Whooping cough is a common childhood disease caused by infection with the bacteria Bordetella pertussis or Bordetella parapertussis. Although previously considered under control within developed countries due to widespread vaccination, whooping cough has undergone a resurgence in many developed countries, with recent outbreaks underscoring the need for new and more effective vaccines. Most crucially, there is a need for vaccines that can be administered during the neonatal period, to protect infants at their most susceptible, and vaccines that will provide long-lasting protection. Due to the functional differences of the neonatal immune system as compared to the adult, there are specific difficulties that must be overcome when attempting to create a vaccine that will be effective in the neonate. The objective of the current research was to examine the immunogenicity of several adjuvants, including CpG ODN, IDRP, and PP, in order to design a combined novel adjuvant platform that could be used with our pertussis vaccine antigen, PTd. After selection of each adjuvant component, we tested the ability of various adjuvant formulations to induce Th1 and Th2 humoral responses in both adult and neonatal mice. We found that a 1:2:1 ratio of CpG ODN: IDRP: PP was most effective, and that pre-complexation of the IDRP and CpG ODN components induced significantly higher Th1 (IgG2a) antibody titres than non-complexed vaccines. Our vaccine platform induced strong Th1 and Th2 antibody titres in both adult and neonatal BALB/c mice, with the immune response being of a mixed Th1/Th2 type. The Th1 type humoral response to our vaccine platform was significantly higher than that seen using current commercial vaccines such as Quadracel®, or when using the standard vaccine adjuvant alum. This Th1 antibody response was extremely long-lasting, with strong IgG2a titres being found up to 2 years post-vaccination. When examining the cell-mediated immune response in adult and neonatal BALB/c mice, a strong secretory IFN-g (Th1) response was present post-vaccination in the splenocytes of platform-vaccinated mice, with a large number of IFN-g secreting cells present. The IL-5 (Th2) response was found to be decreased in mice that received our novel vaccine as compared to mice vaccinated with Quadracel®, with no detectable cytokine secreted by stimulated splenocytes in vitro, and few to no IL-5 secreting cells visible through ELISPOT. To further improve our vaccine, a second antigen, pertactin (PRN), was added to the formulation. Upon live bacterial challenge, mice that received the two-antigen vaccine were completely protected against infection, and showed strong humoral response. This full protection and clearance was superior to the results seen using Quadracel®. Finally, the variability and cell-recruitment functions of the adjuvant platform were examined. The adjuvant platform successfully induced a strong mixed Th1 and Th2 humoral response when combined with the vaccine antigen HBsAg, with a significant increase in the Th1 (IgG2a) antibody response. Replacing the CpG ODN component of the adjuvant platform with Poly I:C through and using various immunization routes also resulted in an induction of IgG2a titres. Thus we have developed a novel vaccine formulation against B.pertussis that induces strong humoral and cell-mediated immune responses in both adult and neonatal mice, with these responses being both long-lasting and protective against infection. Our novel adjuvant platform itself has been shown to be adaptable for use with other vaccine antigens and through several routes of administration, and there is the possibility of adjusting the components while maintaining efficacy.

Indiana University-Purdue University Indianapolis (IUPUI) / Malaria infects more than 240 million people every year, causing more than 640,000 deaths in 2021 alone. The complex interactions between the Plasmodium parasites that cause malaria and host immune system have made it difficult to identify specific mechanisms of vaccine-induced and naturally acquired immunity. After more than half a century of research into potential immunization methods, reliable immune correlates of malaria protection still have yet to be identified, and questions underlying the reduced protective efficacy of malaria vaccines in field studies of endemic populations relative to non-endemic populations still remain. In this thesis, I use computational methods to identify biological determinants of whole-parasite vaccine-induced immunity and immune correlates of protection from clinical malaria. Our systems analysis of a PfSPZ Vaccine clinical trial revealed that innate signatures were predictive of increased antibody response but also a decrease in the cytotoxic response required for sterilizing immunity. Conversely, these myeloid signatures predicted protection against parasitemia for subjects receiving a saline placebo, suggesting a role for myeloid-lineage cells in clearing pre-erythrocytic parasite stages. Based on these findings, I created a structural equation model to examine the interactions between cellular, humoral, and transcriptomic responses and the effects these have on protection outcome. This revealed a direct positive effect of CD11+ monocyte-derived cells on parasitemia outcome post-vaccination that was mediated by the presence of P. falciparum-specific antibodies at pre-vaccination baseline. Additionally, this model illustrates an indirect role of CD14+ monocyte activation in restricting immune priming by the PfSPZ Vaccine. Together, this data supports our hypothesis that innate immune activation and antigen presentation are uncoupled from cytotoxic cell-dependent immunity from the PfSPZ Vaccine and that this effect may be antibody-dependent.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Elizabeth Davis / The immune status of an individual host or among a population is affected by important variables including the source and route of potential natural exposure and for vaccination consist of vaccine type, potency, and virus strain; vaccination route and schedule; and individual host factors. Although, perhaps, often overlooked, it is essential to have a basic understanding of the laboratory methods used to measure and assess the host’s immune status. The precision, accuracy, sensitivity, and specificity of a method must be well defined. Moreover, an “adequate,” acceptable, or diagnostic value for each method must be clearly defined so that a particular test result for a patient can be meaningfully interpreted in relation to the patient’s history and clinical management. The reasons for performing rabies serology can range from diagnosis of infection to investigation of epitope specificity of an anti-rabies virus glycoprotein monoclonal antibody. Characterization of an antibody’s affinity, specificity, quantity, and neutralizing function, and class/subclass are achieved by various methods. Many serological techniques developed over the past five decades differ not only in their ability to detect the function, affinity and specificity of rabies virus antibodies, but also in the ease and practicality with which they are performed. To select an appropriate method and appropriately interpret test results, it is essential to understand the specific strengths, weaknesses, and limitations of available methods. The decision to use a specific assay should start with the purpose of testing and the intended application of results. Other factors to consider are the assay complexity, degree of precision and/or accuracy, specificity and range of detection. Given the importance of RVNA levels in the prevention of human and animal rabies, guidelines for adequate vaccination should be stated in terms that are readily understood by individuals-at-risk and health care providers, both veterinary and medical, who will use the recommendations for clinical management of humans or animals. Across the globe, the standardization of rabies serologic assays has a direct effect on the clinical use of human and animal products, including direct assessment of, and assessment of host responses to, rabies vaccines for the prevention of rabies.

Vaccines play a vital role in public health by preventing infectious disease across the globe. Vaccine formulations represent a weakened form of a microbe or toxin that is injected into the human body to elicit an immune response, generating antibodies to protect against a future infection. To this day, it is a challenge to identify and engineer important antigens and epitopes to focus this immune response in a safe and effective manner. The example of Bordetella pertussis is used to highlight the problems and lessons learned in designing a vaccine for this global epidemic. In particular, this review will focus on the advantages and disadvantages of chemical versus genetic detoxification and whole cell versus acellular vaccines in the context of pertussis. The latter part of this review will provide a summary of general strategies, such as epitope mapping and manipulation, synthesis of truncated variants, reverse vaccinology, and structural vaccinology, that have been successful in addressing increasingly complex diseases. Collectively, these techniques provide an invaluable set of tools to focus the immune response by finding and engineering specific antigens and epitopes. / text

Consistent efficacy in human clinical trials has been achieved by two leading malaria vaccine candidates encoding either the P. falciparum circumsporozoite (CSP) or thrombospondin-related adhesion (TRAP) proteins. However, protection in humans relies on high antibody (Ab) titers or potent T cells, respectively, when these antigens are used individually. Therefore, a concurrent induction of both anti-CSP antibodies and TRAP-specific T cells may further improve the protective efficacy associated with these immunogens. This thesis investigates the protective potential associated with CSP and TRAP combination vaccines by employing a pre-clinical Plasmodium berghei (P. berghei) mouse malaria challenge model. Depletion of CD4⁺ and CD8⁺ T cells indicated that protection by the CSP antigen relied solely on antibodies while TRAP protected through CD8⁺ T cell responses. Moreover, the administration of relatively small amount of anti-CSP monoclonal antibodies (mAb) substantially enhanced the sub-optimal protection elicited by TRAP. A way to maximize both, anti-CSP antibodies by adenovirus/protein (Ad-P) prime-boost vaccinations and anti-TRAP T cell responses using adenovirus/modified vaccinia strain Ankara (Ad-M), was explored. Combination of the two approaches stimulated optimal humoral and cellular responses that afforded sterile protection in the C57BL/6 animal model. Additional analyses of the effector functions of Abs indicated that the efficacy of this vaccine relied on a two-stage attack against the parasite: anti-CS antibodies reduced the number of sporozoites reaching the liver, thus decreasing the number of infected hepatocytes required to be eliminated by the dual action of natural killer (NK) cells and CD8⁺ T cells. These proof-of-concept studies using a wild-type (wt) P. berghei challenge model allowed progression towards the development of human malaria Plasmodium vivax (P. vivax) vaccines using PvCSP and PvTRAP antigens. The immunogenicity of PvCSP and PvTRAP-based vaccine candidates was assessed in multiple mouse strains. Additionally, transgenic (tg) P. berghei parasites expressing P. vivax genes were generated and used to demonstrate the protective efficacy of Ad-P PvCSP and Ad-M PvTRAP vaccines.

Despite 30 years of research, a prophylactic vaccine against HIV-1 is still lacking and is urgently needed in order to control the global AIDS pandemic. The discovery of broadly neutralising antibodies (BNAbs) was an important step for HIV-1 research but no vaccine candidate tested so far has been able to reproduce responses containing such antibodies, and it remains unclear how this could be achieved via immunisation. In this thesis, I attempted to explore this gap of knowledge in two ways. First, certain features (‘signatures’) of the Env protein that were associated with a broadly neutralising response were identified through machine learning. Further characterisation of these signatures revealed several ways by which these naturally-occurring mutations might alter the immunogenicity of the Env protein that could result in the elicitation of a broadly neutralising response. The incorporation of such signatures in future vaccine design could be useful as the Env protein might adopt a conformation that encourages the elicitation of a broadly neutralising response. Second, 3 novel vaccination approaches were proposed aiming to induce a BNAb antibody response. The development of 2 approaches proved to be difficult and was not continued. For the third approach, non-neutralising immunogen-derived antibodies were used to mask immunodominant epitopes on the Env protein (i.e. ‘antibody-shielding’), thus allowing the antibody response to be focused to the highly conserved CD4 binding site (CD4bs). Subsequent immunisation of the antibody-shielded gp120 proteins in mice and rabbits demonstrated that antibody-shielding was able to significantly dampen the V3-specific antibody response while retaining the CD4bs-specific response. However, the antibody response to the V1/V2 loop was enhanced upon V3-dampening which indicates that further optimisation of the antibody-shield is needed in order to eliminate any antibody response towards the immunodominant regions. In conclusion, these results are the first description of a number of novel vaccination ideas and provide valuable insights into how these approaches could be optimised to become effective HIV-1 vaccines that can lead to the elicitation of a broadly neutralising antibody response.

Replication defective adenoviruses have emerged as promising vectors for delivery of vaccine antigens. The development of new vaccine vectors has recently focused on serotypes t, which the human population is less exposed in order to circumvent pre-existing anti vector immunity. This thesis describes the construction and optimisation of ChAdOX1, a new vector based on chimpanzee adenovirus Y2S, which has recently been manufactured to clinical grade for a Phase 1 human trial. Comparative immunogenicity studies between vectors of different serotype were performed in mice, with careful consideration of the infectious titer of vector preparations, since this parameter can confound studies based solely on viral particle estimation. Aft intramuscular administration, HAdV-S (Human adenovirus C) based vectors elicited superior transgene product specific T cell and antibody responses compared to a selection of chimpanzee adenovirus vectors (from Human adenovirus EJ including ChAdOX1. The construction of ChAdOXl in a bacterial artificial chromosome (BA C), enabled precise, and flexible modification of the genome by recombmation mediated genetic engineering. (recombmeering). Reverse genetics was performed to identify vector determinants of immunogenicity. Chimeric ChAdOXl vectors were created by replacement of native virus associated RNA (VA-RNA) and fiber sequences with the corresponding sequences from HAdV-5 Using these chimeric vectors, the importance of innate immunity and vector transduction in determining vector immunogenicity was investigated. Though the mechanisms responsible ultimately remain unclear, superior transgene product specific immune responses with HAdV-5 correlated with higher levels of transgene expression in vivo after vector administration. The current study has conclusively demonstrated that neither VA-RNA sequences, nor the fiber protein, are responsible for differences in immunogenicity between vectors, contrary to hypotheses based on previous studies.

A highly effective vaccine against malaria is urgently needed, with leading vaccination strategies involving the induction of protective antigen-specific CD8⁺ T-cells via heterologous prime-boost viral vector immunization, targeting primarily the pre- erythrocytic liver stages of the Plasmodium falciparum lifecycle. To date, the greatest immunogenicity has been obtained through a heterologous prime boost regimen, where vaccination with an Adenoviral vector is followed 8 weeks later by a Modified Vaccinia Ankara virus (MVA) boost. Experimental work directed at providing a greater understanding of CD8⁺ T-cell memory responses induced by Ad-MVA vaccinations lead to the development of a novel vaccine strategy aimed at priming CD8⁺ T-cells in the periphery and subsequently targeting them to hepatic tissue with protein loaded poly(lactic- co-glycolic acid) nanoparticles or recombinant viral vectors. Durable Ag-specific CD8+ T- cells exhibiting a phenotype of tissue-resident memory T-cells were generated in the liver, with a ten-fold increase over the conventional heterologous vector regimen. Importantly, in P. berghei sporozoite challenge models of liver-stage malaria, this strategy was found to result in unprecedented levels of sterile protection across multiple clinically relevant antigens and mouse strains. This prime and target immunization strategy for liver-stage malaria may provide a novel general approach for prevention or immunotherapy against other hepato-trophic pathogens.

Despite being amongst the most common zoonotic diseases in the world, brucellosis is a neglected disease for which an approved vaccine for human use does not exist. Thus far, the traditional approaches to Brucella antigen selection for subunit vaccine development have yielded unacceptable results. In this work, we evaluated the predictive ability of a multistep Brucella antigen selection process with in vitro immunological and invasion assays and in vivo protection experiments. Initial in silico screening for antigens was performed via genomic sequence analysis where 27 Brucella melitensis open reading frames (ORF) coding for outer membrane proteins bearing MHC epitopes, adhesin and conserved properties were identified. Evidence for a role in any aspect of Brucella virulence (i.e., invasion, co-regulation/expression with known Brucella virulence factors, intracellular adaptation) was then used to narrow the list of candidate antigens. To further increase confidence in the candidate ORF putative role in Brucella pathogenesis, differential expression of candidate ORF was evaluated using previously generated global transcriptomics data in in vitro HeLa and in vivo bovine models of acute Brucella infection. Protein expression in the E. coli heterologous system resulted in the successful expression of OmpW, BtuB, Omp22, Hia, and FlgK. With regards to virulence, the two proteins with the highest predicted adhesin scores conferred an invasive phenotype to the non-invasive BL-21 E. coli strain in alveolar epithelial cells. From an immunogenicity standpoint, all proteins elicited IgG production in Brucella-exposed goats, mouse and humans. Antigen-specific recall responses in splenocytes from C57BL/6 mice immunized with a cocktail of the three proteins with highest MHC scores revealed a mixed Th1/Th2 response with a comparatively greater Th1 response. In protection studies, subcutaneous (SQ) immunization with BtuB, Hia and FlgK, individually, promoted bacterial clearance following a robust intraperitoneal challenge dose of Brucella melitensis 16M. In addition, single SQ inoculation of FlgK enhanced protective efficacy of the vaccine strain B. abortus S19. In contrast, immunization of mice with the three protective antigens in a cocktail formulation elicited immune responses but no protection against intraperitoneal challenge with Brucella melitensis 16M in the spleen and liver. In conclusion, our results indicate that our combinatorial in silico, in vitro and in vivo antigen selection and identification modeling approach provides strong evidence for prediction of Brucella protective antigens, and represent a novel strategy with broad application to other major pathogens.

Tuberculosis, caused by infection with Mycobacterium tuberculosis (M.tb), remains a global health problem. Drug resistance and high rates of HIV infection have fuelled the pandemic and, although a vaccine exists, its ability to protect from pulmonary tuberculosis varies between 0 and 80%. Bacille Calmette Guerin (BCG) has been administered to billions worldwide yet its protective mechanisms remain unknown, as do the reasons for its failure to protect in many parts of the world. Modified Vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel candidate vaccine designed to boost immune responses to BCG and improve protection. An aim of this thesis has been to characterise the innate immune response to an MVA85A boosting vaccination in both UK adults and South African infants. In the former, volunteers develop a strong innate response following vaccination however this does not always translate into a robust adaptive response to antigen 85A (Ag85A), which is determined in part by Treg expansion and the nuclear protein HMGB1 signaling through the TLR1-2-6 axis. By contrast, not all South Africa infants mount a strong innate immune response to MVA85A yet this response is correlated with the magnitude of the adaptive response. The immune response to BCG in both populations is also characterised and an association found between increased production of IL-17, IL-22 and IFN-γ in response to BCG stimulation and control of mycobacterial growth. The results presented here further the knowledge on the links between innate and adaptive responses to vaccination with BCG and MVA85A and the variation in mechanisms involved in different populations.