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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.
Pf8: an open dataset of Plasmodium falciparum genome variation in 33,325 worldwide samples
We describe the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000 Plasmodium falciparum samples from 99 partner studies and 122 locations over more than 50 years. This release provides open access to raw sequencing data and genotypes at over 12 million genomic positions. For the first time, it includes copy-number variation (CNV) calls in the drug-resistance associated genes gch1 and crt. As in Pf7, CNV calls are provided for mdr1 and plasmepsin2/3, along with calls for deletion in hrp2 and hrp3, genes associated with rapid diagnostic test failures. This data resource additionally features derived datasets, interactive web applications for exploring patterns of drug resistance and variation in over 5,000 genes, an updated Python package providing methods for accessing and analysing the data, and open access analysis notebooks that can be used as starting points for further analyses. In addition, informative example analyses show contrasting profiles of the decline of chloroquine resistance-associated mutations in Africa, and variation in copy number variation across 10 distinct sub-populations. To the best of our knowledge, Pf8 is the largest open data set of genome variation in any eukaryotic species, making it an invaluable foundational resource for understanding evolution, including that of pathogens.
Vaccine-induced responses to R21/Matrix-M - an analysis of samples from a phase 1b age de-escalation, dose-escalation trial.
IntroductionThe pre-erythrocytic malaria vaccine R21 vaccine adjuvanted with Matrix-M reported good efficacy (75%) in an ongoing phase 3 trial and was recommended World Health Organization for use in children 5-36 months. Vaccine-induced antibodies against NANP are associated with protection, however, various factors such as age, pre-existing immunity, and vaccine dose have been shown to influence vaccine responses.MethodsSamples from adults (n =18), children (n = 17), and infants (n = 51) vaccinated with R21/Matrix-M in a phase I trial were assayed for vaccine-specific antibody responses. We measured antibodies (quantity) by MSD and ELISA; and function (quality) by complement (C1q) fixation assay, inhibition of sporozoite invasion (ISI) assay, and avidity assay. Pre-existing malaria antibody exposure was assessed using an anti-3D7 Plasmodium falciparum crude parasite lysate ELISA.ResultsVaccine-induced CSP antibodies (against full-length R21, NANP, and C terminus), exhibited complement fixation and inhibition of sporozoites. These were significantly lower in adults compared to children and infants. Additionally, children had a higher rate of decay of vaccine-induced antibodies compared to adults 2 years post-vaccination. Furthermore, a higher Matrix-M adjuvant dose resulted in significantly higher C1q fixation, and ISI than the low adjuvant dose in infants. Importantly, functional measures ISI and C1q-fixation were positively associated with the vaccine-induced antibodies overall, but avidity was not. Interestingly, in adults, previous malaria exposure was negatively associated with ISI but positively correlated with avidity and C1q fixation. At baseline, all the study participants were seropositive for anti-HBsAg IgG above the WHO-required protective threshold of 10 mIU/mL, and titers significantly increased post-vaccination.DiscussionR21/Matrix-M was immunogenic across all age groups, with age and vaccine dose significantly affecting antibody magnitude and function. These findings emphasize the importance of evaluating the right adjuvant and vaccine dose for clinical development progression. This could thus inform the development of next-generation malaria vaccines. However, additional crucial factors need further exploration.
Risk factors of metabolic dysfunction-associated steatotic liver disease in a cohort of patients with chronic hepatitis B.
Background and aimsChronic hepatitis B (CHB) and metabolic dysfunction-associated steatotic liver disease (MASLD) commonly co-exist, with conflicting data in prevalence and disease severity. We aimed to investigate these discrepancies.MethodsThis multicentre study included consecutive CHB patients from 19 European centres. A survey on standard of care for MASLD screening in CHB was circulated.Results1709 CHB patients were included; median age: 53 (42-64), males 60.7%, BMI 25.6 (14-63), 57.3% White. MASLD prevalence (1510 consecutive patients) was 42.3%. BMI (OR=1.27, 95% CI:1.19-1.36), ferritin (OR=1.00, 95% CI:1.00-1.00) and type-2-diabetes (T2DM) (OR=2.60, 95% CI:1.12-6.02) were independently associated with MASLD. The prevalence of advanced fibrosis was 18% (255/1420) in the whole cohort, 25.4% (162/639) among CHB with MASLD, and 13.7% in those without MASLD. Independent predictors of advanced fibrosis were MASLD (OR:2.76, 95%CI:1.50-5.05), BMI (OR:1.08, 95%CI:1.02-1.15), ALT (OR:1.01, 95%CI:1.00-1.03), lower PLTs (OR:0.99, 95%CI:0.98-0.99), insulin-treatment (OR:13.88, 95%CI:2.95-65.28) and long-term antivirals (OR:4.86, 95%CI:2.40-9.85). During follow-up (48 months), only patients without MASLD showed significant LSM improvement over time (p<0.001). Among patients with MASLD, FIB-4 and LSM performed moderately at predicting advanced fibrosis (AUROC 0.71 vs 0.70, p=0.38), against histology. As standard of care, 68.4% centres screened all CHB patients for MASLD. 52.6% followed the same treatment indication in those with CHB and MASLD vs CHB only.ConclusionIn this large European cohort, MASLD and fibrosis were highly prevalent among CHB, while MASLD aggravated liver fibrosis. Though screening strategies remain inconsistent, ferritin levels, increased BMI and T2DM may inform on the presence of MASLD. Biomarkers showed modest performance in predicting fibrosis.
Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine.
Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6-14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4+ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.
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.
Developing the next-generation of adenoviral vector vaccines.
The COVID-19 pandemic saw the first extensive use of adenoviral vector vaccines, with over 3 billion doses produced during the first year of the pandemic alone and an estimated 6 million lives saved. These vaccines were safe and effective, and could be produced at low cost in several continents allowing widespread use in low- and middle-income countries (LMICs). Despite their successful deployment against SARS-CoV-2, their impact has been overshadowed by relatively lower immunogenicity in contrast to mRNA vaccine technologies and very rare but serious adverse events such as vaccine-induced thrombotic thrombocytopaenia (VITT). The next-generation of adenoviral vector vaccines must address these challenges: here, we explore strategies to improve immunogenicity and safety by novel serotype selection, vector engineering, capsid modification and new delivery technologies, and discuss opportunities for next-generation adenoviral vectors against infectious disease and cancer.
Prediction and characterisation of the human B cell response to a heterologous two-dose Ebola vaccine.
Ebola virus disease (EVD) outbreaks are increasing, posing significant threats to affected communities. Effective outbreak management depends on protecting frontline health workers, a key focus of EVD vaccination strategies. IgG specific to the viral glycoprotein serves as the correlate of protection for recent vaccine licensures. Using advanced cellular and transcriptomic analyses, we examined B cell responses to the Ad26.ZEBOV, MVA-BN-Filo EVD vaccine. Our findings reveal robust plasma cell and lasting B cell memory responses post-vaccination. Machine-learning models trained on blood gene expression predicted antibody response magnitude. Notably, we identified a unique B cell receptor CDRH3 sequence post-vaccination resembling known Orthoebolavirus zairense (EBOV) glycoprotein-binding antibodies. Single-cell analyses further detailed changes in plasma cell frequency, subclass usage, and CDRH3 properties. These results highlight the predictive power of early immune responses, captured through systems immunology, in shaping vaccine-induced B cell immunity.
Antibiotic use attributable to RSV infections during infancy-an international prospective birth cohort study.
BackgroundEarly-life antibiotic use impacts microbiome composition and contributes to the emergence of antimicrobial resistance. Despite respiratory syncytial virus (RSV) being a leading cause of acute respiratory infections (ARI), accurate estimates of antibiotic use attributable to RSV are lacking.ObjectivesTo assess RSV-associated antibiotic use during the first year of life.Patients and methodsThe RESCEU birth cohort study followed healthy term infants, born (n = 9154) between 1 July 2017 and 31 July 2020 from five European countries, to identify RSV-ARI hospitalizations during infancy. In a nested cohort (n = 993), we performed active RSV surveillance by collecting nasal swabs in case of ARI symptoms during RSV seasons (October-April). Antibiotic use during hospitalization was identified through chart review, while outpatient data were collected via parental questionnaires.ResultsIn the total cohort, antibiotics were used in 22.8% of RSV hospitalizations (33/145) and 62.5% of RSV intensive care admissions (5/8). In the nested cohort, antibiotics were used in 5.2% of any-severity RSV-ARI (13/250) and 9.9% of medically attended RSV-ARI (13/131). This results in an estimated incidence of 1.3% (95%CI: 0.8-2.0) of healthy term infants receiving ≥1 course of antibiotics associated with RSV infection in their first year, with an incidence rate of 1.1 RSV-associated antibiotic prescriptions per 1000 infant-months (95%CI: 0.6-1.9). As such, RSV accounts for 22.9% of antibiotic prescriptions for ARI during RSV seasons.ConclusionsOne in 77 healthy term infants receives antibiotics during RSV infection before their first birthday. Real-world evidence is needed to establish the impact of RSV immunization on antibiotic use during infancy.Clinical trials registrationNCT03627572.
Ex vivo model of functioning human lymph node reveals role for innate lymphocytes and stroma in response to vaccine adjuvant.
Immunological processes that underpin human immune responses to therapeutics and vaccine components, such as vaccine adjuvants, remain poorly defined due to a paucity of models that faithfully recapitulate immune activation in lymphoid tissues. We describe precision-cut human lymph node (LN) slices as a functioning, architecturally preserved, full-organ cross-sectional model system. Using single-cell transcriptomics and multiplexed imaging, we explore early inflammatory response to a potent, clinically relevant liposomal vaccine adjuvant containing a TLR4-agonist and QS-21 saponin. Both TLR4 and NLRP3 inflammasome activation are involved in the direct initiation of the inflammatory response to adjuvant by monocytes and macrophages (Mon./Mac.) with secretion of interleukin (IL)-1β, but not IL-18, dependent on TLR4 signaling. Innate lymphoid cells, including natural killer cells, are indirectly activated by Mon./Mac.-produced cytokines, signaling downstream to B cells via interferon-γ secretion. Resident LN stromal populations, primed both directly and indirectly by vaccine adjuvant, are instrumental in mediating inflammatory cell recruitment, particularly neutrophils.
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.
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.