NIHRDataInsights/HRCSData huggingface dataset:
Title: Epidemiological modelling to address burden of hepatitis B in resource poor settings: Impact & cost-effectiveness of intervention strategies
Funder: Medical Research Council

Abstract: BACKGROUND: Despite childhood vaccination programmes, Hepatitis B virus (HBV) is still widespread in resource-poor settings (eg. in The Gambia 15-20% of adults are estimated to be chronically infected with HBV). Evidence in high-income countries shows that HBV treatment is effective in reducing HCC, as well as, cost effective (CE). However, there has been minimal action or research into developing similar intervention programmes in sub-Saharan Africa. Disease modelling & CE analyses, demonstrating the likely significant public health impact, may help change this lack of commitment. AIMS & OBJECTIVES: Generation of epidemiological models to address the burden of hepatitis B and hepatocellular carcinoma in resource poor settings: Impact and cost-effectiveness of screening & treatment programmes. METHODOLOGY: The main data source for Africa specific epidemiological and cost data will be the PROLIFICA programme, a 5 year, EU funded, community screening and treatment platform & HCC case control platform in West Africa. After systematic literature review into the natural history of HBV, the development of HBV markov state transmission model, using these transmission parameters, will be developed. Computational programming will use the force of infection, chronic carriage and age dependent models to model HBV related morbidity and mortality and the impact of screening and treatment. Inputting parameters generated from PROLIFICA, will allow outcome predictions specific to West Africa, with potential future applicability, once validated, to other sub-Saharan countries. CE of this hepatitis B screening and treatment programmes from a provider, as well as a societal perspective, will be evaluated by collecting both health and cost data, from the PROLIFICA programme, health facilities in the Gambia and household questionnaires. Embedding these results into the disease burden model will output cost per episode and DALYs averted by screening and treatment.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Defining the reciprocal interaction between neutrophils and human cytomegalovirus
Funder: Medical Research Council

Abstract: Human cytomegalovirus (hCMV) is a highly prevalent opportunistic infection and a major pathogen in immune-compromised patients including HIV-infected individuals and organ transplant recipients, causing disease through primary infection and secondary reactivation. The virus productively infects fibroblasts and macrophages, with detectable viral gene expression and the lytic release of new virions. However, hCMV is not thought to infect neutrophils, one of the main cells involved in innate immunity. Preliminary data indicates that neutrophils in fact respond very effectively to incubation with hCMV. This manifests as profound inhibition of constitutive apoptosis, which does not involve hCMV uptake, lytic viral gene expression, or contaminating LPS or monocytes. hCMV also triggers the secretion of a highly bioactive secretome from neutrophils (but not monocytes), which induces a similar anti-apoptotic effect in fresh neutrophils, and stimulates monocyte chemotaxis and their differentiation to a phenotype permissive for hCMV infection. This project aims to identify the bioactive components within the hCMV-induced neutrophil secretome responsible for the autocrine survival effect and paracrine effects on monocyte differentiation, through proteomic and lipidomic studies and the use of neutralising antibodies, and to define the receptor and cellular signalling mechanisms involved. Additionally, I will investigate the hypothesis that the virus uses the neutrophil as a vehicle for dissemination. This will involve immunophenotyping of monocytes for markers of dendritic cell and macrophage lineage commitment, viral growth curve analysis to determine if monocyte infection is productive or abortive, and co-culture of neutrophils with permissive fibroblasts to look for evidence of infectious virus transfer. This work will shed light on the role of the neutrophil as an inadvertent promoter of hCMV disease, and offer new approaches to combating viral dissemination.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: From malaria control to sustainable elimination: Cluster randomised trial comparing targeted versus generalised vector control in South Africa
Funder: Medical Research Council

Abstract: To achieve malaria elimination, interventions have to be sustainable in low transmission settings. Annual mass treatment of houses with indoor residual spraying (IRS) is costly per case averted when the malaria burden is low and can lead to poor compliance when the perceived risk of malaria is small. An open label two arm cluster randomised non-inferiority trial will compare effectiveness, cost, IRS coverage and householder acceptability between targeted focal IRS, initiated in response to two or more new local cases being reported in an area, no more than 4 weeks apart and within no more than 0.5 km from one another, with generalised annual IRS of all structures. Aggregations of spray localities will be used to form study clusters of between 5,000 and 10,000 inhabitants. Assuming an average of 3 cases/1000 person-years, and a coefficient of variation of 0.4 the trial will require at least 21 clusters per arm (42 in total) for 80% power and 5% significance if cluster populations consist of 6000 persons on average, incidence is measured over a 2 years period and if 1 case/1000 is regarded as the largest difference in the two methods that can be regarded as unimportant. The existence of hotspots of transmission from which cases arise will strengthen the case for focal vector control. Hotspots will be investigated through sero-prevalence surveys in the neighbourhoods of incident cases, compared to control neighbourhoods. Study endpoints will be malaria incidence, IRS coverage, intervention costs, compliance and antibody sero-prevalence. If targeted IRS is shown to be as effective, results in higher coverage, is more acceptable and more economical than mass IRS it will enable countries that have set elimination as a policy objective to make evidence based decisions about mass vector control in the pre-elimination phase.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: The structure and function of the human respiratory syncytial virus M2-1 protein and its critical interaction with viral cofactors
Funder: Medical Research Council

Abstract: Human respiratory syncytial virus (HRSV) is ubiquitous pathogen that is the major cause of severe respiratory tract infections in infants, the elderly and immunocompromised. Recent studies suggest that each year HRSV is responsible for over 34 million infections and between 66,000 and 199,000 deaths. In addition, HRSV infection early in life may contribute towards increased incidence of asthma later in adulthood. There is no HRSV vaccine. The only available specific treatment regime involves prophylactic administration of a humanized anti-HRSV monoclonal antibody, which although being effective, is expensive. Thus there remains a strong need for alternative and complementary anti-HRSV therapies. This proposal describes experiments that will investigate the structure and function of the HRSV M2-1 protein, which is an essential component of the viral polymerase. M2-1 is a phosphoprotein, and is known to associate with viral RNA and also the HRSV P protein. The ability of M2-1 to be phosphorylated, and to interact with RNA and P are critical for its function. Our research will use structural biology techniques paired with functional analysis using biochemical and cell-based assays to reveal critical information regarding the role and activities of M2-1 during the virus life cycle. The research we describe will build on our exciting and extensive preliminary data including the first crystal structure of the M2-1 protein at a resolution of 2.4 Å. We propose to determine the structure of M2-1 bound to both RNA and P protein ligands, and also determine the structural significance of phosphorylation at critical residues. This research program will identify RNA and P binding interfaces on the surface of M2-1, and identify critical residues involved in these processes. This work will identify the structural basis of M2-1 function, and also provide promising targets for structure-based antiviral drug design that can be addressed in future translational research.


Research activity codes: 5.1 PHARMACEUTICALS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: How does the trypanosome haptoglobin-hemoglobin receptor interact with nutrients and immunity molecules? Receptor structure to cellular mechanism.
Funder: Medical Research Council

Abstract: This project combines the technical expertise of the Carrington and Higgins laboratories, allowing an integrated structural and cellular approach to understand the biology of the trypanosome haptoglobin-haemoglobin receptor (HpHbR). We will combine structural techniques (x-ray crystallography, NMR and electron microscopy) with biophysical tools and molecular modeling, to understand how HpHbR interacts with ligands. Bacterial and baculovirus expression systems allow us to produce HpHbRs and haptoglobin variants. We have successfully solved crystal structures of T congolense HpHbR, alone and in complex with haemoglobin, and determined the structure of human HpHb complex. We have crystals (diffracting to 1.9Å resolution) and NMR data showing that we are close to determining structures of HpHbR from T. brucei variants. We will continue with these studies to determine the structure of HpHbR from a human infective trypanosome species in complex with human HpHb and HprHb and to understand the structural effect of polymorphisms that disrupt ligand binding in HpHbR from T. b. gambiense. We will use electron microscopy and image processing to study the architecture of the trypanolytic complexes and their interactions with HpHbR. Cellular studies will allow us to integrate structural information into the context of the dynamic endocytic system and VSG surface coat. Here we follow up the finding that HpHbR can protrude above the VSG layer, making it available to ligands but also accessible to IgG binding. We will use uptake assays and high-resolution microscopy techniques to follow ligand and IgG uptake. We have prepared an HpHbR null mutant of T. brucei and will introduce variant receptors into this context, allowing us to examine the importance of the position of the HpHb binding site relative to the VSG layer. We will use flagella mutants of trypanosomes to study the role of hydrodynamic flow in HpHbR function, ligand uptake and immunoglobulin clearance.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mechanisms of helminth induced antiviral immunity to RSV infection
Funder: Medical Research Council

Abstract: RSV is the main cause of viral bronchiolitis in infants worldwide. It results in hospitalisation of 2% of all infants and, particularly in those with a high viral load at the onset, may cause severe life threatening disease. With significant morbidity and, in developing countries, mortality, RSV bronchiolitis has major health and economic implications. Despite this, only supportive therapy is available and effective and affordable prevention is lacking. The costly use of palivizumab in prevention is limited to small groups of high risk infants in affluent settings. Using a mouse model, we have recently found that viral titres and immune/inflammatory cell responses following RSV infection were significantly reduced in mice previously infected with the strictly enteric nematode Heligmosomoides polygyrus (Hp). This was associated with increased expression of the antiviral genes interferon-beta, viperin and OAS in the lungs of Hp infected mice. We will test the hypothesis that immune mediators/cells induced by gut helminth infection enhance lung antiviral immune responses, thus reducing viral load, lung inflammation, and disease in RSV infection. We will use mouse models to determine if the Hp induced antiviral effects require adaptive immunity and Hp infection with associated tissue damage, or if they can be triggered by Hp products alone. We will then define which innate immune mediators/pathways are required for the Hp antiviral effect and test if these can reduce the severity of RSV infection in the absence of Hp infection. In a parallel clinical study, we will compare Ugandan children with and without gut helminth infection to determine if this also enhances antiviral responses in the human respiratory tract. These translational studies will define the immune mediators/cells responsible for helminth induced enhanced antiviral lung responses and may identify these as new targets for the prevention of severe RSV disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Unraveling type IV pilus assembly
Funder: Medical Research Council

Abstract: Pili are hair-like appendages found in many bacterial species to which they confer adhesive abilities. In numerous human pathogens they promote attachment to host cells and thereby play a key role in pathogenesis. Type IV pili (Tfp) are undoubtedly the most widespread type of pili since they are found in hundreds of very different bacterial species, including many important human pathogens such as our model Neisseria meningitidis. As already demonstrated for better characterized pili, understanding the molecular basis of Tfp assembly is expected to provide leads for the rational design of small molecules interfering with that process. Due to Tfp's exceptionally widespread distribution, such molecules would have a large spectrum of action and be of a tremendous therapeutic potential. However, this will need our understanding of Tfp assembly to be dramatically improved, which is the main objective of the research proposed here. Using a systematic genetic approach in N. meningitidis, we have provided indirect evidence that Tfp assembly relies on a relatively small set of highly conserved proteins, many of which were found to form a sub-complex at the inner membrane. Our recent finding that this sub-complex can self-assemble upon expression of the corresponding genes in E. coli paves the way for the reconstitution of a minimal system for Tfp assembly in the bacterial "workhorse" par excellence. Reconstituting a minimal pilus assembly system in E. coli will allow its subsequent functional and structural characterization, which are the main objectives of this research project. This is expected to have a major impact on Tfp biology. The two aims of this research project are to: 1. reconstitute in E. coli a minimal system capable of assembling Tfp through modular co-expression of optimized synthetic N. meningitidis pil genes, 2. perform and in depth functional characterization of this machinery in order to better understand its mode of action.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Streptococcus pyogenes interaction with the lymphatic hyaluronan receptor LYVE-1 as a mechanism for lymphatic dissemination and disease progression
Funder: Medical Research Council

Abstract: The polysaccharide capsule of the virulent human pathogen Streptococcus pyogenes is comprised of hyaluronan (HA), a large mucopolysaccharide in extracellular matrix and lymph. Building on our previous work demonstrating dissemination of S. pyogenes from a focus of infection to local lymph node, we have now shown that HA-encapsulated S. pyogenes can bind to human lymphatic endothelial cells via the lymphatic endothelial cell (LEC) hyaluronan receptor LYVE-1, providing a potential conduit for extracellular transport of S. pyogenes to lymph nodes. We have three broad questions (1) What is the impact of S. pyogenes binding to LYVE-1 on LEC in vitro? (2) What is the impact of the binding in vivo? (3) Is there evidence of binding in clinical tissues? In this proposal we will determine the impact of S. pyogenes capsular binding to primary human dermal (HD)LEC via LYVE-1, to determine if the interaction promotes internalisation by LEC or invasion/transmigration, as assessed by quantitative microbiology, confocal and 2 photon microscopy. The response of LEC to S. pyogenes binding will also be investigated by confocal microscopy and whole genome transcriptomics followed by targeted analysis of enriched gene products. The specificity of interaction will be underpinned by use of isogenic S. pyogenes HA mutants from leading clinical lineages and by use of LYVE-1 blocking strategies. We will go on to determine the functional significance of S. pyogenes-LYVE-1 binding in upper respiratory tract and soft tissue infections in refined experimental models exploiting availability of LYVE-1 blocking antibodies and homozygous LYVE1-/- knockout mice. Finally we will investigate the clinical relevance of our observations by appropriate immunostaining of tissues from patients that are infected with S. pyogenes and by determining the capacity of S. pyogenes to invade lymphatics of tonsil and soft tissue samples ex vivo.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Studies of hepatic latency in human ovale malaria
Funder: Medical Research Council

Abstract: Ovale malaria is caused by two closely related parasite species, Plasmodium ovale curtisi (Poc) and P. o. wallikeri (Pow). These have recently been shown to differ in the duration of the latent period prior to development of a symptomatic blood-stage infection, implying differences in liver stage biology. The literature contains a single study on liver-stage schizonts (1954) and none on hypnozoites of ovale malaria, yet recent data suggest that ovale parasites can evade chemotherapy in some individuals, presumably through the emergence of hypnozoites into the blood after drug levels have fallen. Thus P. ovale spp. liver-stage biology has important public health consequences for malaria control and elimination efforts in sub-Saharan Africa, where the parasite is widespread. We have established a transient 48 - 72 hour culture method with ex vivo ovale parasites from blood samples submitted to the UK Malaria Reference Laboratory that sustains schizont and gametocyte maturation, but not-erythrocyte invasion. This will permit studies of mRNA expression, sex ratio and ex-flagellation in ovale sexual stage parasites for the first time. We will attempt experimental mosquito infections and initiation of in vitro liver stage cultures by inoculation of primary human hepatocytes and cell lines with sporozoites from both Poc and Pow. The ex vivo blood stage material will also be used to for next-generation sequencing on the LSHTM in-house Illumina platform. Bioinformatic approaches will be used to identify genes shared with the relapsing parasite P. vivax, but not with P. knowlesi, as a means to generate a list of candidate genes important in the formation of hypnozoites. Patterns of ovale relapse in Malian children treated with ACT for falciparum malaria will be deduced from screening of follow-up blood samples in large clinical trials currently underway; this will add to our knowledge of the role of hypnozoites in maintaining ovale transmission in Africa.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Deciphering the role of the host endoplasmic reticulum in Chlamydia inclusion biogenesis
Funder: Medical Research Council

Abstract: Chlamydiae are obligate intracellular bacterial pathogens that have worldwide medical impact. Chlamydiae replicate within a specialised compartment, termed an 'inclusion'. Inclusion biogenesis requires a bacterial type III secretion system (T3SS), a macromolecular machine that deploys effector proteins into the inclusion boundary membrane and beyond into the host cytosol and nucleus. Chlamydial inclusion proteins (Incs) are hydrophobic T3SS substrates that localise to the inclusion membrane from where they subvert host functions. The inclusion membrane is therefore a critical host-pathogen interface, yet the extent of its interaction with cellular organelles and the origin of this membrane remain poorly defined. We have shown that the host rough endoplasmic reticulum (rER) is recruited to inclusions, and that generation of infectious bacterial progeny requires an intact rER. Electron tomography of Chlamydia-infected cells revealed 'pathogen synapses' where ordered arrays of T3SSs connect to the inclusion membrane only at rER contact sites. We propose to address important interrelated questions that arise from our findings using established approaches including protein biochemistry, cell biology, confocal microscopy and electron tomography. We will investigate whether the T3SS directs synapse formation by using effectors to recruit the rER. We wish to establish why the rER is recruited to the inclusion, specifically by investigating whether the translocon is hijacked during chlamydial infection. Our screening of predicted Incs in the genome revealed potential rER-retention signals. We will investigate whether these interact with rER-based machinery and how they might determine Inc partitioning within the inclusion membrane. We will establish how rER morphology influences pathogen synapse formation and the shape and positioning of the inclusion. Together the data will provide a mechanistic understanding of the role of the rER in Chlamydia inclusion biogenesis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION