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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.
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 Using a Bayesian model, we synthesised published data from a systematic literature review and unpublished data shared by international collaborators for estimating the distribution of infant RSV hospitalisations by month of age.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.
Establishing laboratory reference ranges for haematological and biochemical blood parameters in adults and children in Kilifi, Kenya
Background Accurate laboratory reference ranges (RR) are essential for diagnosis and management of patients in routine clinical care and clinical trials. RRs vary between geographical location due to differences in population demographics and blood analysis equipment, so locally derived RRs are essential. Here we establish adult and paediatric RRs for a rural population in Kilifi, Kenya using clinical trial data from KEMRI-Wellcome Trust Research Programme (KWTRP). Methods Data from healthy, non-pregnant participants from six clinical trials conducted between 2016 and 2020 were used. Coulter ACT 5 Diff and Ilab Aries were used for haematological and biochemical analysis respectively. Quality control was undertaken daily prior to sample analysis. Derived RRs were compared with RRs from other African countries and further afield. All analyses were performed using R version 3.6.1 (Reference Intervals package). Results 2338 adults and 2054 children were included, 52% of adults and 51% of children were male, median adult age was 32.5 years. Haemoglobin range was lower in women compared to men (9.5–14.2g/dL and 11.5–16.6g/dL respectively), platelet upper limit of normal (ULN) was higher in women compared to men (397 x 103/μL vs 358 x 103/ μL). Biochemistry values were higher in men (ALT ULN 57 U/L in men and 35 U/L in women, creatinine ULN 113umol/L in men and 91umol/L in women). Paediatric RRs showed differences in multiple parameters depending on the age of the child. In both adults and children, many parameters in 2023 Kilifi RRs differed from those in other countries. There was however little difference between 2023 and 2017 Kilifi paediatric RRs. Conclusions This study provides RRs for adults and children in Kilifi, and the most extensive RRs available for much of East and Southern Africa. We show the need for locally derived reference ranges, highlighting differences between sex, age and geographical location.
Non-typhoidal Salmonella combination vaccines: clinical development plan and regulatory considerations.
Invasive non-typhoidal serovars of Salmonella enterica,S. Typhimurium and S. Enteritidis, (iNTS) are estimated to cause over 500,000 cases of disease leading to more than 79,000 deaths with a high case fatality ratio of 14.5 %. Most infections occur in infants and young children in LMICs in sub-Saharan Africa where host risk factors for iNTS disease such as malaria, malnutrition, HIV infection, and anemia are common. iNTS disease is observed from birth, with a peak incidence early in the second year of life, declining before the age of 3 years. The prevalence of multiple drug resistance of iNTS has increased markedly by decade, emphasizing the need for effective vaccines. A clinical development plan and regulatory pathway for licensure of iNTS vaccines has been shaped following the development of Preferred Product Characteristics and R&D Roadmap through a series of expert consultations. Several iNTS alone or combined with Typhoid Conjugate Vaccine platforms are in early clinical development. Encouraging safety and immunogenicity data have prompted developers and manufacturers to plan efficacy trials, aligned with regulatory expectations. It is critical to clearly communicate iNTS disease burden in endemic countries and to discuss complexities related to iNTS single component or combination vaccine clinical development with regulators. An essential component is the disease burden in infants less than 6 months of age, which will inform the optimal age of first vaccination (less than or from 6 months), compatibility across national expanded programme on immunization schedules, and whether a booster dose would be needed. Early regulatory guidance is essential to make informed regulatory decisions and to guide the clinical development plan and licensure pathway. Continued communication with public health stakeholders and end-user representatives will effectively contribute to better awareness and education about iNTS disease and protection afforded by vaccination.
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.
Nipah virus vaccines evaluated in pigs as a 'One Health' approach to protect public health.
Nipah virus (NiV) causes a severe neurological disease in humans. The first NiV outbreak, in Malaysia, involved pig-to-human transmission, that resulted in significant economic losses to the local pig industry. Despite the risk NiV poses to pig-dense regions, no licensed vaccines exist. This study therefore assessed three NiV vaccine candidates in pigs: (1) adjuvanted soluble NiV (s)G protein, (2) adjuvanted pre-fusion stabilised NiV (mcs)F protein, and (3) adenoviral vectored NiV G (ChAdOx1 NiV G). NiV sG induced the strongest neutralising antibody response, NiV mcsF induced antibodies best able to neutralise cell-cell fusion, whereas ChAdOx1 NiV G elicited CD8+ T-cell responses. Despite differences in immunogenicity, prime-boost immunisation with all candidates conferred a high degree of protection against NiV infection. Follow-up studies demonstrated longevity of immune responses and broadly comparable immune responses in Bangladeshi pigs under field conditions. These studies provide a platform for developing a NiV vaccine for pigs.
Repertoire, function, and structure of serological antibodies induced by the R21/Matrix-M malaria vaccine.
The World Health Organization (WHO) recently recommended the programmatic use of the R21/Matrix-M vaccine for Plasmodium falciparum malaria prevention in children living in malaria-endemic areas. To determine its effects on humoral immunity, we conducted a proteomic analysis of polyclonal IgG antibodies directed against the NANP tetrapeptide of the circumsporozoite protein (CSP), which comprises the vaccine's core immunogen. In 10 malaria-naïve adult volunteers, R21/Matrix-M induced polarized IgG anti-NANP repertoires, heavily skewed for IGHV3-30/3-33 genes bearing minimal somatic mutation, which remained static in composition following a controlled human malaria infection challenge. Notably, these vaccine-generated antibodies cross-reacted with another protective CSP epitope, the N-terminal junction region, despite its absence from the R21 construct. NANP-specific IGHV3-30/3-33 mAbs mined from polyclonal IgG repertoires blocked sporozoite invasion in vitro and prevented parasitemia in vivo. Overall, R21/Matrix-M elicits polarized, minimally mutated, polyclonal IgG responses that can target multiple protective CSP epitopes, offering molecular insight into the serological basis for its demonstrated efficacy against P. falciparum malaria.
Adenoviral vaccines—Infectious disease
Since the early 2000s, adenoviral vectors have been extensively used for the development of infectious disease vaccines. The first clinical vectors were derived from species C human adenovirus type 5 (HAdV-C5) and induced robust T cell and antibody responses against the encoded antigen. However, with widespread prevalence of HAdV-C5 in the human population, pre-existing immunity against the vector often adversely impacts vaccine immunogenicity. To circumvent this, rare human types and nonhuman types have been evaluated as vaccine vectors. Impressively, over 50 adenoviral vectored vaccines have been clinically evaluated against a wide range of pathogens, exploring different dosing regimens and delivery routes. In 2014, the first adenovirus-based vaccine was licensed, utilizing a vector derived from HAdV-D26, a rare human species D adenovirus with low seroprevalence. This adenoviral vector is delivered in a heterologous prime-boost regimen with Modified Vaccinia Ankara vector for prophylaxis against Ebola virus disease. Multiple clinical adenoviral vectored vaccines have since been granted marketing authorization. This success and subsequent widespread administration of adenoviral vectored vaccines is an additional source of antivector immunity, alongside that generated through natural adenovirus infection. This further drives the necessity to understand the mechanisms and impacts of antivector immunity, in addition to developing approaches to negate these. This chapter outlines the breadth of clinical adenoviral vectored vaccines developed against viral, parasitic and bacterial pathogens of humans, defining the clinical needs and associated challenges of such vaccines. The highlights and limitations of these adenoviral vectored vaccines are summarized, alongside vector delivery routes and dosing regimens, populations included during clinical evaluation, vaccine immunogenicity and efficacy outcomes, and the efforts to identify correlates of vaccine-induced protection.