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The Jenner Institute is based within the Nuffield Department of Medicine, University of Oxford, and operates out of the Old Road Campus Research Building, in Headington, Oxford.
Tuberculosis in patients with systemic lupus erythematosus
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tb), with approximately 10 million new cases reported worldwide annually. Patients with immunocompromised states or those receiving immunosuppressive therapy for autoimmune diseases are at higher risk of M. tb infection or reactivation. The chronic autoimmune disease, systemic lupus erythematosus (SLE), is associated with a higher risk of M. tb infection and TB disease during conventional treatment with corticosteroids and immunosuppressants. However, whether risk of TB is influenced by the immune disturbances associated with active SLE when patients are not receiving immunosuppressant treatment remains unclear. In this review, we describe the pathogenesis of TB and SLE and consider how autoimmune responses in SLE could influence TB risk.
Safety and immunogenicity of the ChAdOx1 nCoV-19 (AZD1222) vaccine in children aged 6-17 years: Final results of a phase 2, single-blind, randomised controlled trial (COV006).
Paediatric COVID-19 vaccination programmes were initiated in response to the coronavirus pandemic declared by the World Health Organisation (WHO) in 2020. Ten COVID-19 vaccines received WHO Emergency Use Listing, however, only five were approved for use in children. ChAdOx1 nCoV-19 (AZD1222) was approved in adults in a two-dose regimen. We previously reported interim findings of a phase 2 study of ChAdOx1 nCoV-19 in children with immunogenicity, comparable with adults. Final results after 12 month follow-up are reported. Single-blind, randomised controlled trial across four UK centres, recruiting 261 children and adolescents (aged 6-17 years). Participants received either two doses of ChAdOx1 nCoV-19 or Bexsero vaccine (controls). The primary outcome was safety (adverse events for 28 days following vaccination and serious adverse events throughout), and secondary outcome was immunogenicity (measured by SARS-CoV-2 anti-spike enzyme-linked immunosorbent assay (ELISA) and enzyme-linked immunosorbent spot (ELISpot)). Five serious adverse events and four adverse events of special interest were reported. None were related to study vaccinations, and there were no deaths. Geometric mean titres (GMTs) from an anti-spike (Wuhan) ELISA in participants aged 6-11 years were 1 EU/ml (95% CI 1-2) at baseline versus 796 EU (95% CI 161-3948, n =4) at D364. In participants aged 12-17 years, GMTs were 1 EU/ml (95% CI 1-2, n=3) at baseline versus 1432 EU/ml (95% CI 2337-6083; n=6) at D364 (2 dose regimen at 112-day interval), compared to 3 EU/ml (95% CI 0-62) at baseline versus 392 EU/ml (95% CI 24, 6493; n=3) at D364 (2 dose regimen at a 28-day interval). A two-dose regimen of ChAdOx1 nCoV-19 was immunogenic and safe in the trial population. No vaccine-related serious adverse events were reported. Immune responses persisted to 12 months in participants who did not experience breakthrough infection, This trial was registered with ISRCTN, trial number 15638344. The study was funded by the Department of Health and Social Care, through the National Institute for Health Research, and AstraZeneca.
Evaluation of 1<sup>st</sup> WHO anti-malaria reference reagent for competition ELISA harmonisation and development of ADAMSEL analytical platform.
This study focuses on harmonising the competition ELISA (cELISA) assay for Plasmodium falciparum (P. falciparum), using the 1st WHO reference reagent for anti-malaria (P. falciparum) human reference serum (10/198). Antibody-mediated immune responses against the Apical Membrane Antigen 1 (AMA1) play a significant role in protection against malaria. However, the sequence diversity of AMA1 and cross-reactivity among variants pose challenges in assessing antibody responses. To address this, the cELISA assay was selected to examine cross-reactive antibody responses against different variants. The harmonisation process for cELISA was performed in three laboratories. The 10/198 served as an internal standard for the calculation of IgG concentrations in the cELISA using ADAMSEL software. Additionally, a novel semi-automated analytical tool was developed in the R-statistics environment. This tool is freely available for download and streamlines generating results while minimising human error. This study demonstrated the effectiveness of the 1st WHO reference reagent as a standard for cELISA. Additionally, the ADAMSEL software and R-platform tool provide a user-friendly and accessible tool for the analysis of cELISA data. Its automation capabilities improve efficiency and ensure global accessibility at no cost, benefitting laboratories with limited resources.
Dosing interval is a major factor determining the quality of T cells induced by SARS-CoV-2 mRNA and adenoviral vector vaccines
Functional T cell responses are crucial for protective immunity induced by COVID-19 vaccination, but factors influencing the quality of these responses are incompletely understood. We used an activation-induced marker (AIM) assay and single-cell transcriptomic sequencing to analyze SARS-CoV-2 spike-responsive T cells after mild SARS-CoV-2 infection or after one or two doses of mRNA–lipid nanoparticle (mRNA-LNP) or adenoviral-vectored COVID-19 vaccines. Our findings revealed broad functional and clonal heterogeneity in T cells generated by vaccination or infection, including multiple distinct effector populations. T cell function was largely conserved between COVID-19 vaccine platforms but was distinct compared with SARS-CoV-2 infection. Notably, the dosing interval greatly influenced the quality of T cells after two vaccine doses, particularly after mRNA-LNP vaccination, where a longer interval led to reduced inflammatory signaling and increased secondary proliferation. These insights enhance our understanding of SARS-CoV-2–specific T cells and inform the optimization of mRNA vaccination regimens.
MAIT and other innate-like T cells integrate adaptive immune responses to modulate interval-dependent reactogenicity to mRNA vaccines
Adenoviral (Ad) vectors and mRNA vaccines exhibit distinct patterns of immune responses and reactogenicity, but underpinning mechanisms remain unclear. We longitudinally compared homologous ChAdOx1 nCoV-19 and BNT162b2 vaccination, focusing on cytokine-responsive innate-like lymphocytes—mucosal-associated invariant T (MAIT) cells and Vδ2 + γδ T cells—which sense and tune innate-adaptive cross-talk. Ad priming elicited robust type I interferon (IFN)–mediated innate-like T cell activation, augmenting T cell responses (innate-to-adaptive signaling), which was dampened at boost by antivector immunity. Conversely, mRNA boosting enhanced innate-like responses, driven by prime-induced spike-specific memory T cell–derived IFN-γ (adaptive-to-innate signaling). Extending the dosing interval dampened inflammation at boost because of waning T cell memory. In a separate vaccine trial, preboost spike-specific T cells predicted severe mRNA reactogenicity regardless of the priming platform or interval. Overall, bidirectional innate-like and adaptive cross-talk, and IFN-γ–licensed innate-like T cells, orchestrate interval-dependent early vaccine responses, suggesting modifiable targets for safer, more effective regimens.
Human tonsil organoids reveal innate pathways modulating humoral and cellular responses to ChAdOx1.
The COVID-19 pandemic response demonstrated the effectiveness of adenovirus vector vaccines in inducing protective cellular and antibody responses. However, we still lack mechanistic understanding of the factors regulating immunity induced by this platform, especially innate pathways. We utilized a human tonsil organoid model to study the regulation of adaptive responses to ChAdOx1 nCoV-19. Innate activation and cytokine release occurred within 24 hours and T and B cell activation and antigen-specific antibody secretion occurred during the ensuing 14-day culture. Among the immune cell populations, plasmacytoid dendritic cells (pDCs) exhibited the highest ChAdOx1 transduction levels. pDC-derived IFN-ɑ was critical for humoral responses, but production of antigen in pDCs was dispensable. Furthermore, IL-6 enhanced humoral responses in both IFN-⍺-dependent and independent manners, indicating intricate signaling interplay. IFN-ɑ and IL-6 also regulated the function of vaccine-activated CD4+ T cells, including TFH. These data provide key insights into innate pathways regulating ChAdOx1-induced immunity and highlights the promise of this model for vaccine platform mechanistic studies.
Heterologous COVID-19 vaccine schedule with protein-based prime (NVX-CoV2373) and mRNA boost (BNT162b2) induces strong humoral responses: Results from COV-BOOST trial.
BackgroundHeterologous schedules of booster vaccines for COVID-19 following initial doses of mRNA or adenoviral vector vaccines have been shown to be safe and immunogenic. There are few data on booster doses following initial doses of protein nanoparticle vaccines.MethodsParticipants of the phase 3 clinical trial of the COVID-19 vaccine NVX-CoV2373 (EudraCT 2020-004123-16) enroled between September 28 and November 28, 2020, who received 2 doses of NVX-CoV2373 administered 21 days apart were invited to receive a third dose booster vaccine of BNT162b2 (wild type mRNA vaccine) as a sub-study of the COV-BOOST clinical trial, and were followed up for assessment of safety, reactogenicity and immunogenicity to day 242 post-booster.ResultsThe BNT162b2 booster following two doses of NVX-COV2373 was well-tolerated. Most adverse events were mild to moderate, with no serious vaccine-related adverse events reported. Immunogenicity analysis showed a significant increase in spike IgG titres and T-cell responses post-third dose booster. Specifically, IgG levels peaked at day 14 with a geometric mean concentration (GMC) of 216,255 ELISA laboratory units (ELU)/mL (95% CI 191,083-244,743). The geometric mean fold increase from baseline to day 28 post-boost was 168.6 (95% CI 117.5-241.8). Spike IgG titres were sustained above baseline levels at day 242 with a GMC of 58,686 ELU/mL (95% CI 48,954-74,652), with significant decay between days 28 and 84 (geometric mean ratio 0.58, 95% CI 0.53-0.63). T-cell responses also demonstrated enhancement post-booster, with a geometric mean fold increase of 5.1 (95% CI 2.9-9.0) at day 14 in fresh samples and 3.0 (95% CI 1.8-4.9) in frozen samples as measured by ELISpot. In an exploratory analysis, participants who received BNT162b2 after two doses of NVX-COV2373 exhibited higher anti-spike IgG at Day 28 than those who received homologous three doses of BNT162b2, with a GMR of 5.02 (95% CI: 3.17-7.94). This trend remained consistent across all time points, indicating a similar decay rate between the two schedules.ConclusionsA BNT162b2 third dose booster dose in individuals primed with two doses of NVX-COV2373 is safe and induces strong and durable immunogenic responses, higher than seen in other comparable studies. These findings support the use and investigation of heterologous booster strategies and early investigation of heterologous vaccine technology schedules should be a priority in the development of vaccines against new pathogens.
Comparative performance of the InBios SCoV-2 Detect TM IgG ELISA and the in-house KWTRP ELISA in detecting SARS-CoV-2 spike IgG antibodies in Kenyan populations.
The InBios SCoV-2 Detect™ IgG ELISA (InBios) and the in-house KWTRP ELISA (KWTRP) have both been used in the estimation of SARS-CoV-2 seroprevalence in Kenya. Whereas the latter has been validated extensively using local samples, the former has not. Such validation is important for informing the comparability of data across the sites and populations where seroprevalence has been reported. We compared the assays directly using pre-pandemic serum/plasma collected in 2018 from 454 blood donors and 173 malaria cross-sectional survey participants, designated gold standard negatives. As gold standard SARS-CoV-2 positive samples: we assayed serum/plasma from 159 SARS-CoV-2 PCR-positive patients and 166 vaccination-confirmed participants. The overall agreement on correctly classified samples was >0.87 for both assays. The overall specificity was 0.89 (95% CI, 0.87-0.91) for InBios and 0.99 (95% CI, 0.97-0.99) for KWTRP among the gold standard negative samples while the overall sensitivity was 0.97 (95% CI, 0.94-0.98) and 0.93 (95% CI, 0.90- 0.95) for InBios and KWTRP ELISAs respectively, among the gold standard positive samples. In all, the positive predictive value for InBios was 0.83 (95% CI, 0.79-0.87) and 0.98 (95% CI, 0.96-0.99) for KWTRP while the negative predictive value was 0.98 (95% CI, 0.97- 0.99) and 0.97 (95% CI, 0.95-0.98) for InBios and KWTRP respectively. Overall, both assays showed sufficient sensitivity and specificity to estimate SARS-CoV-2 antibodies in different populations in Kenya.
Respiratory syncytial virus hospitalisation by chronological month of age and by birth month in infants
Understanding the distribution of respiratory syncytial virus (RSV) disease burden by more granular age bands in infants is necessary for optimising infant RSV immunisation strategies. Using a Bayesian model, we synthesised published data from a systematic literature review and unpublished data shared by international collaborators for estimating the distribution of infant RSV hospitalisations by month of age. Based on local RSV seasonality data, we further developed and validated a web-based prediction tool for estimating infant RSV hospitalisation distribution by birth month. Although RSV hospitalisation burden mostly peaked at the second month of life and was concentrated in infants under six months globally, substantial variations were noted in the age distribution of RSV hospitalisation among infants born in different months. Passive immunisation strategies should ideally be tailored to the local RSV disease burden distribution by age and birth month to maximise their per-dose effectiveness before a universal immunisation can be achieved.
Chicken TCRγδ+CD8α+T cells are antigen-specific and protective in H9N2 AIV infection.
TCRγδ+ T cells are a major lymphocyte population of chickens, but their response or contribution to immunity against avian influenza virus (AIV) remains unknown. Here, we report an increase in the proportion and activation state of TCRγδ+CD8α+ T cells in the PBMCs of 3 chicken lines (MHC homozygous H-B2 and H-B21 lines and outbred G-WL line) with the strongest responses observed in the more resistant H-B2 chickens. H9N2 AIV infection induced mRNA upregulation of interferon (IFN)-γ and cytotoxicity-associated molecules, including, Granzyme A, Granzyme K, and perforin in sorted TCRγδ+CD8α+ T cells. Moreover, in ex vivo cultured TCRγδ+CD8α+ T cells in response to H9N2 AIV infected splenocytes, strongly indicates the activation of these cells' cytolytic potential via detection of transcription levels of cytotoxic genes with quantitative reverse transcription polymerase chain reaction (qRT-PCR), and IFN-γ protein level with ELISPOT and an intracellular cytokine staining assays. Most importantly, in vivo depletion of γδ T cells led to reduced H9N2 AIV control, which was particularly evident in the early phase of infection. Taken together, these results indicate that strong TCRγδ+CD8α+T cell response plays a critical role in protecting chicken against H9N2 AIV infection.
Capsid Restructuring Activates Semi-Conservative dsRNA Transcription in Cystovirus ɸ6.
Double-stranded (ds)RNA viruses replicate and transcribe their genome within a proteinaceous viral capsid to evade host cell defenses. While Reovirale s members use conservative transcription, most dsRNA viruses, including cystoviruses, utilize semi-conservative transcription, where the positive strand of the genome functions as mRNA. Here, we visualize semi-conservative transcription activation in cystovirus ɸ6 double-layered particles using cryogenic electron microscopy. We observe nucleotide-triggered disassembly of the domain-swapped outer capsid layer, subsequent expansion of the inner capsid layer, and stepwise assembly of transcription complexes at the opposing poles of the spooled dsRNA genome. These complexes consist of the viral polymerases embedded into a triskelion formed by the minor protein P7, which we show as essential for continuous transcription. The packaging hexamers proximal to the transcription sites channel the viral mRNA exit. Our results define the complex molecular pathway from the quiescent state to activated semi-conservative transcription.
Safety and immunogenicity of varied doses of R21/Matrix-M™ vaccine at three years follow-up: A phase 1b age de-escalation, dose-escalation trial in adults, children, and infants in Kilifi-Kenya.
BackgroundFalciparum malaria remains a global health problem. Two vaccines, based on the circumsporozoite antigen, are available. RTS, S/AS01 was recommended for use in 2021 following the advice of the World Health Organisation (WHO) Strategic Advisory Group of Experts (SAGE) on Immunization and WHO Malaria Policy Advisory Group (MPAG). It has since been pre-qualified in 2022 by the WHO. R21 is similar to RTS, S/AS01, and recently licensed in Nigeria, Ghana and Burkina Faso following Phase 3 trial results.MethodsWe conducted a Phase 1b age de-escalation, dose escalation bridging study after a change in the manufacturing process for R21. We recruited healthy adults and children and used a three dose primary vaccination series with a booster dose at 1-2 years. Variable doses of R21 and adjuvant (Matrix-M ™) were administered at 10µgR21/50 µg Matrix-M™, 5µgR21/25µg Matrix-M™ and 5µgR21/50µg Matrix-M™ to 20 adults, 20 children, and 51 infants.ResultsSelf-limiting adverse events were reported relating to the injection site and mild systemic symptoms. Two serious adverse events were reported, neither linked to vaccination. High levels of IgG antibodies to the circumsporozoite antigen were induced, and geometric mean titres in infants, the target group, were 1.1 (0.9 to 1.3) EU/mL at day 0, 10175 (7724 to 13404) EU/mL at day 84 and (following a booster dose at day 421) 6792 (5310 to 8687) EU/mL at day 456.ConclusionR21/Matrix-M™ is safe, and immunogenic when given at varied doses with the peak immune response seen in infants 28 days after a three dose primary vaccination series given four weeks apart. Antibody responses were restored 28 days after a 4 th dose given one year post a three dose primary series in the young children and infants.RegistrationClinicaltrials.gov (NCT03580824; 9 th of July 2018; Pan African Clinical Trials Registry (PACTR202105682956280; 17 th May 2021).
Rabies glycoprotein engineering for improved stability and expression.
Current rabies vaccines require multiple doses and are relatively expensive, limiting their accessibility. Novel low-cost vaccines capable of inducing a protective antibody response against the rabies virus glycoprotein (RVG) are therefore desirable. Structure-guided engineering of the antigen may enhance its qualitative or quantitative immunogenicity, as may transgene cassette optimisation in the case of vectored vaccines. We investigated the potential of these approaches for the design of improved rabies vaccines. We evaluated twelve candidate cassette designs. While codon optimisation enhanced expression in vitro, it did not translate into improved immunogenicity. Co-expression or RVG with rabies matrix protein (RVM) did not detectably affect expression or immunogenicity. Inserting a C-terminal trimerisation domain was detrimental to expression in vitro and did not improve immunogenicity compared to the wild-type comparator. We screened 72 mutant constructs for in vitro expression and pre-fusion stabilisation. Several mutants enhanced expression and/or pre-fusion stability at low pH. Combination of the previously reported H270P mutation with the H419L substitution achieved enhanced stability. An L271Q + H419L double mutant achieved the greatest positive effect upon expression. Neither of double mutants improved immunogenicity compared to wild-type RVG when tested using an mRNA vaccine platform. These mutant constructs may be of value for protein subunit vaccines, but full length wild-type RVG may be sufficiently conformationally stable and well-expressed for optimal immunogenicity of adenovirus and mRNA vaccines in mice.
Synergistic blockade of TIGIT and PD-L1 increases type-1 inflammation and improves parasite control during murine blood-stage Plasmodium yoelii non-lethal infection
ABSTRACT Pro-inflammatory immune responses are rapidly suppressed during blood-stage malaria but the molecular mechanisms driving this regulation are still incompletely understood. In this study, we show that the co-inhibitory receptors TIGIT and PD-1 are upregulated and co-expressed by antigen-specific CD4 + T cells (ovalbumin-specific OT-II cells) during non-lethal Plasmodium yoelii expressing ovalbumin ( Py NL -OVA ) blood-stage infection. Synergistic blockade of TIGIT and PD-L1, but not individual blockade of each receptor, during the early stages of infection significantly improved parasite control during the peak stages (days 10–15) of infection. Mechanistically, this protection was correlated with significantly increased plasma levels of IFN-γ, TNF, and IL-2, and an increase in the frequencies of IFN-γ-producing antigen-specific T-bet + CD4 + T cells (OT-II cells), but not antigen-specific CD8 + T cells (OT-I cells), along with expansion of the splenic red pulp and monocyte-derived macrophage populations. Collectively, our study identifies a novel role for TIGIT in combination with the PD1-PD-L1 axis in regulating specific components of the pro-inflammatory immune response and restricting parasite control during the acute stages of blood-stage Py NL infection.
Comparative performance of the InBios SCoV-2 DetectTM IgG ELISA and the in-house KWTRP ELISA in detecting SARS-CoV-2 spike IgG antibodies in Kenyan populations
Background The InBios SCoV-2 Detect™ IgG ELISA (InBios) and the in-house KWTRP ELISA (KWTRP) have both been used in the estimation of SARS-CoV-2 seroprevalence in Kenya. Whereas the latter has been validated extensively using local samples, the former has not. Such validation is important for informing the comparability of data across the sites and populations where seroprevalence has been reported. Methods We compared the assays directly using pre-pandemic serum/plasma collected in 2018 from 454 blood donors and 173 malaria cross-sectional survey participants, designated gold standard negatives. As gold standard SARS-CoV-2 positive samples: we assayed serum/plasma from 159 SARS-CoV-2 PCR-positive patients and 166 vaccination-confirmed participants. Results The overall agreement on correctly classified samples was >0.87 for both assays. The overall specificity was 0.89 (95% CI, 0.87–0.91) for InBios and 0.99 (95% CI, 0.97–0.99) for KWTRP among the gold standard negative samples while the overall sensitivity was 0.97 (95% CI, 0.94–0.98) and 0.93 (95% CI, 0.90– 0.95) for InBios and KWTRP ELISAs respectively, among the gold standard positive samples. In all, the positive predictive value for InBios was 0.83 (95% CI, 0.79-0.87) and 0.98 (95% CI, 0.96-0.99) for KWTRP while the negative predictive value was 0.98 (95% CI, 0.97- 0.99) and 0.97 (95% CI, 0.95-0.98) for InBios and KWTRP respectively. Conclusions Overall, both assays showed sufficient sensitivity and specificity to estimate SARS-CoV-2 antibodies in different populations in Kenya.