Malaria transmission-blocking vaccine candidate antigens have been developed to induce antibodies using different delivery systems, mainly protein-in-adjuvant formulations, independently in various laboratories giving varied transmission-blocking activity (TBA). However, only one candidate antigen has been tested in clinical trials. In order to advance the most efficacious target(s) for possible clinical development, a rank order of the leading antigens based on TBA in a head-to-head comparison using a single delivery platform was made. Candidate antigens, AnAPN1, PfsHAP2, Pfs230-C, Pfs25, and Pfs48/45 (with or without N-glycosylation site substitution), were generated as recombinant viral-vectored vaccines using simian adenovirus and modified vaccinia Ankara and administered to mice in a heterologous prime-boost regimen. Vaccine-induced antibody responses were induced to all except PfsHAP2 were maintained up to ten and a half months post-boost. TBA was assessed at the peak response against Plasmodium falciparum NF54 laboratory strain and African field isolates by ex vivo membrane feeding assays in Anopheles stephensi and A. gambiae respectively. Antibodies to three antigens [Pfs230-C, Pfs25 and Pfs48/45+_NGln] had TBA against P. falciparum NF54, and those against Pfs230-C and Pfs25 consistently showed efficacy regardless of the parasite exposure in both mosquito species. Further analysis of antibody responses to these two candidate antigens showed concentration-dependent efficacy against P. falciparum field isolates. In a rabbit study, responses to Pfs230-C, Pfs25 and Pfs48/45+_NGln also showed IgG concentration-dependent efficacy. To assess TBA against AnAPN1, antibody responses to three fragments were tested. TBA was observed only against N-terminal 135 amino acid fragment. Pfs230-C and Pfs25 were generated as fusion vaccines using either a self-cleaving or glycine-proline linker sequence. Comparable antibody responses were induced between the two fusion strategies that had synergistic effects at inhibiting P. falciparum NF54 development in A. stephensi.

Tc17 cells and the semi-invariant human mucosal associated invariant T (MAIT) cells are important CD8+ tissue-homing cell populations. Both are characterized by high expression of CD161 (++) and type-17 differentiation, yet their origins and relationships remain poorly defined. By transcriptional and functional analyses it is demonstrated that a pool of polyclonal, pre-committed type-17 CD161++CD8αβ+ T cells exists in cord blood, from which a prominent MAIT cell (TCR Vα7.2+/Vβ2 or 13.2) population emerges post-natally. During this expansion, CD8αα T-cells appear exclusively within CD161++CD8+/MAIT subset, sharing cytokine production (IL17, IL-22 and IFN-γ), chemokine-receptor expression (CCR2, CCR6 and CXCR6), TCR-usage and transcriptional profiles with their CD161++CD8αβ+ counterparts. These data demonstrate the origin and differentiation pathway of MAIT cells from a naïve type-17 pre-committed CD161++CD8+ T cell pool and the distinct phenotype and function of CD8αα cells in man. The CD161++CD8αβ and CD8αα T cell subsets are reduced in the peripheral circulation in chronic hepatitis B and C and are enriched in the liver in chronic hepatitis C. Their potential role in immunity to chronic viral hepatitis B and C is demonstrated by their expression of activation/exhaustion markers CD69, CD25, HLA-DR and PD-1. In addition a substantial distinct CD161-CD8β^low population is demonstrated in chronic hepatitis B, co-characterised by a CD28^low, HLA-DR^high phenotype and high expression of IFN-γ, with important implications for the development of immunotherapy and vaccination.

Most in-hospital deaths secondary to infections in under-five deaths within sub-Saharan Africa (SSA) occur in the initial 24 hours of admission and shock has been identified as a major risk factor for the early deaths. However, controversies exist on the appropriate clinical diagnosis of shock, choice of ideal fluid for resuscitation (crystalloid or colloid), and safety of fluid resuscitation in severe malnutrition or severe malaria. This thesis investigates these aspects and also reviews the evidence base of current paediatric fluid resuscitation guidelines for children (aged >60 days and ≤12 years) with severe febrile illnesses. Capillary refill time >2 seconds, weak pulse volume, or bradycardia, in the presence of abnormal temperature and severe disease are predictive of impaired perfusion (defined by lactic acidosis) and death. Tachycardia and temperature gradient are neither associated with increased risk of death nor predictive of hypoperfusion. Existing international definitions of shock have low sensitivities (FEAST=44%, WHO=2%, and ACCM=59%) and high specificities (FEAST=82%, WHO=100%, and ACCM=66%) for diagnosis of impaired perfusion. Clinical criteria derived (called derived shock) had a sensitivity of 30% and specificity of 93%. Shock in children with severe febrile illnesses in Kilifi has a complex presentation but mainly presents with hyperdynamic circulation (high cardiac index) and vasodilatation. Cases with low cardiac index (myocardial dysfunction) are relatively rare but increase the risk of mortality when present. Synthetic colloids (gelofusine, hydroxyethyl starch 130/0.4 (HES), and dextran 70) are safe for use in fluid resuscitation in children with severe malaria. However, HES is the most promising compared to other synthetic colloids concerns still remain about its renal safety. However, further evaluation of synthetic colloids for treatment of shock is not warranted due to the findings of FEAST trial. A Pilot trial shows that bolus isotonic fluids are safe, have better efficacy, and produce faster resolution of shock compared to low-sodium solutions at volumes and rates recommended by WHO in children with severe malnutrition. Evidence available from all ten the trials in children with sepsis show that fluid resuscitation using crystalloids and colloids result in similar survival. However, fluid bolus resuscitation results in increased mortality compared to no bolus (control) in children in SSA. This finding excludes children with gastroenteritis, trauma, burns, and malnutrition. Colloids are better than crystalloids for severe dengue shock but both have similar efficacy in moderate dengue shock.

Common mycobacterial diseases, including tuberculosis and leprosy, contribute to major mortality and morbidity worldwide. Despite evidence of an important role of host genetic factors in susceptibility to these infections, few compelling genetic associations have been identified with previous candidate gene and linkage approaches. This thesis investigates the genetic factors of human immunity to these mycobacterial diseases using a high-throughput approach of association testing. To assess genetic susceptibility to tuberculosis, I have conducted a genome-wide association study in the Gambian population as part of the Wellcome Trust Case Control Consortium (WTCCC). The study reveals the region flanking CADM1 as a potential susceptibility locus. Combining this study with a Ghanaian cohort further implicates two genetic loci at chromosome 18q11.2 (P = 9.2x10⁻⁹) and PARD3B (P = 1.4x10⁻⁶). For leprosy, I have performed a gene-centric association study in the New Delhi Indian population. Evidence of significant association was observed in the HLA-DRB1/DQA1 (P = 4.9x10⁻¹⁴) and TLR1 (P = 1.7x10⁻⁹) loci. These studies identify important genomic regions that may be involved in immunity to tuberculosis and leprosy. Further analysis revealed a significant immunogenetic overlap between tuberculosis and leprosy. This provides proof-of-principle for the subsequent aggregate analysis for mycobacterial susceptibility, which suggests that the steroid biosynthesis pathway may be important in anti-mycobacterial immunity. This thesis represents one of the largest studies to identify the genetic factors for human immunity against mycobacteria. These novel findings will further enhance vaccine and pharmaceutical efforts into prevention and treatment of these mycobacterial diseases.

Chronic otitis media (OM) is an archetypal complex disease, which is particularly prevalent in childhood. Epidemiological data suggest high heritability for disease susceptibility, but previous genetic association studies have had methodological flaws, and none have specifically focused on chronic OM phenotypes. Mouse models represent one way to ascertain candidate loci for human association testing. A number of mouse models of middle ear inflammation have been reported, but many susceptibility loci remain undiscovered. I demonstrate that oto-endoscopy is a robust and scalable phenotyping platform for OM in the mouse, and discuss its value in new model discovery. Chronic OM is also a feature of trisomy HSA21 (Down Syndrome). Through an interrogation of the mouse library of segmental trisomy models of Down Syndrome, I identify a critical trisomic region for chronic otitis media. This region may underlie OM susceptibility in Down Syndrome, but could also contribute to disease susceptibility in non-syndromic disease. Mouse models can also be used to interrogate disease mechanisms. Our previous work has shown that the chronically inflamed middle ear is hypoxic, and that hypoxia signalling is a potential therapeutic target. Exploiting the Junbo mouse model, I demonstrate that surgical ventilation of the Junbo ear improves inflammation, and that this is associated with loss of hypoxia signalling. I present preliminary results from transcript analyses of human middle ear effusions showing marked upregulation of hypoxia signalling. A systematic review of existing mouse models suggests that the loci FBXO11, EVI1, SMAD2, and TGIF1 are good candidates genes for human association testing. I detail recruitment and collection of DNA from families in the UK where a child is undergoing grommet insertion. Association testing using a variant of the transmission disequilibrium test shows susceptibility associated with polymorphisms at FBXO11, and possibly also SMAD2 and TGIF1.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common heritable trait whose prevalence mirrors geographic patterns of historic malaria endemicity, is thought to confer a selective advantage owing to partial protection conferred against malaria. Direct evidence supporting this malaria protection hypothesis in the form of clinical association studies remains controversial, however, as conflicting results have been reported with respect to the strength and specificity of a protective effect, if any, conferred to carriers of G6PD deficiency-associated alleles. This thesis examines genetic diversity at the G6PD locus, and then considers how such variation impacts both immediate molecular phenotypes and multifactorial clinical phenotypes. First, Chapter 3 presents a survey of variation at G6PD in several malaria-endemic areas, while Chapter 4 describes a novel technique for polymorphism discovery using pooled massively parallel sequencing. Next, in Chapters 5 and 6, I evaluate the link between genetic variation at the locus and G6PD enzyme activity, identifying major and minor determinants of G6PD deficiency state in an association study conducted in Kenya, and demonstrating a new technique for assaying G6PD deficiency at the level of an individual erythrocyte in a pilot project in Mali. Finally, Chapter 7 addresses the malaria protection hypothesis directly by conducting a fine-mapping case-control association study of severe malaria in the Gambia, where I found that G6PD deficiency alleles exhibited differential direction of association with respect to two important clinical syndromes-- trending towards risk conferred to severe malarial anemia, and protection with respect to cerebral malaria. Overall, these findings suggest that future clinical association studies should consider heterogeneity at the genetic level, as well as at the level of molecular and clinical phenotypes in order to achieve a better mechanistic understanding of the relationship between G6PD deficiency and severe malaria.

Hepatitis C virus (HCV) is a major global pathogen that infects an estimated 170 million people worldwide, and for which currently no vaccine is available. HCV is a highly diverse viral pathogen and exists as 6 major genotypes sharing only 75% sequence homology; developing a vaccine that is cross-reactive between genotypes is a major challenge. Defining immune responses that target different HCV genotypes will facilitate pan-genotypic T cell vaccine development. HCV genotype 3 (gt3) is now the most common infecting genotype in the United Kingdom and large parts of Asia; however, data regarding the T cell antigenic targets of this genotype is very limited. In this thesis, HCV gt3 specific T cell targets were defined in acute, chronic and spontaneously resolved infection: in chronic gt3 infection, T cell responses were low in magnitude and narrowly focused in specificity, similar to those previously reported for gt1; in contrast, resolved infection was associated with a higher magnitude and broader specificity of CD4+ and CD8+ T cell responses across the genome. Overall, T cell specificity in gt3 infection was markedly different to that previously described for gt1, confirming that sequence differences between genotypes result in distinct immunological profiles. Previous work from our laboratory demonstrated that, though T cell responses induced by a potent T cell vaccine containing HCV gt1b non-structural regions do target epitopes dominant in natural infection, induced T cells show limited cross-reactivity against other genotypes. In this thesis, it was assessed whether T cells primed in natural gt3 infection are able to recognize viral sequence variants at dominant epitopes, which would make these potential targets in cross-reactive vaccine design. For seven gt3-specific T cell epitopes identified here as dominant, major sequence variability was observed within and between genotypes, and limited T cell cross-reactivity observed against identified viral variants. This suggests that regions frequently targeted in natural infection may not serve as attractive targets for cross-reactive vaccine design. These results informed the subsequent design of a cross-reactive vaccine based on fragments of HCV that are conserved between genotypes. A generic algorithm was developed to define viral regions conserved between major HCV genotypes (for 1a/1b, 1/3a, 1-6), and these were joined to form immunogens between 819 and 1543 AA long. Possible artificial, non-HCV epitopes formed by junctions were identified using online epitope prediction servers, and abrogated through the insertion of 2-6 amino acid linkers. To address the concern that conserved regions may not be immunogenic, epitopes described in natural HCV infection were mapped on HCV sequences, showing that conserved segments are well populated with epitopes; additionally, strong binding peptides were predicted for conserved segments using online epitope prediction programs, suggesting potential in vivo immunogenicity. In conclusion, HCV T cell specificity is distinct between genotypes, with limited T cell cross-reactivity between viral variants. Leading from this result, vaccine immunogens were designed entirely based on conserved viral regions. This work paves the way for future studies of novel HCV immunogens based on conserved viral segments between genotypes.

Yersinia pestis is a human pathogen and the causative agent of bubonic plague, responsible for causing three massive pandemics, resulting in hundreds of millions of deaths in the 14th century alone. Yersinia’s virulence stems from its ability to overcome host immune defences by the injection of six Yersinia outer proteins (Yops) into the host cells via its Type III secretion system. One of these Yops, YopO specifically disables the actin polymerization machinery, leading to the crippling of phagocytosis. YopO consists of a GDI domain which sequesters Rac and Rho, and a kinase domain, the activity of which is dependent on host actin. Little is known about the targets of the kinase domain and the mechanism of function of YopO remains incomplete. In this work, YopO was crystallized in complex with actin, revealing that YopO binds to actin on subdomain 4, away from the 'hotspot’ between subdomains 1 and 3 which is involved in binding most actin-binding proteins. The structure reveals how recruitment of YopO-bound actin monomers stalls actin polymerization by steric hindrance. The structure also demonstrates how YopO uses actin for self-activation and suggests that actin is being used by YopO as bait for recruitment into actin machineries. Using SILAC mass spectrometry, actin cytoskeletal machineries within macrophages that recruit YopO are identified and these include, amongst others: VASP family proteins, gelsolin family proteins, formins and WASP. Of these, VASP, EVL, diaphanous1, WASP and gelsolin have been identified to be phosphorylated by YopO and were validated by in vitro phosphorylation. This work demonstrates that YopO uses actin as a scaffold for selection of kinase substrates, enabling targeted phosphorylation of the actin machinery and provides insight into the regulation of the actin cytoskeleton by phosphorylation under non-pathogenic conditions.

L'émergence de maladies telles que le SRAS et le SIDA au cours des dernières décennies a fait prendre conscience des liens étroits existant entre santé animale, santé humaine et santé des écosystèmes. En effet, les pathogènes émergents ont pour la plupart une origine zoonotique (i.e. ils circulaient à l'origine au sein des populations animales). Les risques sanitaires associés à ces émergences sont en constante évolution sous l'influence des changements globaux qui modifient les écosystèmes et les contacts entre les hôtes. La prévention et le contrôle des maladies infectieuses émergentes nécessitent la compréhension de leur dynamique dans l'ensemble des compartiments dans lesquels elles circulent. Le travail présenté ici avait pour objectif d'améliorer cette compréhension au sein des zones humides méditerranéennes en ce concentrant sur deux pathogènes émergents : les virus Influenza A (VIA) et le virus West Nile. Il a été structuré selon trois axes de recherche : i) Utiliser la surveillance épidémiologique de l'avifaune sauvage pour comprendre la circulation du virus West Nile dans le bassin méditerranéen ii) Comprendre la dynamique des VIA au sein des différents compartiments où ils circulent et à leur interface iii) Comprendre le rôle des conditions environnementales dans la dynamique des VIA notamment au sein des populations humaines. Nos résultats mettent en évidence l'intérêt de mener des études multidisciplinaires sur le long terme pour comprendre l'épidémiologie des maladies émergentes. Ils soulignent également le rôle des activités anthropiques et des conditions environnementales dans la dynamique de ces maladies. Nos études apportent des éléments de réflexion pour allier gestion des risques d'émergence et gestion des écosystèmes et des populations. Elles encouragent à développer ce type d'approche afin de relever le défi de la prévention et du contrôle des pathogènes émergents. / During the last decades, the emergence of numerous infectious diseases such as SARS and AIDS has raised awareness of the close links that exist between animal health, human health and ecosystem health. Many of the emerging pathogens have a zoonotic origin (i.e. they originally circulated among animal populations). The health risks associated with the emergence of these diseases are progressing under the influence of global changes that affect ecosystems and contacts between hosts. The prevention and control of emerging infectious diseases require an in-depth understanding of their dynamics in all the compartments in which they occur. The aim of the present work is to improve our understanding of these phenomena within the context of Mediterranean wetlands by focusing on two emerging pathogens: Influenza A viruses (IAV) and West Nile virus. The thesis is structured around three research axes i) Using epidemiological surveillance of wild birds to investigate the circulation of West Nile virus in the Mediterranean Basin ii) Exploring IAV dynamics in the different compartments in which they circulate and at their interface iii) Determining the role of environmental conditions in IAV dynamics, especially within human populations. Our results highlight the value of long-term interdisciplinary studies for the understanding of the epidemiology of emerging diseases. They also emphasize the role of human activities and environmental conditions in the dynamics of these diseases. Our studies open up perspectives for combining emerging disease risk management and the management of ecosystems and populations. They also argue in favour of further developing this type of approach in order to meet the challenge of emerging pathogen prevention and control.

A malária é a doença infecciosa mais prevalente em regiões tropicais e subtropicais e a Reação em Cadeia da Polimerase (PCR) com primers do 18S rRNA (4-8 cópias/parasito) no formato semi-nested ou nested-PCR são empregadas como referência. O genoma mitocondrial dos plasmódios é pequeno (6 kb) contendo três genes que codificam a enzima citocromo c oxidase I (cox I), a citocromo c oxidase III (cox III) e a citocromo b (cyt b), com número de cópias variando de 20-150/parasito. Esta pesquisa desenvolveu uma multiplex-PCR baseada na amplificação de cox I, cox III e cytb para a detecção simultânea de Plasmodium das espécies falciparum, vivax e malariae. A utilização de três pares de primers espécie-específicos, em uma única etapa de amplificação em lugar de uma nested-PCR (18S rRNA) poderia minimizar a ocorrência de contaminações (carry-over), reduzindo o custo das reações e o tempo para a liberação de resultados. A seleção dos primers empregou a estratégia ASO (Allele Specific Oligonucleotide), os amplificados das três espécies foram clonados e os plasmídeos contendo os insertos (controles positivos) foram usados em diluições seriadas determinar o limite de detecção que foi de 22,5 cópias para P. falciparum, 28,7 cópias para P. vivax e 32 cópias para P. malariae. Como cada parasito possui entre 20-150 cópias dos genes mitocondriais, a multiplex-PCR detectou 1 parasito das três espécies. Na etapa de validação, amostras antigas e recentes provenientes de regiões endêmicas foram testadas, todas com diagnóstico de gênero e espécie de Plasmodium. A multiplex-PCR foi mais sensível que a microscopia (gota espessa) quando 104 amostras foram testadas, e tão sensível quanto a semi-nested (n=60), a nested-PCR (n=6) e a PCR em Tempo Real (n=38). No entanto, na análise das espécies de Plasmodium, houve discordâncias da multiplex-PCR tanto em relação a gota espessa, quanto com a semi-nested-PCR principalmente na detecção de infecções mistas, havendo mais espécies detectadas pela semi-nested-PCR. Não houve discordâncias com a nested-PCR e a PCR em Tempo Real. Testes de especificidade da multiplex-PCR utilizando DNA de outros microrganismos e de doadores de banco de sangue não encontraram reações cruzadas (100% de especificidade). O estudo concluiu que a multiplex-PCR foi desenvolvida com sucesso, com especificidade de 100%, apresentando sensibilidade superior à gota espessa e equivalente à semi-nested-PCR, nested-PCR e PCR em Tempo Real, no entanto com discordâncias na identificação de espécies. Estudos prospectivos com amostras apresentando resultados discordantes nos testes moleculares de referência deverão ser testadas para avaliar se a nova ferramenta molecular possui sensibilidade superior. / Malaria is the most prevalent infectious disease in tropical and subtropical regions and the Polymerase Chain Reaction (PCR) based on the 18S rRNA sequence (4-8 copies/parasite) in semi-nested and nested-PCR formats are the reference tests. Plasmodium mitochondrial genome is small (6 kb) containing three genes encoding cytochrome c oxidase I (cox I), cytochrome c oxidase III (cox III) and cytochrome b (cyt b), with number of copies varying from 20-150/parasite. This research developed a multiplex-PCR based on the amplification of cox I, cox III and cytb for the simultaneous detection of Plasmodium falciparum, vivax and malariae. The use of three pairs of species-specific primers in a single amplification step rather than a nested-PCR (18S rRNA) could minimize the occurrence of carry-over, reducing the cost of reactions and the time to release of results. The selection of primers employed the ASO (Allele Specific Oligonucleotide) strategy. Amplification products of the three species were cloned and the plasmids containing the inserts (positive controls) were used in serial dilutions to determine the limit of detection (LoD) of 22.5 copies for P. falciparum, 28.7 copies for P. vivax and 32 copies for P. malariae. As each parasite has between 20-150 copies of the mitochondrial genes, the multiplex-PCR was able to detect 1 parasite of the three species. In the validation stage, old and recent samples from endemic regions were tested, all with diagnosis of genus and Plasmodium species. The multiplex-PCR was more sensitive than the thick blood smear when 104 samples were tested, and was as sensitive as the semi-nested (n=60), the nested-PCR (n=6) and the Real-Time PCR (n=38). However, in relation to Plasmodium species, there were disagreements of the multiplex-PCR with respect to both, the thick blood smear and the semi-nested PCR, mainly in the detection of mixed infections, with more species detected by the semi-nested-PCR. There were no disagreements with the nested-PCR and the Real-Time PCR. Multiplex-PCR specificity tests using DNA from other microorganisms and from blood bank donors found no cross-reactivity (100% specificity). The study concluded that the multiplex-PCR was successfully developed with specificity of 100%, presenting higher sensitivity than the thick blood smear and equivalent sensitivity to the semi-nested-PCR, the nested-PCR and the real-time PCR, however with disagreements in the identification of species. Prospective studies are needed to test the multiplex-PCR on samples with discordant results in reference molecular tests to assess whether the new molecular tool has superior sensitivity.