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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.
Technological Approaches for Improving Vaccination Compliance and Coverage.
Vaccination has been well recognised as a critically important tool in preventing infectious disease, yet incomplete immunisation coverage remains a major obstacle to achieving disease control and eradication. As medical products for global access, vaccines need to be safe, effective and inexpensive. In line with these goals, continuous improvements of vaccine delivery strategies are necessary to achieve the full potential of immunisation. Novel technologies related to vaccine delivery and route of administration, use of advanced adjuvants and controlled antigen release (single-dose immunisation) approaches are expected to contribute to improved coverage and patient compliance. This review discusses the application of micro- and nano-technologies in the alternative routes of vaccine administration (mucosal and cutaneous vaccination), oral vaccine delivery as well as vaccine encapsulation with the aim of controlled antigen release for single-dose vaccination.
Core-shell microcapsules compatible with routine injection enable prime/boost immunization against malaria with a single shot.
Inadequate booster uptake threatens the success of immunization campaigns as seen with the recently rolled-out R21 malaria vaccine. The ability to administer both prime and boost immunizations with a single injection would therefore save lives and alleviate health care burdens. We present a platform for delayed delivery of the booster dose that is scalable with existing technology, easily injectable, and protective against malaria in vivo. Using chip-based microfluidics, we encapsulated the R21 malaria vaccine in polymer microcapsules that release their content weeks to months postinjection. Coinjecting microcapsules with the priming dose of the R21 vaccine elicited strong antibody responses in a mouse model and provided 85% of the protection of a standard prime/boost schedule. If confirmed in humans, these results would pave the way for rapid deployment of single-shot prime/boost vaccination, an urgently needed global health intervention.
Acute Plasmodium yoelii 17XNL Infection During BCG Vaccination Limits T Cell Responses and Mycobacterial Growth Inhibition.
Tuberculosis and malaria overlap in many sub-Saharan African countries where Bacillus Calmette Guérin (BCG) vaccination is routinely administered. The aim of this study was to determine whether the timing of BCG vaccination in relation to a malaria infection has implications for BCG vaccine efficacy. Mice were intradermally vaccinated with BCG either 4 weeks before infection with blood-stage Plasmodium yoelii 17XNL, at 13 days post-infection (during an acute blood-stage malaria infection) or 21 days post-infection (after clearance of P. yoelii 17XNL infection). Ex vivo control of mycobacterial growth by splenocytes was used as a surrogate of protective efficacy, and PPD-specific T-cell responses were quantified by flow cytometry. No differences in mycobacterial growth control were detected between BCG vaccinated mice and groups receiving vaccination prior to or after clearance of P. yoelii 17XNL infection. Poorer control of mycobacterial growth was observed following BCG vaccination administered during an acute malarial infection compared to BCG vaccination only or BCG vaccination after blood-stage malaria infection, and mycobacterial growth negatively correlated with the magnitude of total cytokine production from PPD-specific CD4+ T cells (p
Roles and responsibilities of participants, researchers, and the media in the communication of vaccine trials: Experience from the United Kingdom's first COVID-19 vaccine trial.
BackgroundThe media have played an important part in presenting arguments for and against vaccination. The potential for the media to influence public attitudes to vaccines is becoming increasingly crucial to address.MethodsTo understand the differing roles and responsibilities in the communication of vaccine trials we draw insight from a retrospective study of 349 survey responses and 102 semi-structured interviews conducted in 2020 with participants in the United Kingdom's first-in-human clinical trial of the Oxford-AstraZeneca COVID-19 vaccine.ResultsWe found that trial participants had mixed views as to whether their participation conferred responsibility to communicate more widely about their trial experiences. Some participants perceived themselves to have an altruistic obligation to communicate to the media about the trial, and others felt that those who did share their participation had 'attention-seeking' motives. When participants did speak out they preferred to do so anonymously. Frustration was also reported with sensationalised and false media stories. Social media was viewed as a means to accelerate misinformation or as a force for recruitment and public education about trials. Participants were pleased to see trial investigators and trial team playing prominent roles in the media and this instilled confidence in the vaccine and the trial. We discuss these evolving roles and responsibilities for trial communication, concentrating on the views of participants about experiences, opportunities, and risks.ConclusionsWe argue that the pandemic has demonstrated the need for clinical trials to be made more transparent as a scientific practice that requires better public understanding and engagement. For high-profile vaccine trials we recommend; (1) explicit and comprehensive guidance aimed at all participants for interactions with the media; (2) prioritising having open and effectively expressed accounts of trial composition, processes, and participation; (3) offering support and a direct communication channel for journalists to report trials by utilising internal press officers to engage with journalists.
A roadmap of priority evidence gaps for the co-implementation of malaria vaccines and perennial malaria chemoprevention
Progress in malaria control will rely on deployment and effective targeting of combinations of interventions, including malaria vaccines and perennial malaria chemoprevention (PMC). Several countries with PMC programmes have introduced malaria vaccination into their essential programmes on immunizations, but empirical evidence on the impact of combining these two interventions and how best to co-implement them are lacking. At the American Society of Tropical Medicine and Hygiene 2023 annual meeting, a stakeholder meeting was convened to identify key policy, operational and research gaps for co-implementation of malaria vaccines and PMC. Participants from 11 endemic countries, including representatives from national malaria and immunization programmes, the World Health Organization, researchers, implementing organizations and funders attended. Identified evidence gaps were prioritized to select urgent issues to inform co-implementation. The output of these activities is a strategic roadmap of priority malaria vaccine and PMC co-implementation evidence gaps, and solutions to address them. The roadmap was presented to stakeholders for feedback at the 2024 Multilateral Initiative on Malaria meeting and revised accordingly. The roadmap outlines four key areas of work to address urgent evidence gaps for co-implementation: (1) support to the global and national policy process, (2) implementation support and research, (3) clinical studies, and (4) modelling. Together, these areas will provide practical guidance on the co-implementation of the interventions, and robust evidence to inform decision-making on how best to design, optimize and scale-up co-implementation in different contexts, including if and in what contexts the co-implementation is cost-effective, and the optimal schedule for co-implementation. This will work towards supporting the policy process on co-implementation of malaria vaccines and PMC, and achieving the most impactful use of available resources for the prevention of malaria in children.
Respiratory viral detection in children hospitalized with pneumonia during periods of major population disruptions in Nepal, 2014-2018.
BackgroundRespiratory viruses commonly cause pneumonia in children. We aimed to identify respiratory viral nucleic acids in the nasopharynx of children admitted with pneumonia from 2014 to 2018, a period including a major earthquake (April 2015), PCV10 introduction (August 2015), and a fuel shortage (October 2015 to March 2016).MethodsChildren 2 months to 14 years admitted to Patan Hospital between March 2014 and February 2018 with a clinical diagnosis of pneumonia had nasopharyngeal swabs collected and tested with a multiplex panel for the presence of genetic material from 23 respiratory pathogens.ResultsOf 1343 children with pneumonia, 974 (72.5%) had the nucleic acids of at least one respiratory virus in the nasopharynx. The median age of children with any viral genetic material detected was lower than those without (1.18, IQR: 0.59-2.39 years; versus 2.01 years, IQR: 0.81-4.34 years; p<0.001). Commonly detected viral nucleic acids included those of RSV (21.0%), rhino/enterovirus (30.8%), and parainfluenza (7.4%). The odds of detecting any respiratory viral genetic material in children with pneumonia increased by 1.88 (95% confidence interval: 1.15, 3.06) in the year after the earthquake, when there were several aftershocks and a fuel crisis, relative to other periods and accounting for other potential confounding factors.ConclusionsThese findings highlight the importance of viral diagnostics in pediatric pneumonia and suggest that public health measures addressing environmental conditions during disasters might help reduce respiratory infections.
Integrating Artificial Intelligence in Cybersecurity Education: A Pedagogical Framework and Case Studies
The increasing adoption of Artificial Intelligence (AI) in cybersecurity demands a new approach to education that combines technical skills with critical thinking and problem-solving. This paper presents a pedagogical framework focused on constructivist learning, scaffolding, and experiential learning to integrate AI concepts into cybersecurity education effectively. The framework enables students to actively engage in solving real-world cybersecurity problems using AI, while gradually building their knowledge and confidence through structured support and hands-on experiences. The framework is demonstrated through three practical case studies: phishing detection using supervised learning, malware classification with decision trees, and anomaly detection in network traffic through clustering algorithms. These case studies illustrate how students progress from foundational AI concepts to advanced applications in cybersecurity, fostering a deeper understanding of both fields. This paper highlights the anticipated outcomes of this approach, including increased student engagement, enhanced technical performance, and better preparation for AI-driven cybersecurity roles. By emphasizing active learning, guided progression, and real-world application, this work offers a scalable and impactful method for transforming cybersecurity education.
Iron deficiency causes aspartate-sensitive dysfunction in CD8+ T cells.
Iron is an irreplaceable co-factor for metabolism. Iron deficiency affects >1 billion people and decreased iron availability impairs immunity. Nevertheless, how iron deprivation impacts immune cell function remains poorly characterised. We interrogate how physiologically low iron availability affects CD8+ T cell metabolism and function, using multi-omic and metabolic labelling approaches. Iron limitation does not substantially alter initial post-activation increases in cell size and CD25 upregulation. However, low iron profoundly stalls proliferation (without influencing cell viability), alters histone methylation status, gene expression, and disrupts mitochondrial membrane potential. Glucose and glutamine metabolism in the TCA cycle is limited and partially reverses to a reductive trajectory. Previous studies identified mitochondria-derived aspartate as crucial for proliferation of transformed cells. Despite aberrant TCA cycling, aspartate is increased in stalled iron deficient CD8+ T cells but is not utilised for nucleotide synthesis, likely due to trapping within depolarised mitochondria. Exogenous aspartate markedly rescues expansion and some functions of severely iron-deficient CD8+ T cells. Overall, iron scarcity creates a mitochondrial-located metabolic bottleneck, which is bypassed by supplying inhibited biochemical processes with aspartate. These findings reveal molecular consequences of iron deficiency for CD8+ T cell function, providing mechanistic insight into the basis for immune impairment during iron deficiency.
Identification of cross-stage, cross-species malaria CD8+ T cell antigens.
Malaria is one of the most prevalent parasitic diseases in the world. In 2023, 263 million malaria cases were estimated worldwide. Two species of Plasmodium, P. falciparum and P. vivax, cause most human malaria. Despite the licensing of two partially protective vaccines for P. falciparum, there is no vaccine capable of providing long-term control or elimination. A major limitation for vaccine development is the lack of validated T cell epitopes for either species that could be targeted by vaccines. P. vivax is the most widespread human malaria parasite and is the major species causing malaria in the Americas and Asia while P. falciparum is more prevalent in Africa1. P. vivax exclusively infects reticulocytes in peripheral blood, which, unlike the mature erythrocytes infected by P. falciparum, still retain RNA and therefore retain host protein translation capabilities. We previously reported that P. vivax-infected reticulocytes express the major human leukocyte antigen class I (HLA-I), which allows parasite sensing by CD8+ T cells and consequent killing of parasite-infected host cells and intracellular parasites. Here we report by immunopeptidomic analysis the first unbiased identification of Plasmodium spp. antigens presented via HLA-I on infected reticulocytes. We identified 453 unique peptides that mapped to 166 different proteins. Most of these antigens were housekeeping proteins that are constitutively expressed at multiple stages of the parasite life cycle. Common peptides were presented in different individuals by the same or distinct HLA-ABC alleles as well as by non-classical HLA-E. Many peptide sequences were highly conserved in P. falciparum and P. vivax. The immunogenicity of the newly identified epitopes was validated in both P. vivax- and P. falciparum-infected patient samples. Furthermore, several of these antigens were immunogenic in the blood and liver of non-human primates following Plasmodium infection and attenuated parasite immunization. Two antigens were also the target of protective CD8+ T cell-mediated immunity in rodents. Thus, these antigens have potential for use in a cross-stage and cross-species malaria vaccine.
Virion Structure
Picornaviruses were the first animal viruses whose structure was determined in atomic detail and, as of October 2009, the Protein Data Bank (PDB) registered 53 structure depositions for picornaviruses. These data have contributed significantly to the understanding of picornavirus evolution, assembly, host-cell interaction, host adaptation, and antigenic variation and are providing the basis for novel therapeutic strategies. Subsequently classified as a picornavirus, the general morphology of FMDV could not be visualized until the advent of the electron microscope, when negative-stained images to a resolution of 4 to 5 nm revealed rather smooth round particles of ˜30 nm diameter. The current classification of picornaviruses is based on genome and protein sequence properties which are derived from the interplay of the error-prone replication mechanism of the virus with the process of natural selection. Differences in physical properties, such as buoyant density in cesium chloride and pH stability, underpinned the early classification of picornaviruses. Virus capsids recognize susceptible cells by attachment to specific receptors on the host cell membrane, thereby determining the host range and tropism of infection. The majority of antibodies are weak neutralizers that appear to operate by using the two arms of the antibody to cross-link different virus particles, causing aggregation.
An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis.
Peptides presented by HLA-E, a molecule with very limited polymorphism, represent attractive targets for T cell receptor (TCR)-based immunotherapies to circumvent the limitations imposed by the high polymorphism of classical HLA genes in the human population. Here, we describe a TCR-based bispecific molecule that potently and selectively binds HLA-E in complex with a peptide encoded by the inhA gene of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis in humans. We reveal the biophysical and structural bases underpinning the potency and specificity of this molecule and demonstrate its ability to redirect polyclonal T cells to target HLA-E-expressing cells transduced with mycobacterial inhA as well as primary cells infected with virulent Mtb. Additionally, we demonstrate elimination of Mtb-infected cells and reduction of intracellular Mtb growth. Our study suggests an approach to enhance host T cell immunity against Mtb and provides proof of principle for an innovative TCR-based therapeutic strategy overcoming HLA polymorphism and therefore applicable to a broader patient population.
Asparagine availability controls germinal center B cell homeostasis
The rapid proliferation of germinal center (GC) B cells requires metabolic reprogramming to meet energy demands, yet these metabolic processes are poorly understood. By integrating metabolomic and transcriptomic profiling of GC B cells, we identified that asparagine (Asn) metabolism was highly up-regulated and essential for B cell function. Asparagine synthetase (ASNS) was up-regulated after B cell activation through the integrated stress response sensor GCN2. Conditional deletion of Asns in B cells impaired survival and proliferation in low Asn conditions. Removal of environmental Asn by asparaginase or dietary restriction compromised the GC reaction, impairing affinity maturation and the humoral response to influenza infection. Furthermore, metabolic adaptation to the absence of Asn required ASNS, and oxidative phosphorylation, mitochondrial homeostasis, and synthesis of nucleotides were particularly sensitive to Asn deprivation. These findings demonstrate that Asn metabolism acts as a key regulator of B cell function and GC homeostasis.
The TyphiNET data visualisation dashboard: unlocking Salmonella Typhi genomics data to support public health
Abstract Background Salmonella enterica subspecies enterica serovar Typhi (abbreviated as ‘Typhi’) is the bacterial agent of typhoid fever. Effective antimicrobial therapy reduces complications and mortality; however, antimicrobial resistance (AMR) is a major problem in many endemic countries. Prevention through vaccination is possible through recently-licensed typhoid conjugate vaccines (TCVs). National immunisation programs are currently being considered or deployed in several countries where AMR prevalence is known to be high, and the Gavi vaccine alliance has provided financial support for their introduction. Pathogen whole genome sequence data are a rich source of information on Typhi variants (genotypes or lineages), AMR prevalence, and mechanisms. However, this information is currently not readily accessible to non-genomics experts, including those driving vaccine implementation or empirical therapy guidance. Results We developed TyphiNET (https://www.typhi.net), an interactive online dashboard for exploring Typhi genotype and AMR distributions derived from publicly available pathogen genome sequences. TyphiNET allows users to explore country-level summaries such as the frequency of pathogen lineages, temporal trends in resistance to clinically relevant antimicrobials, and the specific variants and mechanisms underlying emergent AMR trends. User-driven plots and session reports can be downloaded for ease of sharing. Importantly, TyphiNET is populated by high-quality genome data curated by the Global Typhoid Pathogen Genomics Consortium, analysed using the Pathogenwatch platform, and identified as coming from non-targeted sampling frames that are suitable for estimating AMR prevalence amongst Typhi infections (no personal data is included in the platform). As of February 2024, data from a total of n = 11,836 genomes from 101 countries are available in TyphiNET. We outline case studies illustrating how the dashboard can be used to explore these data and gain insights of relevance to both researchers and public health policy-makers. Conclusions The TyphiNET dashboard provides an interactive platform for accessing genome-derived data on pathogen variant frequencies to inform typhoid control and intervention strategies. The platform is extensible in terms of both data and features, and provides a model for making complex bacterial genome-derived data accessible to a wide audience.
Early mucosal responses following a randomised controlled human inhaled infection with attenuated Mycobacterium bovis BCG
Abstract The development of an effective vaccine against Mycobacterium tuberculosis is hampered by an incomplete understanding of immunoprotective mechanisms. We utilise an aerosol human challenge model using attenuated Mycobacterium bovis BCG, in BCG-naïve UK adults. The primary endpoint of this study (NCT03912207) was to characterise the early immune responses induced by aerosol BCG infection, the secondary endpoint was to identify immune markers associated with in-vitro protection. Blinded volunteers were randomised to inhale 1 × 107 CFU aerosolised BCG or 0.9% saline (20:6); and sequentially allocated to bronchoscopy at day 2 or 7 post-inhalation (10 BCG, 3 saline each timepoint). In the bronchoalveolar lavage post-aerosol BCG infection, there was an increase in frequency of eosinophils, neutrophils, NK cells and Donor-Unrestricted T cells at day 7, and the frequency of antigen presenting cells decreased at day 7 compared with day 2. The frequency of interferon-gamma+ BCG-specific CD4+ T cells increased in the BAL and peaked in the blood at day 7 post-BCG infection compared to day 2. BAL cells at day 2 and day 7 upregulated gene pathways related to phagocytosis, MHC-II antigen loading, T cell activation and proliferation. BCG’s lack of key virulence factors and its failure to induce granulomas, may mean the observed immune responses do not fully recapitulate Mycobacterium tuberculosis infection. However, human infection models can provide unique insights into early immune mechanisms, informing vaccine design for complex pathogens.