Variant antigen profiling: a novel genomic tool for diagnosis and surveillance of animal African trypanosomiasis.

非洲动物锥虫病(AAT)是一种家畜疾病，对动物健康和撒哈拉以南国家的发展具有频繁和破坏性的影响。这种被忽视的热带疾病是由寄生虫刚果锥虫引起的，这种寄生虫通过叮咬苍蝇传播，感染血液，导致慢性贫血、虚弱，如果不治疗，最终会死亡。与人类非洲锥虫病(昏睡病)不同，人类锥虫病是由一种相关的寄生虫布氏锥虫引起的，经过成功的干预和大量研究后正在下降，但AAT仍然非常常见，知之甚少。然而，据估计，37个国家每年的疾病和治疗费用约为45亿美元。粮农组织认为，非洲农业技术援助是“非洲与贫困作斗争的核心”，也是其千年目标的核心。大多数关于非洲锥虫的研究是针对模式生物布氏锥虫，但鉴于AAT对动物和人的深刻影响，我们需要专门针对兽医寄生虫的研究，以确定寄生虫变异如何影响疾病的进程和严重程度。所有非洲锥虫都利用抗原变异来避免宿主的免疫反应。这包括每次宿主产生针对该蛋白质的抗体时，更换覆盖在寄生虫表面的蛋白质外壳。这种蛋白质被称为变异型表面糖蛋白(VSG)，对寄生虫的生存和疾病的严重程度至关重要，决定了感染的时间长短和对宿主天然防御的抵抗力。布氏木霉和孔氏木霉的基因组都包含数百个VSG基因，其中只有一个基因在特定的表达部位一次表达。总而言之，这种替代VSG基因的谱系是锥虫基因组的一个普遍存在但高度可变的特征，它会随着宿主免疫而不断变化。我们可以用这个曲目来了解寄生虫是如何在空间和时间上变化的，以及这对疾病有什么影响。这个项目的目的是测量弓形虫种群中VSG谱系的变异，然后根据其VSG谱系产生一种新的工具来快速预测菌株的性质。我将产生40个分离自奶牛弓形虫感染的分离株的基因组序列。到目前为止，一直避免对VSG曲目进行总体规模的分析，因为它们的复杂性使得不可能使用标准工具。在此之前，我发现龙须草VSG分为不同的类型，每种类型都由独特的蛋白质基序定义。我将通过将每个弓形虫分离株的VSG与这些蛋白质基序进行比较来量化其VSG谱系。VSG类型的相对丰富将为每个分离株产生一个‘变异抗原图谱’(VAP)。为了使VAP具有一定的预测能力，我将通过鉴定存在于特定表达部位并在寄生虫细胞表面表达的活性VSG基因，来确定哪些VSG实际上用于抗原变异，以及那些可能起到其他作用的VSG。我还将确定VAP与地理、时间、疾病严重程度和寄生虫相关性的显著相关性。一个生成和解释VAP的工具将在网上获得，这使得使用变异抗原图谱从基因组序列数据中预测任何弓形虫分离物的性质成为可能。AAT对非洲的动物健康和经济发展来说是一个巨大的挑战，但我们还不知道弓形虫如何变异以及这与我们看到的疾病种类有何关系。这些信息将改善诊断、药物治疗和控制措施的效率，导致对患病动物进行更早和更适当的治疗，甚至可能识别可以作为疫苗靶标的蛋白质。现在是时候开发一种快速而简单的方法来理解VSG的多样性，从而释放锥体基因组学的潜力，以了解AAT，估计其风险并减轻其影响。

Animal African trypanosomiasis (AAT) is a livestock disease with frequent and devastating effects on animal health and on the development of sub-Saharan nations. This neglected tropical disease is caused by the parasite Trypanosoma congolense, which is spread by biting flies and infects the blood causing chronic anaemia, wastage and ultimately death if untreated. Unlike Human African trypanosomiasis ('sleeping sickness'), which is caused by a related parasite T. brucei, and is declining after successful intervention and much research, AAT remains very common and poorly known. Yet the annual costs of disease and treatment are estimated at ~$4.5 billion across 37 countries. The FAO considers AAT to "lie at the heart of Africa's struggle against poverty", and central to its Millennium Goals. Most research on African trypanosomes is directed at the model organism T. brucei, but given the profound effects of AAT on animals and people, we need research dedicated to the veterinary parasites to determine how parasite variation affects the course and severity of disease.All African trypanosomes use antigenic variation to avoid the immune response of their host. This involves the replacement of the protein coat covering the parasite surface each time the host produces antibodies to the protein. The protein is called the Variant Surface Glycoprotein (VSG) and is crucial to parasite survival and the severity of disease, determining the length of infection and resistance to innate host defences. The genomes of both T. brucei and T. congolense contain hundreds of VSG genes, of which just one is expressed at a time from a specific expression site. Together, this repertoire of alternative VSG genes is a ubiquitous, but highly variable, feature of trypanosome genomes that constantly changes in response to host immunity. We can use this repertoire to understand how parasites change through space and time, and what effect this has on disease. This project aims to measure variation in VSG repertoire across the T. congolense population, and then produce a novel tool for rapidly predicting the properties of a strain based on its VSG repertoire.I will produce genome sequences for 40 isolates sampled from T. congolense infections of cows. Until now, analysis of VSG repertoires on a population scale has been avoided because their complexity makes it impossible to use standard tools. Previously, I discovered that T. congolense VSG are divided into distinct types, each defined by unique protein motifs. I will quantify the VSG repertoire in each T. congolense isolate by comparing its VSG to these protein motifs. The relative abundance of the VSG types will produce a 'variant antigen profile' (VAP) for each isolate. To give the VAP some predictive power, I will identify which VSG are actually used in antigenic variation, (and those that might perform some other role), by identifying the active VSG gene present in the specific expression site and expressed on the parasite cell surface. I will also identify significant correlations of VAPs with geography, time, disease severity and parasite relatedness. A tool to generate and interpret a VAP will be accessible online, making it possible to predict the properties of any T. congolense isolate from genome sequence data using variant antigen profiling.AAT represents an enormous challenge to animal health and economic development in Africa and yet we have no detailed knowledge of how T. congolense varies and how this relates to the kind of disease we see. Such information would improve diagnosis, the efficiency of drug therapy and control measures, lead to earlier and more appropriate treatment for sick animals, and perhaps even identify proteins that could serve as vaccine targets. The time is right to develop a fast and simple approach to making sense of VSG diversity that can unlock the potential of trypanosome genomics for understanding AAT, estimating its risk and mitigating its effects.