV-2 infection or vaccination and establish a comparative archive of T-cell response "traces."

Single-cell sequencing to multi-omics: technologies and applications

Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged as one of the most vibrant research fields today. With the optimization and innovation of single-cell sequencing technologies, the intricate multidimensional details concealed within cells are gradually unveiled. The combination of scRNA-seq and other multi-omics is at the forefront of the single-cell field. This involves simultaneously measuring various omics data within individual cells, expanding our understanding across a broader spectrum of dimensions. Single-cell multi-omics precisely captures the multidimensional aspects of single-cell transcriptomes, immune repertoire, spatial information, temporal information, epitopes, and other omics in diverse spatiotemporal contexts. In addition to depicting the cell atlas of normal or diseased tissues, it also provides a cornerstone for studying cell differentiation and development patterns, disease heterogeneity, drug resistance mechanisms, and treatment strategies. Herein, we review traditional single-cell sequencing technologies and outline the latest advancements in single-cell multi-omics. We summarize the current status and challenges of applying single-cell multi-omics technologies to biological research and clinical applications. Finally, we discuss the limitations and challenges of single-cell multi-omics and potential strategies to address them.

The characteristics of BCR-CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccinated volunteers

The global COVID-19 pandemic has caused more than 1 billion infections, and numerous SARS-CoV-2 vaccines developed rapidly have been administered over 10 billion doses. The world is continuously concerned about the cytokine storms induced by the interaction between SARS-CoV-2 and host, long COVID, breakthrough infections postvaccination, and the impact of SARS-CoV-2 variants. BCR-CDR3 repertoire serves as a molecular target for monitoring the antiviral response "trace" of B cells, evaluating the effects, mechanisms, and memory abilities of individual responses to B cells, and has been successfully applied in analyzing the infection mechanisms, vaccine improvement, and neutralizing antibodies preparation of influenza virus, HIV, MERS, and Ebola virus. Based on research on BCR-CDR3 repertoire of COVID-19 patients and volunteers who received different SARS-CoV-2 vaccines in multiple laboratories worldwide, we focus on analyzing the characteristics and changes of BCR-CDR3 repertoire, such as diversity, clonality, V&J genes usage and pairing, SHM, CSR, shared CDR3 clones, as well as the summary on BCR sequences targeting virus-specific epitopes in the preparation and application research of SARS-CoV-2 potential therapeutic monoclonal antibodies. This review provides comparative data and new research schemes for studying the possible mechanisms of differences in B cell response between SARS-CoV-2 infection or vaccination, and supplies a foundation for improving vaccines after SARS-CoV-2 mutations and potential antibody therapy for infected individuals.

Breakthrough infection evokes the nasopharyngeal innate immune responses established by SARS-CoV-2-inactivated vaccine

Nasopharyngeal immune responses are vital for defense against SARS-CoV-2 infection. Although vaccination via muscle immunization has shown a high efficacy in reducing severity and death in COVID-19 infection, breakthrough infection frequently happens because of mutant variants and incompletely established mucosal immunity, especially in the upper respiratory tract. Here, we performed a single-cell RNA and T-cell receptor repertoire sequencing and delineated a high-resolution transcriptome landscape of nasopharyngeal mucosal immune and epithelial cells in vaccinated persons with breakthrough infection and non-vaccinated persons with natural infection as control. The epithelial cells showed anti-virus gene expression diversity and potentially recruited innate immune cells into the nasopharyngeal mucous of vaccinated patients. Upon infection, they released significant pro-inflammatory cytokines and chemokines by macrophages and monocytes and expressed antigen-presenting relevant genes by dendritic cells. Such immune responses of nasopharyngeal innate immune cells would facilitate the strengthened expression of cytotoxic genes in virus-specific T-cell or B-cell differentiation into antibody-secreting cells at the early stage of breakthrough infection through cell interaction between innate and adaptive immune cells. Notably, these alterations of nasopharyngeal immune cells in breakthrough infection depended on the activated Nuclear factor-κB (NF-κB) and NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) signaling rather than type I interferon responses due to the general reduction in interferon-stimulated gene expression. Our findings suggest that vaccination potentially strengthens innate immune barriers and virus-specific memory immune cell responses, which could be quickly activated to defend against variant breakthrough infection and maintain nasopharyngeal epithelial cell integrity. Thus, this study highlights the necessity of a boost via nasal mucous after intramuscular immunization.