Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

T-cell responses to highly conserved SARS-CoV-2 epitopes in Hispanic Americans receiving an mRNA COVID-19 vaccine

This study reports the pre-clinical evaluation of peptides from EPV-CoV-19, a T cell epitope-based SARS-CoV-2 vaccine candidate, following spike-mRNA vaccination of a predominantly Hispanic American cohort. EPV-COV-19 peptides' potential to boost T cell responses to spike protein vaccines was evaluated, confirming previously observed memory recall responses in donors with prior immunity to COVID-19. The vaccinated subjects' averaged immune responses to the 15-peptide EPV-CoV-19 pool achieved 85% of the observed response to a spike protein peptide array containing a 7-fold greater epitope content, suggesting that the EPV-CoV-19 peptides have a higher relative concentration of T cell epitope content per-peptide. Ten of the 15 peptides contained spike epitopes conserved in the majority of variants of concern (VOC) evaluated over the 2020-2024 period. While commercial vaccines exhibited gradual loss of T cell epitope conservation with VOC over time, the EPV-CoV-19 epitope-peptides maintained conservation until the XBB variant emerged. The addition of one new peptide to the vaccine design reestablished broad T cell epitope coverage. These findings underscore the importance of identifying highly conserved T cell epitopes for vaccine designs that target rapidly-mutating strains of emergent pathogens, while also documenting broad memory T cell response to the vaccine in a predominantly Hispanic American cohort.

The presenting HLA determines fidelity of SARS-CoV-2 spike protein epitope prediction

Early in the COVID-19 pandemic, multiple studies used prediction methods to identify candidate peptides to be included in prospective vaccines. While subsequent studies identified epitopes from convalescent and vaccinated subjects, few studies have compared the predicted to identified epitopes. Here we used three methods to predict SARS-CoV-2 spike protein helper T cell epitopes and compared the results to experimentally determined peptide binding as well as published epitopes. The correspondence between the predicted and experimental binding results and published epitopes depended more on the HLA being investigated than the prediction method used. Lastly, these observations were used to predict peptides which bind to the most HLAs. These peptides were previously identified and predicted to maintain HLA binding in the current variants of interest. This study highlights which prediction methods and conditions lead to the most reliable prediction results which would be of great interest for improving the design of future vaccines.

In-house assays for detecting anti-SARS-CoV-2 antibodies in serum and urine: Correlation with COVID-19 severity from a cohort study in Qatar

BACKGROUND

Serological assays targeting antibodies against key viral proteins, including the Spike (S1), Receptor Binding Domain (RBD), and Nucleocapsid, play a critical role in understanding immunity and supporting diagnostic efforts during COVID-19 pandemic, and afterward. This study aimed to develop and validate in-house assays for detecting anti-SARS-CoV-2 antibodies in serum and urine.

METHODS

ELISA-based assay was developed to detect IgG and IgM antibodies against SARS-CoV-2. The assay was examined in serum and urine samples of two different cohort of patients affected by COVID-19 disease with different severity and compared to age and sex matched control group. Neutralizing antibody activity was evaluated using an RBD-ACE2 binding inhibition assay. Additionally, a Sengenics protein microarray platform was employed to assess epitope-specific antibody responses.

RESULTS

The in-house ELISA assay reliably detected antibodies in both 163 serum and 64 urine samples compared to 50 serum samples from healthy control, with strong correlations observed between antibody levels in the two biofluids. Neutralizing antibody levels correlated positively with disease severity, highlighting their clinical relevance. The performance of the in-house assays was comparable to commercial kits, and the Sengenics microarray provided detailed insights into antibody profiles, identifying dominant epitopes within the Nucleocapsid core domain and RBD.

CONCLUSIONS

The developed in-house assay demonstrated robust performance and versatility, offering a cost-effective and scalable alternative to commercial kits. Their ability to detect antibodies in both serum and urine highlighted their potential as non-invasive diagnostic tools. These findings contribute to advancing sero-diagnostic capabilities, improving understanding of immune responses to SARS-CoV-2, and supporting global efforts to monitor and manage COVID-19 effectively.

Methodological approach to identify immunogenic epitopes candidates for vaccines against emerging pathogens tailored to defined HLA populations

Vaccines stimulate cells of the adaptive immune system, generating a protective and lasting memory, and are the main public health strategy to protect the world population from emerging pathogens such as the SARS-CoV-2 virus, responsible for millions of deaths in the recent COVID-19 pandemic. Several in-silico algorithms have facilitated the selection of antigens as vaccine candidates; however, their predictive capacity remains limited and it is necessary to continue training them, using information obtained in immunological assays. In this work, the SARS-CoV-2 proteome was sampled using a series of concatenated algorithms that allowed us to define a series of candidate viral peptides for a vaccine against SARS-CoV-2 in individuals from Colombian, whose haplotypes for HLA-I and II were incorporated as part of the algorithm. The immunogenicity of the peptides predicted with three tools or with the combination of them was evaluated and found that short peptides predicted and selected as highly immunogenic peptides were capable of expanding memory CD8 T lymphocytes with an activation phenotype. Altogether, our results outline a pipeline that combines a bioinformatic and immunological approach useful to select immunogenic epitopes from emerging pathogens as vaccine candidates tailored to the population's HLA-Haplotypes.

Evaluation of broad-spectrum protection by novel mRNA vaccines against SARS-CoV-2 variants (Delta, Omicron-BA.5, XBB-EG.5) in the golden hamster model

BACKGROUND

The SARS-CoV-2 virus has continuously evolved, with new variants like Delta, Omicron-BA.5, and XBB-EG.5 posing challenges to vaccine efficacy. mRNA vaccines have emerged as a promising tool due to their rapid development and adaptability. This study evaluates the protective efficacy of six novel mRNA vaccine candidates against these variants using a golden hamster model.

METHODS

Six mRNA vaccines were designed, targeting the spike (S) and nucleocapsid (N) proteins of SARS-CoV-2. The vaccines were tested on golden hamsters, which were immunized and then challenged with Delta, Omicron-BA.5, and XBB-EG.5 variants. Key outcomes measured included body weight, viral RNA loads in various tissues, cytokine levels, and lung tissue pathology.

RESULTS

Hamsters vaccinated with the novel mRNA vaccines showed reduced weight loss, lower viral RNA loads in throat swabs and lung tissues, and reduced levels of pro-inflammatory cytokines compared to control groups. Additionally, vaccinated animals exhibited significantly less lung damage as evidenced by both histological and immunofluorescence analyses, especially in groups vaccinated with RBD-Fe, RE-N, and COVID-19 epitope formulations.

CONCLUSIONS

These mRNA vaccines demonstrated broad protective efficacy against multiple SARS-CoV-2 variants. They elicited immune responses, reduced viral RNA loads, and mitigated inflammatory and pathological damage, highlighting their potential in combating rapidly evolving SARS-CoV-2 variants.

SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform

To address the need for broadly protective SARS-CoV-2 vaccines, we developed an attenuated a SARS-CoV-2 vaccine virus that lacks the open reading frames of two viral structural proteins: the envelope (E) and membrane (M) proteins. This vaccine virus (ΔEM) replicates in a cell line stably expressing E and M but not in wild-type cells. Vaccination with ΔEM elicits a CD8 T-cell response against the viral spike and nucleocapsid proteins. Two vaccinations with ΔEM provide better protection of the lower respiratory tissues than a single dose against the Delta and Omicron XBB variants in hamsters. Moreover, ΔEM is effective as a booster in hamsters previously vaccinated with an mRNA-based vaccine, providing higher levels of protection in both respiratory tissues compared to the mRNA vaccine booster. Collectively, our data demonstrate the feasibility of a SARS-CoV-2 ΔEM vaccine candidate virus as a vaccine platform.

T cell memory response to MPXV infection exhibits greater effector function and migratory potential compared to MVA-BN vaccination

In 2022, a global mpox outbreak occurred, and remains a concern today. The T cell memory response to MPXV (monkeypox virus) infection has not been fully investigated. In this study, we evaluate this response in convalescent and MVA-BN (Modified Vaccinia Ankara - Bavarian Nordic) vaccinated individuals using VACV-infected cells. Strong CD8+ and CD4+ T cell responses are observed, and T cell responses are biased towards viral early expressed proteins. We identify seven immunodominant HLA-A*02:01 restricted MPXV-specific epitopes and focus our detailed phenotypic and scRNAseq analysis on the immunodominant HLA-A*02:01-G5R18-26-specific CD8+ T cell response. While tetramer+CD8+ T cells share similar differentiation and activation phenotypes, T cells from convalescent individuals show greater cytotoxicity, migratory potential to site of infection and TCR clonal expansion. Our data suggest that effective functional profiles of MPXV-specific memory T cells induced by Mpox infection may have an implication on the long-term protective responses to future infection.

Predicting immune protection against outcomes of infectious disease from population-level effectiveness data with application to COVID-19

Quantifying the extent to which previous infections and vaccinations confer protection against future infection or disease outcomes is critical to managing the transmission and consequences of infectious diseases. We present a general statistical model for predicting the strength of protection conferred by different immunising exposures (numbers, types, and strains of both vaccines and infections), against multiple outcomes of interest, whilst accounting for immune waning. We predict immune protection against key clinical outcomes: developing symptoms, hospitalisation, and death. We also predict transmission-related outcomes: acquisition of infection and onward transmission in breakthrough infections. These enable quantification of the impact of immunity on population-level transmission dynamics. Our model calibrates the level of immune protection, drawing on both population-level data, such as vaccine effectiveness estimates, and neutralising antibody levels as a correlate of protection. This enables the model to learn realised immunity levels beyond those which can be predicted by antibody kinetics or other correlates alone. We demonstrate an application of the model for SARS-CoV-2, and predict the individual-level protective effectiveness conferred by natural infections with the Delta and the Omicron B.1.1.529 variants, and by the BioNTech-Pfizer (BNT162b2), Oxford-AstraZeneca (ChAdOx1), and 3rd-dose mRNA booster vaccines, against outcomes for both Delta and Omicron. We also demonstrate a use case of the model in late 2021 during the emergence of Omicron, showing how the model can be rapidly updated with emerging epidemiological data on multiple variants in the same population, to infer key immunogenicity and intrinsic transmissibility characteristics of the new variant, before the former can be more directly observed via vaccine effectiveness data. This model provided timely inference on rapidly evolving epidemic situations of significant concern during the early stages of the COVID-19 pandemic. The general nature of the model enables it to be used to support management of a range of infectious diseases.

CD47-amyloid-β-CD74 signaling triggers adaptive immunosuppression in sepsis

Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. However, how this dysregulation occurs remains to be elucidated. In this study, we use single-cell RNA sequencing (scRNA-seq) and conventional RNA-seq to analyze the immune landscape of sepsis and observe that adaptive immunity is acutely and strongly suppressed. This systemic immunosuppression occurs not only in the peripheral blood but also in all other immune compartments, including the spleen, lymph nodes, and bone marrow. Clinical data show that these adaptive immunity-related genes may have the potential to be used to distinguish patients with sepsis from those with common infections. CD47 is found to play a pivotal role in this immunosuppression by inducing the production of amyloid-β (Aβ), which interacts with CD74 on B cells, leading to B-cell suppression and subsequent adaptive immunosuppression. Blocking CD47-Aβ signaling significantly reduces organ injury and improves the survival rate of septic mice by restoring phagocytic cell functions and alleviating B-cell suppression and adaptive immunosuppression.

Targeting SARM1 as a novel neuroprotective therapy in neurotropic viral infections

Viral encephalitis, resulting from neurotropic viral infections, leads to severe neurological impairment, inflammation, and exhibits high mortality rates with poor prognosis. Currently, there is a lack of effective targeted treatments for this disease, which poses a significant public health concern. SARM1 has been identified as the pivotal mediator of axonal degeneration and inflammation across various neuropathies, activated by an elevation in the NMN/NAD+ ratio. However, comprehensive in vivo investigations into the role of SARM1-mediated pathogenesis in viral encephalitis are still lacking. In this study, we established mouse models of viral encephalitis using Japanese encephalitis virus (JEV), herpes simplex virus-1 (HSV-1), and rabies virus (RABV) as representative pathogens. Our findings demonstrate that neurotropic virus infections elicit robust axonal degeneration, mitochondrial dysfunction, and profound neuropathological damage in cortical neurons via the activation of SARM1. In mouse models of viral encephalitis, deletion or inhibition of SARM1 effectively preserved axonal morphology and maintained mitochondrial homeostasis, while also attenuating the infiltration of CD45+ leukocytes in the cortex. Consequently, these interventions ameliorated neuropathological damage and enhanced survival outcomes in mice. Our findings suggest that SARM1-mediated axonal degeneration and brain inflammation exacerbate the pathological progression of viral encephalitis. Therapies targeting SARM1 emerge as viable and promising strategies for protecting neuronal function in the context of neurotropic viral infections.

Intranasal replicon SARS-CoV-2 vaccine produces protective respiratory and systemic immunity and prevents viral transmission

While mRNA vaccines have been effective in combating SARS-CoV-2, the waning of vaccine-induced antibody responses and lack of vaccine-induced respiratory tract immunity contribute to ongoing infection and transmission. In this work, we compare and contrast intranasal (i.n.) and intramuscular (i.m.) administration of a SARS-CoV-2 replicon vaccine delivered by a nanostructured lipid carrier (NLC). Both i.m. and i.n. vaccines induce potent systemic serum neutralizing antibodies, bone marrow-resident immunoglobulin G-secreting cells, and splenic T cell responses. The i.n. vaccine additionally induces robust respiratory mucosal immune responses, including SARS-CoV-2-reactive lung-resident memory T cell populations. As a booster following previous i.m. vaccination, the i.n. vaccine also elicits the development of mucosal virus-specific T cells. Both the i.m.- and i.n.-administered vaccines durably protect hamsters from infection-associated morbidity upon viral challenge, significantly reducing viral loads and preventing challenged hamsters from transmitting virus to naive cagemates. This replicon-NLC vaccine's potent systemic immunogenicity, and additional mucosal immunogenicity when delivered i.n., may be key for combating SARS-CoV-2 and other respiratory pathogens.

The immunopathogenesis of SARS-CoV-2 infection: Overview of lessons learned in the first 5 years

This review provides a broad overview of lessons learned in the five years since COVID-19 was identified. It is a bimodal disease, starting with an initially virus-driven phase, followed by resolution or ensuing inappropriate immune activation causing severe inflammation that is no longer strictly virus dependent. Humoral immunity is beneficial for preventing or attenuating the early stage, without benefit once the later stage begins. Neutralizing antibodies elicited by natural infection or vaccination are short-lived and highly vulnerable to viral sequence variation. By contrast, cellular immunity, particularly the CD8+ T cell arm, has a role in preventing or attenuating severe disease, is far less susceptible to viral variation, and is longer-lived than antibodies. Finally, an ill-defined phenomenon of prolonged symptoms after acute infection, termed "long COVID," is poorly understood but may involve various immunologic defects that are hyperactivating or immunosuppressive. Remaining issues include needing to better understand the immune dysregulation of severe disease to allow more tailored therapeutic interventions, developing antibody strategies that cope with the viral spike sequence variability, prolonging vaccine efficacy, and unraveling the mechanisms of long COVID to design therapeutic approaches.

Patients With Mild COVID-19 Exhibit Low Functional Avidity of SARS-CoV-2 Membrane Protein-Reactive CD4+ T Cells

Herein, we found that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-unexposed individuals exhibited an increased frequency of CD4+ T cells against SARS-CoV-2 membrane (M) protein, suggesting that SARS-CoV-2 M-reactive cells may be primed by previous infection with common cold coronaviruses (CCCoVs). We confirmed that CCCoV M-reactive CD4+ T cells cross-recognize SARS-CoV-2 M in unexposed individuals. Among coronavirus disease 2019 (COVID-19) convalescents and unexposed individuals, SARS-CoV-2 M-reactive CD4+ T cells exhibited significantly lower functional avidity than CD4+ T cells reactive to other viruses. Importantly, convalescents from mild COVID-19 had SARS-CoV-2 M-reactive CD4+ T cells with significantly lower functional avidity than convalescents from severe COVID-19. The current data suggest that pre-existing CCCoV M-specific memory CD4+ T cells may contribute to controlling SARS-CoV-2 infection by cross-reactivity, leading to mild disease but leaving memory cells with low functional avidity to SARS-CoV-2 M due to incomplete homology. These data provide indirect evidence that pre-existing cross-reactive CD4+ T cells contribute to protection from severe COVID-19.

Natural Infection of Omicron BA.5.2 in Patients Provides Broad Immune Responses Against SARS-CoV-2

The implementation of COVID-19 policy and the rapid development of SARS-CoV-2 vaccines in the early pandemic significantly contained numerous outbreaks and reduced the severity and mortality of COVID-19. However, the population immunity induced by existing vaccines was insufficient to prevent SARS-CoV-2 outbreaks. The host immunity induced by the wide spread of Omicron variants and its influence on emerging SARS-CoV-2 variants are attracting broad attention. In this study, a clinical data analysis of the patients indicated that pre-vaccination reduced inflammatory responses and mitigated the severity of COVID-19 cases caused by natural infection with Omicron BA.5.2. The analysis of adaptive immune responses indicated that natural infection with BA.5.2 induced robust and broad immune responses, including both humoral and T cell-mediated immune responses (IFN-γ) against highly conserved viral antigens, and provided cross-reactive neutralization against various viral variants. Collectively, we report that the natural infection with Omicron BA.5.2 induced broad cross-reactive immunity against SARS-CoV-2 variants, which suggests that the development of a live attenuated SARS-CoV-2 vaccine with desired safety, high efficacy, broad spectrum, and long-term immune persistence is feasible. Therefore, we suggest that herd immunity, achieved through vaccination with attenuated vaccines, combined with booster doses of existing vaccines and antiviral therapy for people with high viral loads, may contribute to the eradication of this virus.

mRNA vaccine-induced SARS-CoV-2 spike-specific IFN-γ and IL-2 T-cell responses are predictive of serological neutralization and are transiently enhanced by pre-existing cross-reactive immunity

The contributions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells to vaccine efficacy and durability are unclear. We investigated relationships between mRNA vaccine-induced spike-specific interferon- gamma (IFN-γ) and interleukin-2 (IL-2) T-cell responses and neutralizing antibody development in long-term care home staff doubly vaccinated with BNT162b2 or mRNA-1273. The impacts of pre-existing cross-reactive T-cell immunity on cellular and humoral responses to vaccination were additionally assessed. Mathematical modeling of the kinetics of spike-specific IFN-γ and IL-2 T-cell responses over 6 months post-second dose was bifurcated into recipients who exhibited gradual increases with doubling times of 155 and 167 days or decreases with half-lives of 165 and 132 days, respectively. Differences in kinetics did not correlate with clinical phenotypes. Serological anti-spike IgG, anti-receptor binding domain (RBD) IgG, anti-spike IgA, and anti-RBD IgA antibody levels otherwise decayed in all participants with half-lives of 63, 57, 79, and 46 days, respectively, alongside waning neutralizing capacity (t1/2 = 408 days). Spike-specific T-cell responses induced at 2-6 weeks positively correlated with live viral neutralization at 6 months post-second dose, especially in hybrid immune individuals. Participants with pre-existing cross-reactive T-cell immunity to SARS-CoV-2 exhibited greater spike-specific T-cell responses, reduced anti-RBD IgA antibody levels, and a trending increase in neutralization at 2-6 weeks post-second dose. Non-spike-specific T-cells predominantly targeted SARS-CoV-2 non-structural protein at 6 months post-second dose in cross-reactive participants. mRNA vaccination was lastly shown to induce off-target T-cell responses against unrelated antigens. In summary, vaccine-induced spike-specific T-cell immunity appeared to influence serological neutralizing capacity, with only a modest effect induced by pre-existing cross-reactivity.

IMPORTANCE

Our findings provide valuable insights into the potential contributions of mRNA vaccine-induced spike-specific T-cell responses to the durability of neutralizing antibody levels in both uninfected and hybrid immune recipients. Our study additionally sheds light on the precise impacts of pre-existing cross-reactive T-cell immunity to severe acute respiratory syndrome coronavirus 2 on the magnitude and kinetics of cellular and humoral responses to vaccination. Accordingly, our data will help optimize the development of next-generation T cell-based coronavirus vaccines and vaccine regimens to maximize efficacy and durability.

Robust mucosal SARS-CoV-2-specific T cells effectively combat COVID-19 and establish polyfunctional resident memory in patient lungs

Mucosal antigen-specific T cells are pivotal for pathogen clearance and immune modulation in respiratory infections. Dysregulated T cell responses exacerbate coronavirus disease 2019 severity, marked by cytokine storms and respiratory failure. Despite extensive description in peripheral blood, the characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells in the lungs remain elusive. Here we conducted integrated single-cell profiling of SARS-CoV-2-specific T cells in 122 bronchoalveolar lavage fluid (BALF) and 280 blood samples from 159 patients, including 27 paired BALF and blood samples from 24 patients. SARS-CoV-2-specific T cells were robustly elicited in BALF irrespective of prior vaccination, correlating with diminished viral loads, lessened systemic inflammation and improved respiratory function. SARS-CoV-2-specific T cells in BALF exhibited profound activation, along with proliferative and multi-cytokine-producing capabilities and a glycolysis-driven metabolic signature, which were distinct from those observed in peripheral blood mononuclear cells. After viral clearance, these specific T cells maintained a polyfunctional tissue-resident memory phenotype, highlighting their critical roles in infection control and long-term protection.

Age and Latent Cytomegalovirus Infection Do Not Affect the Magnitude of De Novo SARS-CoV-2-Specific CD8+ T Cell Responses

Immunosenescence, age-related immune dysregulation, reduces immunity upon vaccinations and infections. Cytomegalovirus (CMV) infection results in declining naïve (Tnaïve) and increasing terminally differentiated (Temra) T cell populations, further aggravating immune aging. Both immunosenescence and CMV have been speculated to hamper the formation of protective T-cell immunity against novel or emerging pathogens. The SARS-CoV-2 pandemic presented a unique opportunity to examine the impact of age and/or CMV on the generation of de novo SARS-CoV-2-specific CD8+ T cell responses in 40 younger (22-40 years) and 37 older (50-66 years) convalescent individuals. Heterotetramer combinatorial coding combined with phenotypic markers were used to study 35 SARS-CoV-2 epitope-specific CD8+ T cell populations directly ex vivo. Neither age nor CMV affected SARS-CoV-2-specific CD8+ T cell frequencies, despite reduced total CD8+ Tnaïve cells in older CMV- and CMV+ individuals. Robust SARS-CoV-2-specific central memory CD8+ T (Tcm) responses were detected in younger and older adults regardless of CMV status. Our data demonstrate that immune aging and CMV status did not impact the SARS-CoV-2-specific CD8+ T cell response. However, SARS-CoV-2-specific CD8+ T cells of older CMV- individuals displayed the lowest stem cell memory (Tscm), highest Temra and PD1+ populations, suggesting that age, not CMV, may impact long-term SARS-CoV-2 immunity.

Impairment of the T cell memory response in chronic lymphocytic leukemia patients after SARS-CoV-2 vaccination

CLL patients face increased vulnerability to COVID-19 because of weakened immune systems from comorbidities and treatments. Therefore, the need for these patients of vaccination is of outermost importance. In our study we have evaluated T cell-mediated responses to COVID19 vaccines by performing the activation-induced markers (AIM) assay which allows to determine spike-specific CD4+ and CD8+ T cell responses. A CD4+ T cell memory response was registered in all healthy control (HC) (responders), while 28.60 % of CLL patients did not respond to the stimulation (non-responders). CD8+ T cell memory response was impaired in 61.90 % of CLL patients and in 33.33 % of HC. In addition, CLL responders showed a significant impairment of the magnitude of memory response in CD8 subset. Interestingly, impairment of the CD4+ AIM+ memory was associated to a more severe COVID-19 infection. Ibrutinib therapy had negative impact on IL-2 production by CD8+ cells, while the duration of the treatment positively affected the memory response. The majority of CLL patients don't respond well to vaccination, leaving clinicians in need of a reliable way to identify non-responders and assess the protection levels of those who do. Our findings suggest the AIM test as a promising method for screening and categorizing patients, potentially addressing this need.

MERS-CoV spike vaccine-induced N-terminal domain-specific antibodies are more protective than receptor binding domain-specific antibodies

The COVID-19 pandemic underscores the need to prepare for future emerging coronavriuses (CoVs) by understanding the principles behind effective CoV vaccine design such as protective immunity and antibody responses. To study which epitopes and subdomains contribute to in vivo protection, we utilized the prefusion-stabilized spike protein of MERS-CoV, MERS S-2P, as a vaccine immunogen. Vaccination with MERS S-2P elicited both receptor-binding domain (RBD)- and non-RBD-specific antibodies, including N-terminal domain (NTD)-specific G2-and CDC2-A2-like antibodies. Intriguingly, the immunogen MERS S-2P_ΔRBD, MERS S-2P with the RBDs removed, protects comparably to S1 and S-2P immunogens against MERS-CoV challenge. Moreover, passive transfer studies of polyclonal IgG from MERS S-2P immunized mice depleted of subdomain-specific antibodies demonstrated that non-RBD antibodies protected more than non-NTD antibodies. Altogether, these findings illustrate that in-vivo protection is not solely driven by RBD-specific antibodies and highlights the importance of targeting non-RBD sites in future CoV vaccine designs.

Pulchinenoside B4 alleviates DSS-induced colitis by inhibiting CD1d-dependent NLRP3 inflammasome activation in macrophages

Ulcerative colitis (UC) represents a significant challenge to global health, underscoring the importance of developing novel alternative anti-colitis agents. Inhibition of the NLRP3 inflammasome in macrophages has emerged as a potential therapeutic strategy for UC. Pulchinenoside B4 (PB4) is a major component of traditional medicinal plants that demonstrated to possess promising anti-inflammatory properties. The aim of the present study was to assess whether PB4 alleviates dextran sodium sulfate (DSS)-induced colitis by inhibiting the NLRP3 inflammasome in macrophages and its potential molecular mechanism. We constructed DSS-induced colitis in C57BL/6 mice, and isolated mouse intestinal macrophages and epithelial cells to investigate the effect of PB4 on NLRP3 inflammasome, and confirmed our findings in DSS-induced NLRP3-/- mice. In addition, we constructed lipopolysaccharides (LPS)-induced macrophages in vitro and identified the target and molecular mechanism of PB4 through biolayer interference (BLI) and cell thermal migration (CETSA) in conjunction with dss induced macrophage-specific CD1d depletion (CD1d-/-) colitis. This study showed that PB4 had a strong anti-inflammatory effect on WT mice induced by DSS, but the protective effect on NLRP3-/- mice was no longer enhanced. Interestingly, PB4 inhibited the activation of NLRP3 inflammasome in colon macrophages without affecting intestinal epithelial cells. Mechanistically, PB4 may target CD1d, thereby reducing the AKT-STAT1-PRDX1-NF-κB signaling pathway and ultimately inhibiting the activation of the NLRP3 inflammasome. Macrophage-specific CD1d loss has been shown to reverse the protective effects of PB4. These findings have paved the way for the development of CD1d/NLRP3-based novel anti-colitis agents and will facilitate the future clinical translation of the plant-derived drug PB4.

Ocular neuroinflammatory response secondary to SARS-CoV-2 infection-a review

With the consistent occurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the prevalence of various ocular complications has increased over time. SARS-CoV-2 infection has been shown to have neurotropism and therefore to lead to not only peripheral inflammatory responses but also neuroinflammation. Because the receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2), can be found in many intraocular tissues, coronavirus disease 2019 (COVID-19) may also contribute to persistent intraocular neuroinflammation, microcirculation dysfunction and ocular symptoms. Increased awareness of neuroinflammation and future research on interventional strategies for SARS-CoV-2 infection are important for improving long-term outcomes, reducing disease burden, and improving quality of life. Therefore, the aim of this review is to focus on SARS-CoV-2 infection and intraocular neuroinflammation and to discuss current evidence and future perspectives, especially possible connections between conditions and potential treatment strategies.

Screening for immunodominant epitopes of SARS-CoV-2 based on CD8+ T cell responses from individuals with HLA-A homozygous alleles

PURPOSE

SARS-CoV-2-specific CD8+ cytotoxic T lymphocytes (CTLs) are crucial in viral clearance, disease progression, and reinfection control. However, numerous SARS-CoV-2 immunodominant CTL epitopes theoretically are still unidentified due to the genetic polymorphism of human leukocyte antigen class I (HLA-I) molecules.

METHODS

The CTL epitopes of SARS-CoV-2 were predicted by the epitope affinity and immunogenicity prediction platforms: the NetMHCpan and the PromPPD. Individuals with HLA-A homozygous alleles were screened from 252 COVID-19 vaccinees, including the Ad5-nCoV vaccine (CanSino, n = 183) and the CoronaVac inactivated vaccine (Sinovac, n = 69) using MiSeqDx™ generation sequencing, and their PBMCs were further stimulated by the predicted peptides to screen the immunodominant epitopes according to the secretion of IFN-γ from CD8+ T cells. Peptide-MHC tetramers were constructed and used to detect the frequency of antigen specific CTLs in vivo.

RESULTS

Individuals with HLA-A homozygous alleles including HLA-A*01 (n = 1), -A*02 (n = 9), - A*03 and -A*11 (n = 12), and -A*24 (n = 7) supertypes were selected. Twelve immunodominant CTL epitopes for these HLA-A allotypes were finally screened based on the frequency of IFN-γ+CD8+ T cells in homozygous individuals. The SARS-CoV-2 specific CTLs from Omicron variant infected patients were successfully evaluated by these novel peptide-HLA tetramers.

CONCLUSION

A set of immunodominant CTL epitopes of SARS-CoV-2 was identified, and the antigen-specific CD8+ T cells in viral infected patients or COVID-19 vaccinees could be rapidly detected by a mixture of the peptide-MHC tetramers.

Enhancing the immunogenicity of lipid-nanoparticle mRNA vaccines by adjuvanting the ionizable lipid and the mRNA

To elicit optimal immune responses, messenger RNA vaccines require intracellular delivery of the mRNA and the careful use of adjuvants. Here we report a multiply adjuvanted mRNA vaccine consisting of lipid nanoparticles encapsulating an mRNA-encoded antigen, optimized for efficient mRNA delivery and for the enhanced activation of innate and adaptive responses. We optimized the vaccine by screening a library of 480 biodegradable ionizable lipids with headgroups adjuvanted with cyclic amines and by adjuvanting the mRNA-encoded antigen by fusing it with a natural adjuvant derived from the C3 complement protein. In mice, intramuscular or intranasal administration of nanoparticles with the lead ionizable lipid and with mRNA encoding for the fusion protein (either the spike protein or the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)) increased the titres of antibodies against SARS-CoV-2 tenfold with respect to the vaccine encoding for the unadjuvanted antigen. Multiply adjuvanted mRNA vaccines may improve the efficacy, safety and ease of administration of mRNA-based immunization.

T-cell immunobiology and cytokine storm of COVID-19

The 2019 coronavirus illness (COVID 2019) first manifests as a newly identified pneumonia and may quickly escalate to acute respiratory distress syndrome, which has caused a global pandemic. Except for individualized supportive care, no curative therapy has been steadfastly advised for COVID-19 up until this point. T cells and virus-specific T lymphocytes are required to guard against viral infection, particularly COVID-19. Delayed immunological reconstitution (IR) and cytokine storm (CS) continue to be significant barriers to COVID-19 cure. While severe COVID-19 patients who survived the disease had considerable lymphopenia and increased neutrophils, especially in the elderly, their T cell numbers gradually recovered. Exhausted T lymphocytes and elevated levels of pro-inflammatory cytokines, including IL6, IL10, IL2, and IL17, are observed in peripheral blood and the lungs. It implies that while convalescent plasma, IL-6 blocking, mesenchymal stem cells, and corticosteroids might decrease CS, Thymosin α1 and adaptive COVID-19-specific T cells could enhance IR. There is an urgent need for more clinical research in this area throughout the world to open the door to COVID-19 treatment in the future.

Mixed lipopeptide-based mucosal vaccine candidate induces cross-variant immunity and protects against SARS-CoV-2 infection in hamsters

The global dissemination of SARS-CoV-2 led to a worldwide pandemic in March 2020. Even after the official downgrading of the COVID-19 pandemic, infection with SARS-CoV-2 variants continues. The rapid development and deployment of SARS-CoV-2 vaccines helped to mitigate the pandemic to a great extent. However, the current vaccines are suboptimal; they elicit incomplete and short-lived protection and are ineffective against evolving virus variants. Updating the spike antigen according to the prevailing variant and repeated boosters is not the long-term solution. We have designed a lipopeptide-based, mucosal, pan-coronavirus vaccine candidate, derived from highly conserved and/or functional regions of the SARS-CoV-2 spike, nucleocapsid, and membrane proteins. Our studies demonstrate that the designed lipopeptides (LPMix) induced both cellular and humoral (mucosal and systemic) immune responses upon intranasal immunization in mice. Furthermore, the antibodies bound to the wild-type and mutated S proteins of SARS-CoV-2 variants of concern, including Alpha, Beta, Delta and Omicron, and also led to efficient neutralization in a surrogate viral neutralization assay. Our sequence alignment and 3-dimensional molecular modeling studies demonstrated that spike-derived epitopes, P1 and P2, are sequentially and/or structurally conserved among the SARS-CoV-2 variants. The addition of a novel mucosal adjuvant, heat-killed Caulobacter crescentus, to the lipopeptide vaccine significantly bolstered mucosal antibody responses. Finally, the lipopeptide-based intranasal vaccine demonstrated significant improvement in lung pathologies in a hamster model of SARS-CoV-2 infection. These studies are fundamentally important and open new avenues in the investigation of an innovative, broadly protective intranasal vaccine platform for SARS-CoV-2 and its variants.

Polymorphisms Influence the Expression of the Fas and FasL Genes in COVID-19

The apoptotic molecule Fas and its ligand FasL are involved in the process of T-lymphocyte death, which may lead to lymphopenia, a characteristic of severe coronavirus disease 2019 (COVID-19). In this study, we investigated the influence of polymorphisms in the FAS and FASL genes, FAS and FASL gene expression, and plasma cytokine levels on COVID-19 severity and long COVID occurrence. A total of 116 individuals with severe COVID-19 and 254 with the non-severe form of the disease were evaluated. In the post-COVID-19 period, samples from 196 individuals with long COVID and 67 from people who did not have long COVID were included. Genotyping and quantification of gene expression were performed via real-time PCR, and cytokine measurement was performed via flow cytometry. The AA genotype for FAS rs1800682 (A/G) and the TT genotype for FASL rs763110 (C/T) were associated with increased FAS and FASL gene expression, respectively (p < 0.005). Higher plasma IFN-γ levels were associated with higher FAS and FASL gene expression (p < 0.05). Among individuals with non-severe COVID-19, carriers of the AA genotype for FAS rs1800682 (A/G) had higher levels of FAS expression, more symptoms, and higher IFN-γ levels (p < 0.05). No association of the evaluated markers with long COVID were observed. The AA genotype of FAS rs1800682 (A/G) and the TT genotype of FASL rs763110 (C/T) influence the levels of FAS and FASL gene expression. Higher gene expression of FAS and FASL may lead to greater inflammation in COVID-19 patients, with higher levels of IFN-γ and T lymphocyte death.

Magnitude and dynamics of the T-cell response to SARS-CoV-2 infection at both individual and population levels

Introduction

T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection.

Methods

Here, we combined two high-throughput immune profiling methods to create a quantitative picture of the T-cell response to SARS-CoV-2. First, at the individual level, we deeply characterized 3 acutely infected and 58 recovered COVID-19 subjects by experimentally mapping their CD8 T-cell response through antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I presented viral peptides. Then, at the population level, we performed T-cell repertoire sequencing on 1,815 samples (from 1,521 COVID-19 subjects) as well as 3,500 controls to identify shared "public" T-cell receptors (TCRs) associated with SARS-CoV-2 infection from both CD8 and CD4 T cells.

Results

Collectively, our data reveal that CD8 T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the T-cell response to SARS-CoV-2 peaks about one to two weeks after infection and is detectable for at least several months after recovery. As an application of these data, we trained a classifier to diagnose SARS-CoV-2 infection based solely on TCR sequencing from blood samples, and observed, at 99.8% specificity, high early sensitivity soon after diagnosis (Day 3-7 = 85.1% [95% CI = 79.9-89.7]; Day 8-14 = 94.8% [90.7-98.4]) as well as lasting sensitivity after recovery (Day 29+/convalescent = 95.4% [92.1-98.3]).

Discussion

The approaches described in this work provide detailed insights into the adaptive immune response to SARS-CoV-2 infection, and they have potential applications in clinical diagnostics, vaccine development, and monitoring.

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.

A 10 Year Long-Lived Cellular and Humoral MERS-CoV Immunity Cross-Recognizing the Wild-Type and Variants of SARS-CoV-2: A Potential One-Way MERS-CoV Cross-Protection Toward a Pan-Coronavirus Vaccine

MERS is a respiratory disease caused by MERS-CoV. Multiple outbreaks have been reported, and the virus co-circulates with SARS-CoV-2. The long-term (> 6 years) cellular and humoral immune responses to MERS-CoV and their potential cross-reactivity to SARS-CoV-2 and its variants are unknown. We comprehensively investigated long-lasting MERS-CoV-specific cellular and humoral immunity, and its cross-reactivity against SARS-CoV-2 and its variants, in individuals recovered from MERS-CoV infection 1-10 years prior. Two cohorts of MERS-CoV survivors (31 unvaccinated, 38 COVID-19 vaccinated) were assessed for MERS-CoV IgG, memory CD4+/CD8+ T cells, and neutralizing antibodies against MERS-CoV and SARS-CoV-2 variants. MERS-CoV IgG levels and T cell responses were higher in the 1-5 vs 6-10 year postinfection groups. Vaccinated MERS-CoV survivors had significantly elevated MERS-CoV IgG and neutralization compared to unvaccinated. Both groups demonstrated cross-reactive neutralization of SARS-CoV-2 variants. MERS-CoV survivors vaccinated against SARS-CoV-2 had higher anti-MERS IgG, cellular immunity, and neutralization than unvaccinated survivors. MERS-CoV immune responses can persist for a decade. COVID-19 vaccination boosted humoral and cellular immunity in MERS-CoV survivors, suggesting the benefits of vaccination for this population. These findings have implications for pan-coronavirus vaccine development.

Allogeneic CD5-specific CAR-T therapy for relapsed/refractory T-ALL: a phase 1 trial

Refractory or relapsed T cell acute lymphoblastic leukemia (r/r T-ALL) patients have poor prognoses, due to the lack of effective salvage therapies. Recently, CD7-targeting chimeric antigen receptor (CAR)-T therapies show efficacy in patients with r/r T-ALL, but relapse with CD7 loss is common. This study evaluates a CD5-gene-edited CAR-T cell therapy targeting CD5 in 19 r/r T-ALL patients, most of whom had previously failed CD7 CAR-T interventions. CAR-T products were derived from previous transplant donors (Cohort A) or newly matched donors (Cohort B). Primary endpoints were dose-limiting toxicity at 21 days and adverse events within 30 days. Secondary endpoints were responses, pharmacokinetics and severe adverse events after 30 days. A total of 16 received infusions, 10 at target dose of 1 × 106 kg-1. All encountered grade 3-4 cytopenias and one had a grade 3 infection within 30 days. All patients (100%) achieved complete remission or complete remission with incomplete blood count recovery by day 30. At a median follow-up of 14.3 months, four received transplantation; three were in remission and one died of infection. Of 12 untransplanted patients, 2 were in remission, 3 relapsed, 5 died of infection and 2 of thrombotic microangiopathy. CAR-T cells persisted and cleared CD5+ T cells. CD5- T cells, mostly CD5-gene-edited, increased but remained below normal levels. These results suggest this CD5-specific CAR-T intervention has a high remission rate for T-ALL patients. Evidence also suggests the risk of late-onset severe infection may be mitigated with consolidative transplantation. This study provides insights that could help to optimize this promising intervention. ClinicalTrials.gov registration: NCT05032599 .

Consensus Statements on Assessments and Vaccinations Prior to Commencement of Advanced Therapies for the Treatment of Inflammatory Bowel Diseases

BACKGROUND

Given the introduction of new advanced therapies for inflammatory bowel diseases (IBDs), expanded risk mitigation strategies are essential.

AIMS

To create a comprehensive set of statements on assessment procedures and vaccinations before starting monoclonal antibodies, Janus kinase (JAK) inhibitors or sphingosine-1-phosphate (S1P) modulators for IBD.

METHODS

We examined literature, guidelines and drug product information regarding vaccination and assessment recommendations for initiating advanced IBD therapies. Using a modified Delphi approach, delegates voted anonymously on the acceptability of these statements prior to and following consensus discussion.

RESULTS

We developed eight statements on the domains of infectious diseases screening, vaccinations and assessments prior to commencing JAK inhibitors and S1P modulators. Six statements received agreement. Pre-advanced therapy screening for infectious diseases was established, and the vaccination protocol was revised. Malignancy, cardiovascular and thromboembolic risk assessments are necessary before initiating JAK inhibitors. Those starting S1P modulators need cardiac and ophthalmic assessments.

CONCLUSIONS

These consensus statements combine vaccination and assessments on the currently available advanced therapies for IBD as a single comprehensive document that may reduce IBD complications associated with use of advanced therapies. Knowledge gaps identified during the consensus process will provide further research opportunities.

Sustained Vascular Inflammatory Effects of SARS-CoV-2 Spike Protein on Human Endothelial Cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has been associated with systemic inflammation and vascular injury, which contribute to the development of acute respiratory syndrome (ARDS) and the mortality of COVID-19 infection. Moreover, multiorgan complications due to persistent endothelial dysfunction have been suspected as the cause of post-acute sequelae of SARS-CoV-2 infection. Therefore, elucidation of the vascular inflammatory effect of SARS-CoV-2 will increase our understanding of how endothelial cells (ECs) contribute to the short- and long-term consequences of SARS-CoV-2 infection. Here, we investigated the interaction of SARS-CoV-2 spike protein with human ECs from aortic (HAoEC) and pulmonary microvascular (HPMC) origins, cultured under physiological flow conditions. We showed that the SARS-CoV-2 spike protein triggers prolonged expression of cell adhesion markers in both ECs, similar to the effect of TNF-α. SARS-CoV-2 spike treatment also led to the release of various cytokines and chemokines observed in severe COVID-19 patients. Moreover, increased binding of leucocytes to the endothelial surface and a procoagulant state of the endothelium were observed. Transcriptomic profiles of SARS-CoV-2 spike-activated HPMC and HAoEC showed prolonged upregulation of genes and pathways associated with responses to virus, cytokine-mediated signaling, pattern recognition, as well as complement and coagulation pathways. Our findings support experimental and clinical observations of the vascular consequences of SARS-CoV-2 infection and highlight the importance of EC protection as one of the strategies to mitigate the severe effects as well as the possible post-acute complications of COVID-19 disease.

Trivalent recombinant protein vaccine induces cross-neutralization against XBB lineage and JN.1 subvariants: preclinical and phase 1 clinical trials

The immune escape capacities of XBB variants necessitate the authorization of vaccines with these antigens. In this study, we produce three recombinant trimeric proteins from the RBD sequences of Delta, BA.5, and XBB.1.5, formulating a trivalent vaccine (Tri-Vac) with an MF59-like adjuvant at a 1:1:4 ratio. Tri-Vac demonstrates immunogenicity in female NIH mice, inducing cross-neutralization against various SARS-CoV-2 variants, including pre-Omicron and Omicron BA.2.75, BA.5, and XBB lineages. It elicits measurable antigen-specific T cell responses, germinal center B cell responses, and T follicular helper responses, effectively protecting against live Omicron XBB.1.16 challenges. Protective immunity is maintained long-term, with sustained neutralizing antibodies and T cell responses, as well as memory B cells and long-lived plasma cells observed by day 210 post-immunization. Tri-Vac also serves as a candidate booster for enhancing immunity after three doses of inactivated virus or mRNA vaccines. A phase 1 investigator-initiated trial was initiated to assess safety and immunogenicity in humans, focusing on the primary endpoint of adverse reactions within 7 days and key secondary endpoints including the geometric mean titers (GMTs) of serum neutralizing antibodies within 30 days and 6 months post-vaccination, as well as adverse events within 30 days and serious adverse events within 6 months post-vaccination. Preliminary data indicate Tri-Vac has good safety and immunogenicity, improving neutralization against multiple variants, including JN.1, in previously vaccinated individuals, highlighting its clinical potential for protecting against SARS-CoV-2 variants. The registration number of this clinical trial is ChiCTR2200067245.

Mucosal Immunization with an Influenza Vector Carrying SARS-CoV-2 N Protein Protects Naïve Mice and Prevents Disease Enhancement in Seropositive Th2-Prone Mice

Background/Objectives: Intranasal vaccination enhances protection against respiratory viruses by providing stimuli to the immune system at the primary site of infection, promoting a balanced and effective response. Influenza vectors with truncated NS1 are a promising vaccine approach that ensures a pronounced local CD8+ T-cellular immune response. Here, we describe the protective and immunomodulating properties of an influenza vector FluVec-N carrying the C-terminal fragment of the SARS-CoV-2 nucleoprotein within a truncated NS1 open reading frame. Methods: We generated several FluVec-N recombinant vectors by reverse genetics and confirmed the vector's genetic stability, antigen expression in vitro, attenuation, and immunogenicity in a mouse model. We tested the protective potential of FluVec-N intranasal immunization in naïve mice and seropositive Th2-prone mice, primed with aluminium-adjuvanted inactivated SARS-CoV-2. Immune response in immunized and challenged mice was analyzed through serological methods and flow cytometry. Results: Double intranasal immunization of naïve mice with FluVec-N reduced weight loss and viral load in the lungs following infection with the SARS-CoV-2 beta variant. Mice primed with alum-adjuvanted inactivated coronavirus experienced substantial early weight loss and eosinophilia in the lungs during infection, demonstrating signs of enhanced disease. A single intranasal boost immunization with FluVec-N prevented the disease enhancement in primed mice by modulating the local immune response. Protection was associated with the formation of specific IgA and the early activation of virus-specific effector and resident CD8+ lymphocytes in mouse lungs. Conclusions: Our study supports the potential of immunization with influenza vector vaccines to prevent respiratory diseases and associated immunopathology.

Co-immunization with spike and nucleocapsid based DNA vaccines for long-term protective immunity against SARS-CoV-2 Omicron

The continuing evolution of SARS-CoV-2 variants challenges the durability of existing spike (S)-based COVID-19 vaccines. We hypothesized that vaccines composed of both S and nucleocapsid (N) antigens would increase the durability of protection by strengthening and broadening cellular immunity compared with S-based vaccines. To test this, we examined the immunogenicity and efficacy of wild-type SARS-CoV-2 S- and N-based DNA vaccines administered individually or together to K18-hACE2 mice. S, N, and S + N vaccines all elicited polyfunctional CD4+ and CD8+ T cell responses and provided short-term cross-protection against Beta and Omicron BA.2 variants, but only co-immunization with S + N vaccines provided long-term protection against Omicron BA.2. Depletion of CD4+ and CD8+ T cells reduced the long-term efficacy, demonstrating a crucial role for T cells in the durability of protection. These findings underscore the potential to enhance long-lived protection against SARS-CoV-2 variants by combining S and N antigens in next-generation COVID-19 vaccines.

Crystal structure of the human LAG-3-HLA-DR1-peptide complex

T cell activity is governed by T cell receptor (TCR) signaling and constrained by immune checkpoint molecules, including programmed cell death protein 1 (PD-1), cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), and lymphocyte activation gene 3 (LAG-3). The basis for how LAG-3 binds to human leukocyte antigen class II molecules (HLA-II) remains unknown. Here, we present the 3.4-angstrom crystal structure of a LAG-3-peptide-HLA-II complex and probe the energetics of the complex interface. Coincident with the HLA-II binding site of the ancestrally related, monomeric CD4 receptor, the LAG-3 homodimer laterally engages two HLA-II molecules via distal D1 domain surfaces, imposing a 38° angular offset. The LAG-3-HLA-II interface is discontinuous and lacks involvement of the D1 extra loop, a binding site for anti-LAG-3 therapeutic monoclonal antibodies. Upon HLA-II binding, intrinsically mobile loops of the LAG-3 molecule become ordered, with contact residues highly conserved across HLA-DR, DQ, and DP allomorphs. Our data provide a structural foundation for development of immunomodulatory approaches targeting LAG-3.

Comparison of a SARS-CoV-2 mRNA booster immunization containing additional antigens to a spike-based mRNA vaccine against Omicron BA.5 infection in hACE2 mice

The emergence of SARS-CoV-2 variants presents challenges to vaccine effectiveness, underlining the necessity for next-generation vaccines with multiple antigens beyond the spike protein. Here, we investigated a multiantigenic booster containing spike and a chimeric construct composed of nucleoprotein (N) and membrane (M) proteins, comparing its efficacy to a spike-only booster against Omicron BA.5 in K18-hACE2 mice. Initially, mice were primed and boosted with Beta (B.1.351) spike-only mRNA, showing strong spike-specific T cell responses and neutralizing antibodies, albeit with limited cross-neutralization to Omicron variants. Subsequently, a spike-NM multiantigenic vaccine was then examined as a second booster dose for protection in hACE2-transgenic mice. Mice receiving either homologous spike-only or heterologous spike-NM booster had nearly complete inhibition of infectious virus shedding in oral swabs and reduced viral burdens in both lung and nasal tissues following BA.5 challenge. Examination of lung pathology further revealed that both spike-only and spike-NM boosters provided comparable protection against inflammatory infiltrates and fibrosis. Moreover, the spike-NM booster demonstrated neutralization efficacy in a pseudovirus assay against Wuhan-Hu-1, Beta, and Omicron variants akin to the spike-only booster. These findings indicate that supplementing spike with additional SARS-CoV-2 targets in a booster immunization confers equivalent immunity and protection against Omicron BA.5. This work highlights a promising strategy for individuals previously vaccinated with spike-only vaccines, potentially offering enhanced protection against emerging coronaviruses.

SpiN-Tec: A T cell-based recombinant vaccine that is safe, immunogenic, and shows high efficacy in experimental models challenged with SARS-CoV-2 variants of concern

The emergence of new SARS-CoV-2 variants of concern associated with waning immunity induced by natural infection or vaccines currently in use suggests that the COVID-19 pandemic will become endemic. Investing in new booster vaccines using different platforms is a promising way to enhance protection and keep the disease under control. Here, we evaluated the immunogenicity, efficacy, and safety of the SpiN-Tec vaccine, based on a chimeric recombinant protein (SpiN) adjuvanted with CTVad1 (MF59-based adjuvant), aiming at boosting immunity against variants of concern of SARS-CoV-2. Immunization of K18-hACE-2 transgenic mice and hamsters induced high antibody titers and cellular immune response to the SpiN protein as well as to its components, RBD and N proteins. Importantly in a heterologous prime/boost protocol with a COVID-19 vaccine approved for emergency use (ChAdOx1), SpiN-Tec enhanced the level of circulation neutralizing antibodies (nAb). In addition to protection against the Wuhan isolate, protection against the Delta and Omicron variants was also observed as shown by reduced viral load and lung pathology. Toxicity and safety tests performed in rats demonstrated that the SpiN-Tec vaccine was safe and, based on these results, the SpiN-Tec phase I/II clinical trial was approved.

Characteristics of Norovirus capsid protein-specific CD8+ T-Cell responses in previously infected individuals

Norovirus (NV) infection causes acute gastroenteritis in children and adults. Upon infection with NV, specific CD8+ T cells, which play an important role in anti-infective immunity, are activated in the host. Owing to the NV's wide genotypic variability, it is challenging to develop vaccines with cross-protective abilities against infection. To aid effective vaccine development, we examined specific CD8+ T-cell responses towards viral-structural protein (VP) epitopes, which enable binding to host susceptibility receptors. We isolated peripheral blood mononuclear cells from 196 participants to screen and identify predominant core peptides towards NV main and small envelope proteins using ex vivo and in vitro intracellular cytokine staining assays. Human leukocyte antigen (HLA) restriction characteristics were detected using next-generation sequencing. Three conservative immunodominant VP-derived CD8+ T-cell epitopes, VP294-102 (TDAARGAIN), VP2153-161 (RGPSNKSSN), and VP1141-148 (FPHIIVDV), were identified and restrictively presented by HLA-Cw * 0102, HLA-Cw * 0702, and HLA-A *1101 alleles, separately. Our findings provide useful insights into the development of future vaccines and treatments for NV infection.

The characterization of CD8+ T-cell responses in COVID-19

This review gives an overview of the protective role of CD8+ T cells in SARS-CoV-2 infection. The cross-reactive responses intermediated by CD8+ T cells in unexposed cohorts are described. Additionally, the relevance of resident CD8+ T cells in the upper and lower airway during infection and CD8+ T-cell responses following vaccination are discussed, including recent worrisome breakthrough infections and variants of concerns (VOCs). Lastly, we explain the correlation between CD8+ T cells and COVID-19 severity. This review aids in a deeper comprehension of the association between CD8+ T cells and SARS-CoV-2 and broadens a vision for future exploration.

Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions

T cell receptors (TCR) and gene expression provide two complementary and essential aspects in T cell understanding, yet their diversity presents challenges in integrative analysis. We introduce TCRclub, a novel method integrating single-cell RNA sequencing data and single-cell TCR sequencing data using local harmony to identify functionally similar T cell groups, termed 'clubs'. We applied TCRclub to 298,106 T cells across seven datasets encompassing various diseases. First, TCRclub outperforms the state-of-the-art methods in clustering T cells on a dataset with over 400 verified peptide-major histocompatibility complex categories. Second, TCRclub reveals a transition from activated to exhausted T cells in cholangiocarcinoma patients. Third, TCRclub discovered the pathways that could intervene in response to anti-PD-1 therapy for patients with basal cell carcinoma by analyzing the pre-treatment and post-treatment samples. Furthermore, TCRclub unveiled different T-cell responses and gene patterns at different severity levels in patients with COVID-19. Hence, TCRclub aids in developing more effective immunotherapeutic strategies for cancer and infectious diseases.

Obtaining HBV core protein VLPs carrying SARS-CoV-2 nucleocapsid conserved fragments as vaccine candidates

The Hepatitis B core antigen (HBcAg) has been used as a carrier of several heterologous protein fragments based on its capacity to form virus-like particles (VLPs) and to activate innate and adaptive immune responses. In the present work, two chimeric proteins were designed as potential pancorona vaccine candidates, comprising the N- or C- terminal domain of SARS-CoV-2 nucleocapsid (N) protein fused to HBcAg. The recombinant proteins, obtained in E. coli, were named CN-1 and CND-1, respectively. The final protein preparations were able to form 10-25 nm particles, visualized by TEM. Both proteins were recognized by sera from COVID-19 convalescent donors; however, the antigenicity of CND-1 tends to be higher. The immunogenicity of both proteins was studied in Balb/C mice by intranasal route without adjuvant. After three doses, only CND-1 elicited a positive immune response, systemic and mucosal, against SARS-CoV-2 N protein. CND-1 was evaluated in a second experiment mixed with the CpG ODN-39 M as nasal adjuvant. The induced anti-N immunity was significantly enhanced, and the antibodies generated were cross-reactive with N protein from Omicron variant, and SARS-CoV-1. Also, an anti-N broad cellular immune response was detected in spleen, by IFN-γ ELISpot. The nasal formulation composed by CND-1 and ODN-39 M constitutes an attractive component for a second generation coronavirus vaccine, increasing the scope of S protein-based vaccines, by inducing mucosal immunity and systemic broad humoral and cellular responses against Sarbecovirus N protein.

COVID-19 progression and convalescence in common variable immunodeficiency patients show dysregulated adaptive immune responses and persistent type I interferon and inflammasome activation

Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency, marked by hypogammaglobulinemia, poor antibody responses, and increased infection susceptibility. The COVID-19 pandemic provided a unique opportunity to study the effects of prolonged viral infections on the immune responses of CVID patients. Here we use single-cell RNA-seq and spectral flow cytometry of peripheral blood samples before, during, and after SARS-CoV-2 infection showing that COVID-19 CVID patients display a persistent type I interferon signature at convalescence across immune compartments. Alterations in adaptive immunity include sustained activation of naïve B cells, increased CD21low B cells, impaired Th1 polarization, CD4+ T central memory exhaustion, and increased CD8+ T cell cytotoxicity. NK cell differentiation is defective, although cytotoxicity remains intact. Monocytes show persistent activation of inflammasome-related genes. These findings suggest the involvement of intact humoral immunity in regulating these processes and might indicate the need for early intervention to manage viral infections in CVID patients.

Rapid progression of CD8 and CD4 T cells to cellular exhaustion and senescence during SARS-CoV2 infection

Risk factors for the development of severe COVID-19 include several comorbidities, but age was the most striking one since elderly people were disproportionately affected by SARS-CoV-2 infection. Among the reasons for this markedly unfavorable response in the elderly, immunosenescence and inflammaging appear as major drivers of this outcome. A finding that was also notable was that hospitalized patients with severe COVID-19 have an accumulation of senescent T cells, suggesting that immunosenescence may be aggravated by SARS-CoV-2 infection. The present work was designed to examine whether these immunosenescence changes are characteristic of COVID-19 and whether it is dependent on disease severity using cross-sectional and longitudinal studies. Our cross-sectional data show that COVID-19, but not other respiratory infections, rapidly increased cellular senescence and exhaustion in CD4 and CD8 T cells during early infection. In addition, longitudinal analyses with patients from Brazil and Portugal provided evidence of increased frequencies of senescent and exhausted T cells over a 7-d period in patients with mild/moderate and severe COVID-19. Altogether, the study suggests that accelerated immunosenescence in CD4 and especially CD8 T-cell compartments may represent a common and unique outcome of SARS-CoV2 infection.

Features of Highly Homologous T-Cell Receptor Repertoire in the Immune Response to Mutations in Immunogenic Epitopes

CD8+ T-cell immunity, mediated through interactions between human leukocyte antigen (HLA) and the T-cell receptor (TCR), plays a pivotal role in conferring immune memory and protection against viral infections. The emergence of SARS-CoV-2 variants presents a significant challenge to the existing population immunity. While numerous SARS-CoV-2 mutations have been associated with immune evasion from CD8+ T cells, the molecular effects of most mutations on epitope-specific TCR recognition remain largely unexplored, particularly for epitope-specific repertoires characterized by common TCRs. In this study, we investigated an HLA-A*24-restricted NYN epitope (Spike448-456) that elicits broad and highly homologous CD8+ T cell responses in COVID-19 patients. Eleven naturally occurring mutations in the NYN epitope, all of which retained cell surface presentation by HLA, were tested against four transgenic Jurkat reporter cell lines. Our findings demonstrate that, with the exception of L452R and the combined mutation L452Q + Y453F, these mutations have minimal impact on the avidity of recognition by NYN peptide-specific TCRs. Additionally, we observed that a similar TCR responded differently to mutant epitopes and demonstrated cross-reactivity to the unrelated VYF epitope (ORF3a112-120). The results contradict the idea that immune responses with limited receptor diversity are insufficient to provide protection against emerging variants.

B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity

In single-cell studies, cells can be characterized with multiple sources of heterogeneity (SOH) such as cell type, developmental stage, cell cycle phase, activation state, and so on. In some studies, many nuisance SOH are of no interest, but may confound the identification of the SOH of interest, and thus affect the accurate annotate the corresponding cell subpopulations. In this paper, we develop B-Lightning, a novel and robust method designed to identify marker genes and cell subpopulations corresponding to an SOH (e.g. cell activation status), isolating it from other SOH (e.g. cell type, cell cycle phase). B-Lightning uses an iterative approach to enrich a small set of trustworthy marker genes to more reliable marker genes and boost the signals of the SOH of interest. Multiple numerical and experimental studies showed that B-Lightning outperforms existing methods in terms of sensitivity and robustness in identifying marker genes. Moreover, it increases the power to differentiate cell subpopulations of interest from other heterogeneous cohorts. B-Lightning successfully identified new senescence markers in ciliated cells from human idiopathic pulmonary fibrosis lung tissues, new T-cell memory and effector markers in the context of SARS-COV-2 infections, and their synchronized patterns that were previously neglected, new AD markers that can better differentiate AD severity, and new dendritic cell functioning markers with differential transcriptomics profiles across breast cancer subtypes. This paper highlights B-Lightning's potential as a powerful tool for single-cell data analysis, particularly in complex data sets where SOH of interest are entangled with numerous nuisance factors.

Analysis of Measles and Rubella Immunoglobulin G Titers in COVID-19 Patients

Background

The objective of this study is to compare the measles immunoglobulin G (IgG) and rubella IgG levels in patient groups with mild and severe COVID-19 disease and reveal the possible relationship.

Methods

This study was conducted among COVID-19-confirmed patients over 18, under 65 years of age. This study involved 75 participants- divided into two groups. The first group usually comprised asymptomatic patients who did not require hospitalization (n=43), and the second group consisted of patients who had diffuse pneumonia on thoracic CT and required hospitalization (n=32).

Results

Anti-measles and anti-rubella IgG titers were detected to be higher in the group with severe disease compared to the group with mild disease (p=0.001 and p=0.001, respectively). The analyses were repeated by taking n=27 in Group 1 and n=27 in Group 2, which were similar in terms of age, gender and number. In the analysis performed without any age difference between the groups, no significant difference was found between the two groups in terms of Anti Measles IgG antibody titers (p=0.068). However, Anti Rubella antibody titers were found to be higher in the group with severe COVID-19 disease than in those with mild disease (p=0.03). Regardless of the severity of the disease, there was a positive correlation between Anti Rubella and Anti Measles IgG antibody titers and age (p=<0.001 Spearman's rho 0.517; p=0.008 Spearman's rho 0.304, respectively).

Conclusion

We believe that the pre-existing Anti-Rubella IgG antibodies in the patient may increase in parallel with the patient's viral load by recognizing the common macrodomain of SARS-CoV-2 and Rubella viruses. The common macrodomain of SARS-CoV-2 and Rubella viruses is also present in the attenuated rubella virus used in the MMR vaccine4. In this case, we predict that previously administered MMR vaccine may be protective for COVID-19 patients. disease compared to those with mild disease.

Self-Adjuvanting Adenoviral Nanovaccine for Effective T-Cell-Mediated Immunity and Long-Lasting Memory Cell Activation against Tuberculosis

An enhanced vaccine is immediately required to swap the more than 100 year-old bacillus Calmette-Guerin (BCG) vaccine against tuberculosis. Here, trimethyl chitosan-loaded inactivated Mycobacterium smegmatis (MST), along with potent adenovirus hexon protein (AdHP), and toll-like receptor (TLR)-1/2 as a nanovaccine, was developed against tuberculosis (TB). The nanoformulation increased the bioavailability of MST and elicited the targeting ability. Nanovaccines have a size range of 183.5 ± 9.5 nm with a spherical morphology and uniform distribution. The nanovaccine exhibited a higher release of antigen in acidic pH, and this is mainly due to protonation of ionizable groups in polymeric materials. The nanovaccine facilitated the effective cellular uptake of bone-marrow-derived dendritic cells and progressive endosomal escape in a shorter period. In vitro analyses indicated that the nanovaccine activated cytokine and T-cell production and also assisted in humoral immunity by producing antibodies. The nanovaccine was able to induce more cellular and humoral memory cells and a better protective immune response. Nanomaterials effectively delivered the MST, AdHP, and TLR1/2 antigens to the major histocompatibility complex class I and II pathways to generate protective cytotoxic CD8+ and CD4+ T-cells. In vivo experiments, compared with free MST and BCG, showed that mice immunized with the nanovaccine induced more specific CD4+, CD8+, and memory T-cell activations. Overall, the fabricated nanovaccine was able to control the release of antigens and adjuvants and enhance memory cell activation and humoral immunity against TB.

Marker gene fishing for single-cell data with complex heterogeneity

In single-cell studies, cells can be characterized with multiple sources of heterogeneity such as cell type, developmental stage, cell cycle phase, activation state, and so on. In some studies, many nuisance sources of heterogeneity (SOH) are of no interest, but may confound the identification of the SOH of interest, and thus affect the accurate annotate the corresponding cell subpopulations. In this paper, we develop B-Lightning, a novel and robust method designed to identify marker genes and cell subpopulations correponding to a SOH (e.g., cell activation status), isolating it from other sources of heterogeneity (e.g., cell type, cell cycle phase). B-Lightning uses an iterative approach to enrich a small set of trustworthy marker genes to more reliable marker genes and boost the signals of the SOH of interest. Multiple numerical and experimental studies showed that B-Lightning outperforms existing methods in terms of sensitivity and robustness in identifying marker genes. Moreover, it increases the power to differentiate cell subpopulations of interest from other heterogeneous cohorts. B-Lightning successfully identified new senescence markers in ciliated cells from human idiopathic pulmonary fibrosis (IPF) lung tissues, new T cell memory and effector markers in the context of SARS-COV-2 infections, and their synchronized patterns which were previously neglected. This paper highlights B-Lightning's potential as a powerful tool for single-cell data analysis, particularly in complex data sets where sources of heterogeneity of interest are entangled with numerous nuisance factors.

Identification of virus epitopes and reactive T-cell receptors from memory T cells without peptide synthesis

Identifying epitopes and their corresponding T-cell receptor (TCR) sequences is crucial in the face of rapidly mutating viruses. Peptide synthesis is often required to confirm the exact epitope sequences, which is time-consuming and expensive. In this study, we introduce a scalable workflow to identify the exact sequences of virus epitopes and reactive TCRs targeting the epitopes from memory T cells. Following the narrowing down of epitopes to specific regions via the tandem minigene (TMG) system, our workflow incorporates the utilization of peptide-major histocompatibility complex-displaying yeasts (pMHC-displaying yeasts) to rapidly screen immunogenic epitopes' precise sequences, obviating the necessity for the chemical synthesis of peptides. Focusing on SARS-CoV-2, we identify the precise sequences of reactive TCRs, targeting conserved epitopes across the Coronaviridae family, from the blood of COVID-19-recovered individuals over 8 months. Notably, we reveal that at least 75% (6/8) of the tested donors harbor T cells targeting a shared epitope, KTFPPTEPK, derived from the N protein. Furthermore, several identified TCRs exhibit cross-reactivity to mutant epitopes, suggesting a potential mechanism for sustained T-cell responses against emerging SARS-CoV-2 variants.