UK-Indonesian Consortium to Identify Biomarkers Predictive of Dengue Disease Severity.

登革热是人类最重要的蚊媒疾病。印度尼西亚在东南亚承担着最大的登革热负担和经济成本。印度尼西亚的登革出血热发病率从1968年的0.05/10万人急剧增加到2013年的35-40/10万人。感染登革病毒（DENV）可导致一系列临床疾病，从使人衰弱但自限性的登革热，到更严重和可能致命的登革出血热，但导致不同疾病严重程度的因素尚未完全了解。尽管大多数登革热病例可以在家中得到治疗，但由于缺乏一种诊断测试来预测那些从轻度疾病发展到严重疾病的人，迫使患者和卫生保健提供者出于“安全目的”寻求住院治疗，从而使已经不堪重负的卫生保健系统饱和。通过对临床结果明确的患者外周血进行综合分析，我们的总体目标是将疾病严重程度与以下因素联系起来：a) DENV遗传多样性或其他共发病因素（如共感染）；b)宿主转录组学和蛋白质组学变化；c)血小板功能、内皮细胞活化和通透性的改变。为了实现我们的目标，我们将分析一个非常有特征的患者样本生物库，这些样本是回顾性和前瞻性地从患有不同登革热疾病进展的患者中收集的。我们将使用复杂的方法观察在印度尼西亚流行的登革热病毒和其他节肢动物传播的病毒（如基孔肯雅病毒和寨卡病毒）的毒株，并确定我们可以在血液中检测到的患者RNA或蛋白质的任何变化，这些变化可能与登革热病毒感染相关的严重疾病有关。该方法将具有高通量和非常敏感的特点，因此即使是低水平转录本或蛋白质丰度的变化也将被检测到。我们还将能够检测到病毒微小变化的频率，并调查这些变化是否可能与疾病有关。采用互补的方法，我们还将检查a)患者血液样本中的血小板数量和功能，b)不同疾病结局的患者血清在体外试验中介导内皮通透性变化的能力。结果将产生大量数据，这些数据将通过计算方法汇集在一起，这些计算方法要么是可用的，要么是由英国合作伙伴开发的。英国合作伙伴在所需的生物信息学工具方面有特别的经验，并将在整个项目期间通过短期科学交流访问向他们的印度尼西亚同行提供这些工具。数据集的计算分析将使我们能够识别患者的生物标志物，这将通过前瞻性收集的样本进行验证。经过验证后，任何生物标志物都可以用于开发诊断测试，以预测那些有发展为严重疾病风险的个体，并监测DENV变异性。此外，我们的宏基因组分析还将评估其他虫媒病毒，如基孔肯雅病毒和寨卡病毒，是否可能被误诊为登革热感染，这些病毒在印度尼西亚的状况尚不清楚。总的来说，该项目将极大地支持印度尼西亚的研究能力建设。至关重要的是，联合王国合作伙伴提供的培训和技术转让将有助于建立一个适用于印度尼西亚许多其他传染病领域的适应性技术框架。

Dengue is the most important mosquito-borne disease of humans. Indonesia bears the largest dengue disease burden and economic cost in Southeast Asia. The incidence of dengue haemorrhagic fever has increased dramatically in Indonesia from 0.05/100000 individuals in 1968 to ~35-40/100000 in 2013. Infection with dengue virus (DENV) causes a spectrum of clinical illnesses, ranging from dengue fever, a debilitating but self-limited condition, to the more severe and potentially fatal dengue haemorrhagic fever, but the factors contributing to differential disease severity are not entirely understood. Although most dengue cases could be managed at home, the lack of a diagnostic test to predict those individuals who progress from mild to severe disease forces patients and healthcare providers to seek hospital admissions for "safety purposes", saturating an already overwhelmed healthcare system.Our OVERALL OBJECTIVE, by adopting an integrated analysis of peripheral blood from patients who have well-defined clinical outcomes, is to correlate disease severity with a) DENV genetic diversity or other co-morbidity factors (e.g. co-infection), b) host transcriptomic and proteomic changes and c) alterations in platelet function and endothelial activation and permeability. In order to achieve our objective we will analyse a very well characterised biobank of patient samples, collected both retrospectively and prospectively from patients with different dengue disease outcomes as the disease progresses. We will use sophisticated methods to look at the strains of DENV and other arthropod-borne viruses (such as chikungunya and Zika virus) that are circulating in Indonesia and also identify any changes in patient RNA or proteins which we can detect in blood that might be linked to serious disease associated with DENV infection. The methods will be both high throughput and very sensitive so that even changes in the abundance of low-level transcripts or proteins will be detected. We will also be able to detect the frequency of minor changes in the virus and investigate whether these may be linked to disease. Using complementary approaches we will also examine a) platelet number and function in patient blood samples and b) the ability of patient serum from different disease outcomes to mediate changes in endothelial permeability using in vitro assays. The results will produce large amounts of data that will be brought together using computational methods, either available or to be developed by the UK partners. The UK partners have particular experience with the bioinformatics tools needed and will provide these to their Indonesian counterparts through short-term scientific exchange visits throughout the project.Computational analysis of the datasets will allow us to identify biomarkers in patients, which will be verified using prospectively collected samples. After verification, any biomarkers can then be used to develop diagnostic tests to predict those individuals at risk of progressing to severe disease and to monitor DENV variability. In addition, our metagenomic analysis will also assess whether other arboviruses such as chikungunya and Zika virus, whose status in Indonesia is unknown, may have been misdiagnosed as dengue infection. Overall, the project will significantly support the building of research capacity in Indonesia. Critically, the training and technology transfer provided by the UK partners will help to establish an adaptable technological framework that is also relevant to many other infectious disease areas in Indonesia.