NIHRDataInsights/HRCSData huggingface dataset:
Title: CoV-Ind-UK: Prospective investigation of the determinants for COVID-19 outcomes amongst South Asians in India and the United Kingdom.
Funder: Medical Research Council

Abstract: South Asian people are at high risk both for infection with SARS-CoV2 virus, and for developing severe or fatal COVID-19. Addressing this inequality is a major public health priority. In this study, we will identify incident COVID-19, amongst ~30,000 South Asian men and women who are participants of our established prospective population studies in India and the UK. Participants will undergo testing for SARS-CoV2, and complete a validated questionnaire to assess symptoms, relevant behaviours, attitudes to vaccination, and adverse outcomes. We will use our available comprehensive baseline phenotypic data, including molecular characterisation and stored biological samples, collected before the COVID-19 pandemic, to determine what are the major risk factors for infection with SARS-CoV2, severe COVID-19, or prolonged COVID-19, amongst South Asians in India and the UK. We will focus initially on recognised risk factors such as adiposity, raised blood pressure, diabetes, cardiovascular disease, health behaviours, socio-economic indicators, and biochemical measures. We will compare our results in South Asians with equivalent data for Europeans, to determine whether these known risk factors explain the high risk of COVID-19 in Asians. We will develop simple tools for predicting risk of COVID-19 in South Asians, that can prioritise people for vaccination or behavioural interventions, and thus protect them from COVID-19. We will report on vaccine hesitancy in South Asians and the main reasons for this. Finally, we will use 'all-of-the-data', including available health and genetic data, to search for novel risk factors or biological processes that might contribute to COVID-19 in South Asians. Our research will thereby determine the reasons underlying the high burden of COVID-19 in South Asians and generate knowledge that will inform health policy and practice for prevention and control of the disease amongst South Asians in India, the UK and globally.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS
Health categories: INFECTION
Title: Explaining the differential severity of COVID-19 between Indians in India and the UK
Funder: Medical Research Council

Abstract: Emerging data suggest that Indian residents may be less susceptible to severe COVID-19 than Indians in the diaspora. It remains unclear whether these differences are real or due to data artefact. Hypothesized mechanisms for protection from COVID-19 include lower burden of obesity and cardio-metabolic disease, greater exposure to vitamin D, and cross-immunity from past infections and vaccinations. The aim of this study is to determine whether the risk of severe COVID-19 (defined as COVID-19 related hospitalisation or death) differs between Indian populations in India and the UK and the extent to which this is explained by differences in data quality, age structure, co-morbidities, and cross-immunity. This project will comprise two work packages: The first is an epidemiological study comparing the population prevalence of severe COVID-19 in India and the UK. Using anonymised longitudinal electronic health record data for 400,000 people of Indian ethnicity in the UK, we will quantify the prevalence of severe COVID-19 adjusted for age, sex, and co-morbidities. A parallel analysis will be conducted in India using COVID-19 surveillance and chronic disease registry data from 220,000 people in the extended cohorts of two established studies in the states of Karnataka and Telangana. The second work package will use detailed biomarker and phenotyping data available in a 10,000 person subset of the two Indian cohorts to conduct an in-depth mechanistic study to elucidate hypothesized relationships between COVID-19 severity, environmental (vitamin D levels) and socio-economic factors (cross-immunity from greater exposure to infections and lower rates of obesity and cardiometabolic co-morbidities due to undernutrition). Findings will be used to triangulate evidence on the differential severity of COVID-19 in global Indian populations and translated into recommendations for clinical and policy use targeted at reducing risk of severe COVID-19 in Indian populations worldwide.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Primary care response to domestic violence and abuse in the COVID-19 pandemic: interrupted time series and qualitative study
Funder: Medical Research Council

Abstract: Aim To understand the impact of UK-wide COVID-19 social isolation policies on domestic violence and abuse (DVA) in the context of the general practice response during the pandemic and its aftermath, Research questions 1. What is the impact of COVID-19 social isolation policies on referral to specialist DVA support for patients experiencing abuse? 2. In remote consultations, how have GPs managed asking about/identifying abuse, giving support and offering referral to patients experiencing DVA amd how have they adapted to online DVA training? Methods Question 1: Interrupted-time series (ITS) and non-linear regression analysis including sensitivity analyses, using practice level referral data across 30 areas. Incidence rate ratios (IRR) and 95% confidence intervals of changes in referral rate before, during and reversal of social isolation policies, quantifying the impact of these COVID-19 prevention policies on DVA referrals. The analysis will cover one year before and one year after the implementation of social isolation (23/03/2019 - 22/03/2021) and the sudden national shift - for at least part of the second period - to online GP consultations. Question 2: Observation and interview-based qualitative study in a purposive sample of practices by ethnic and SES of population, and referral rates. Sampling of 30 GPs within selected practices and 10 other professionals (practice managers, DVA advocate educators); observation of 10 online training sessions. Thematic analysis. Triangulation of ITS with qualitative findings, exploring variation in the referral rates between areas, rapidly reporting relevance, feasibility, and safety of GP responses to DVA during the COVID-19 pandemic and its aftermath.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: INFECTION
Title: Experimentally induced blood-stage malaria in Kenyan adults: understanding disease mechanisms and protection in the context of background immunity
Funder: Medical Research Council

Abstract: Plasmodium falciparum malaria causes substantial morbidity and mortality in Africa. A high-efficacy vaccine is essential. The current lead malaria vaccine confers ~30% protection over 4 years and is based on the major antigen on the surface of pre-erythrocytic sporozoite parasite stages. An attractive strategy to build on this partial efficacy is a multi-stage vaccine including immunity against blood-stages of the parasites. However, there is no analogous single major antigen for blood stage parasites, and vaccines based on several different blood stage antigens have not been successful. Adults in endemic areas acquire immunity to blood-stage parasites after repeated malaria exposure. Identifying the underlying mechanisms of naturally acquired immunity has the potential to inform rational vaccine design e.g. antigen selection. We recently completed controlled human malaria infection (CHMI) studies in Kenyan adults using cryopreserved sporozoites (PfSPZ) and identified 33 out of 142 volunteers who remained uninfected by sensitive blood PCR for malaria parasites. The PCR negative volunteers are likely to have high levels of acquired immunity, and imply an excellent model for vaccine development. However the protection may have resulted either from immunity to pre-erythrocytic or to blood-stage parasites. The distinction is critical for further study and vaccine design. We now propose a blood-stage challenge experiment for these previously protected volunteers since this will bypass pre-erythrocytic stages to determine the contribution of blood-stage immunity and mechanisms. We aim to: (a) test whether a key component of malaria immunity is through an immune response to blood-stage infection; and (b) test whether individuals who are especially immune are able to control higher inoculums of parasites; and (c) define immunological mechanisms associated protection and/or disease pathogenesis to inform the development of the next generation of blood-stage malaria vaccines.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Longitudinal immune and inflammatory responses in the respiratory mucosa and blood of patients after hospitalisation with COVID-19.
Funder: Medical Research Council

Abstract: This study will test the hypothesis that natural infection with SARS-CoV-2 results in virus-specific IgA and T cell responses in the nasal mucosa, which are sustained for up to one year. In order to study the longevity of immune responses, 400 participants who have been hospitalized with COVID-19 will have blood and nasal samples collected at 3, 6 and 12 months post-discharge. Nasosorption allows collection of concentrated nasal fluid which is amenable to studies of antibody specificity. ELISA will be used to determine mIgA/IgG titres at each time-point to longitudinally assess the mucosal antibody response. Responses to viral epitopes including spike and nucleocapsid will be measured. Participant vaccination status and timing will be recorded during the study. This will allow comparison of spike and non-spike antibody titres following vaccination in order to compare the course of natural immunity and vaccine boosted immunity. This will also identify if vaccination can boost mucosal immune responses to SARS-CoV-2. MHC Tetramer staining on nasal curette samples will be used to analyse virus-specific tissue resident CD8+ and CD4+ T cell responses. This will be assessed at each time point to determine the strength and durability of responses. Cytokine levels in plasma and nasal mucosa will be measured through multiplex ELISA. This will be related to data from flow cytometry in selected patients, characterising neutrophil and NK cell populations in the blood and nasal mucosa. This will enable study of the chronic inflammatory response in those with symptoms of Long COVID. This is the first study to provide insights into long-term mucosal antibody and T cell responses to SARS-CoV-2 in convalescent patients. This study will identify if mucosal responses are a potential correlate of protection which can be evaluated further in mechanistic studies. This has important implications for vaccine development and understanding the future course of the pandemic.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding HIV-1 latency in 3D
Funder: Medical Research Council

Abstract: A cure for HIV-1 infection is a priority. Treatment interruption triggers viral rebound from a "reservoir" largely composed of memory CD4+ T cells latently infected with HIV-1. HIV-1 cure strategies aim either at reactivating latent HIV-1 to trigger immune-recognition and elimination of infected cells, or to make latency irreversible to prevent virus rebound upon treatment interruption. However, we have limited understanding of how HIV-1 latency is established or reversed, which presents a major barrier to either of these strategies. Spectacular advances in chromosome conformation capture techniques (3C) are revealing how the three dimensional (3D) organization of chromatin regulates gene expression in a cell type specific way. For example, genes and enhancers that are vastly distant from one another on the "linear" genome can cluster together in proximity in the folded chromatin, resulting in their transcriptional co-regulation. It is known that HIV-1 preferentially integrates into groups of active genes. It is not known how HIV-1 expression is influenced by the spatial organization of the genes in which the virus preferentially integrates. We hypothesize that the spatial location of the integrated provirus within chromatin is key to understand regulation of HIV-1 gene expression and latency. Specifically, we hypothesize that a) HIV-1 has evolved preferentially to integrate into specific spatial domains of chromatin resulting in coordinated expression of HIV-1 and groups of host genes located within the same domain and b) latency depends on the spatial rearrangement of such TADs and compartments. We will address these hypotheses by a combination of cutting-edge technologies to map HIV-1 integration sites onto 3D chromatin in active and latently infected cells, and determine if changes in 3D chromatin regulate latency. This research will provide new key knowledge on HIV-1 latency potentially revealing ways to modulate it for therapeutic purposes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Development of a CRISPR/Cas9 gene editing platform to correct Severe Combined Immunodeficiency caused by mutations in the IL7RA gene
Funder: Medical Research Council

Abstract: The severe combined immunodeficiencies (SCID) are a diverse set of diseases caused by numerous genetic mutations that share a common pathophysiological path of a quantitative deficiency in T-cell numbers. IL7RA deficiency causes the third most common form of SCID. Absence of T lymphocytes results in profound failure of the immune response, with severe and opportunistic infections leading to fatal outcome. While allogeneic hematopoietic stem cell transplantation is curative for all forms of SCID, incomplete immune reconstitution and toxicities cause significant morbidities, meaning alternative cures should be developed. Gene therapy has been successfully developed for ADA SCID and SCID X1, however its application to IL7RA SCID showed that constitutive and unregulated expression of the gene predisposes to leukemia. An alternative to gene therapy is to utilize genome editing, which could correct the endogenous IL7RA locus while avoiding issues of unregulated transgene expression. The goal of this proposal is to develop a CRISPR/Cas9-based genome editing platform to functionally correct mutations in the IL7RA gene in hematopoietic stem and progenitor cells (HSPCs) derived from SCID patients. Our preliminary results showed that by delivering our optimized CRISPR/Cas9 reagents together with an AAV6 donor template we are able to efficiently knock-in a reporter cassette into the IL7RA locus in up to 47% of HSPCs, while maintaining high cell viability and colony forming ability. We now aim to move forward and restore IL7R expression in IL7RA-deficient cells from SCID patients, to establish a viable gene editing-based therapeutic approach to treat IL7RA deficiency and potentially other blood disorders that require correction at the stem cell level.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: A Functional Analysis of Resistance to Pyrethroid Insecticides in the malaria vector Anopheles gambiae
Funder: Medical Research Council

Abstract: Understanding the nature of target site resistance to pyrethroid insecticides is of paramount importance, given that this is the only class of insecticide approved for use in insecticide-treated bednets, which remain our most potent weapon against malaria transmission. Huge collaborative efforts to sequence the genomes of wild caught mosquitoes from different malarial settings have highlighted a range of mutations, in the voltage-gated sodium channel that is the molecular target of pyrethroids, that may be associated with resistance. However, the strength of contribution of these mutations to insecticide resistance is unclear, as is how these mutations actually affect pyrethroid interaction. These are essential questions in order to: 1- improve diagnostic assays designed to track the most epidemiologically relevant mutations in a population; 2- open the possibility of rational design of improved insecticide formulations that are not subject to the same resistance. The work proposed here takes a two-pronged approach: firstly, using CRISPR genome editing to introduce putative resistant mutations in vivo on a uniform genetic background to unambiguously measure their effect on resistance and any pleiotropic effects on mosquito fitness; secondly, by using an electrophysiology approach in parallel to measure, at fine scale, the nature of the alteration to the sodium channel conferred by these mutations. Together, this information will allow a prioritisation of causative mutations according to effect size which can be used directly to improve the resolution of resistance monitoring in vector control programs, to better understand the dynamics of selection for resistance in the wild and, most importantly, allow more informed decisions when adapting control practice to combat resistance.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Molecular mechanisms of host restriction of arenaviruses and viral antagonism
Funder: Medical Research Council

Abstract: The importance of cell-intrinsic or host restriction factors of the innate immune response in shaping the life cycle of arenaviruses, which pose a significant global disease burden, is poorly understood. I discovered the cell-intrinsic inhibitory activity of the zinc metalloprotease ZMPSTE24 against arenavirus entry and identified that interferon-induced transmembrane proteins (IFITMs) co-operatively enhance ZMPSTE24-mediated viral restriction. Their expression affects cellular endocytosis kinetics implying a virus invasion barrier mechanism, and that membrane structure perturbation impacts on their activity, highlighting the importance of membrane integrity for arenavirus fusion. This proposal will define the restriction mechanism of ZMPSTE24 and IFITMs and determine their role in arenavirus infection dynamics: Objective 1 will determine their effects on host membrane structure and dynamics by measuring in-cell restriction factor-imposed differences in the freedom of motion of membranes by site-directed spin labelling coupled to Electron Paramagnetic Resonance spectroscopy. Heterogeneity in cell lipid order will also be monitored by two-photon emission and confocal with spectral emission microscopy using the membrane probe, NR12S. Objective 2 will elucidate whether arenavirus matrix protein Z, which interacts with ZMPSTE24, has a direct role in antagonising ZMPSTE24 activity, informed by mutagenesis and virus budding assays; thereby highlighting an immune escape strategy. Objective 3 will reveal how ZMPSTE24 restriction impacts on the life cycle of arenaviruses: quantitative proteomics will measure viral and host protein changes at different infection stages in the presence of ZMPSTE24 and IFITMs and identify key processes modulated by these restriction factors. Altogether, this multidisciplinary approach will unravel the impact of host restriction mechanisms on arenavirus pathogenesis and open up avenues for targeted therapeutic strategies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Characterization of critical differences between human and parasite respiratory complex II
Funder: Medical Research Council

Abstract: Apicomplexan parasites are global killers and their ability to infect and to disseminate depends on the function of their mitochondrial complex II. Surprisingly, the apicomplexan complex II is missing two canonical subunits that are thus far considered necessary for function. Through biochemical characterisation and functional studies of putative new complex II subunits we will unravel the functional mechanism of this complex. This work will improve our understanding of how divergent eukaryotes execute fundamental cellular processes, and inform future drug discovery. Aims 1. A group of Toxoplasma complex II subunit candidates identified by complexome profiling will be validated and/or expanded through pull-downs with in hand lines where known complex subunits are tagged. Co-localisation in immunofluorescence assays and co-migration in native gel will provide support for complex II assignment. 2. Via our routinely used genetic tools we will generate conditional gene depletions for each candidate. Then, our well-established cell-biology assays will provide additional support for complex assignment, and highlight subunits which are essential for complex assembly and function, for the formation of supercomplexes, and for parasite viability. 3. We will screen for domains and amino acids in each new and essential subunit that are necessary for function. This will be done via genetic complementation of each depletion line with a series of differently mutated copies of the depleted gene, following by analysis of rescue of parasites growth, complex assembly and complex function. Mutagenesis will be guided by analysis of sequence conservation across apicomplexans. Identification and validation of new complex II subunits is the first step for future studies seeking to understand how this essential complex works in apicomplexans. Dissection of the domains and residues necessary for function will provide mechanistic understanding of how it works.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: MICA: Defining the two-step relay mechanism of action of the 8-aminoquinolines: A precondition for optimal combination therapies for relapse malaria
Funder: Medical Research Council

Abstract: The 8-aminoquinolines (8AQs) that include primaquine (PQ) and tafenoquine (TQ), are the only licensed drugs capable of treating relapse malaria. TQ possesses improved pharmacokinetic properties over PQ and is likely to replace PQ in future treatment regimens. However it is very significant, that a recent Phase III trial of TQ + dihydroartemisinin-piperaquine for the radical cure of P. vivax, failed to demonstrate the prevention of relapses. This observation raises a major public health issue for future deployment of TQ in countries where ACTs are standard therapy. We have recently shown that the MoA of PQ operates via a two-step biochemical relay. Step 1 of the MoA relates to the metabolic generation of redox-active metabolites, whilst Step 2 describes the mechanism by which redox-active metabolites exert parasite killing. In an expansion of this model to include TQ and other 8-AQs, we hypothesise that there is convergence amongst 8-AQs for step 2 and that parasite killing occurs as a result of H2O2 production, via the cycling of redox-active metabolites. However, we further hypothesise that PQ and TQ and other 8-AQ, display significant differences in Step 1 of the MoA, specifically the routes and rates of generation of redox-active metabolites. We present initial supporting evidence for this hypothesis including evidence that the choice of combination partner drug can significantly affect the generation H2O2 and in vitro malaria parasite liver-stage efficacy. Significant knowledge gaps remain with regards to Step1 as we do not know the identity of TQ metabolites, we do not know the antimalarial efficacy and toxicity of the metabolites and critically we have no information of the routes and rates of metabolite generation. This information is central to defining the therapeutic window of this drug class, and central to understanding why malaria relapse prevention by TQ and PQ is affected by the choice of the drug combination partner.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION