Using whole genome sequence data to develop molecular barcodes to profile Plasmodium malaria parasites

疟疾是由疟原虫属寄生虫引起的一种重要疾病。虽然近年来疟疾发病率有所下降，但负担仍然很大，2015年约有2.12亿新发疟疾病例。输入性疟疾可能危及疾病的控制和消除，并且由于旅行的增加，其流行率可能会增加。在评估一个国家是否成功消除疟疾时，有必要将输入病例与当地传播病例区分开来。恶性疟原虫分子条形码已经被开发出来，用于预测寄生虫起源的地理区域，准确率很高（约90%）。该条形码是通过研究两种寄生虫细胞器（线粒体和顶质体）的遗传变异而开发的。这些细胞器存在于所有疟原虫物种中，并且都含有特定的DNA序列。在这些基因组中存在区域遗传多样性，这种多样性可以在条形码中用于预测寄生虫的起源。开发的条形码可能被证明是控制疟疾的一个重要工具，但是存在局限性，如果克服这些局限性将提高其性能。恶性疟原虫是世界范围内疟疾相关死亡的主要原因，然而还有许多其他人类感染的疟原虫，包括间日疟原虫、疟疾疟原虫、诺氏疟原虫、瓦利克氏疟原虫和柯氏疟原虫。我建议扩大条形码的范围，包括额外的遗传标记来分析多种疟原虫。此外，以前的条形码是使用来自西非、东非、东南亚以及南美洲和大洋洲的少数国家的寄生虫样本开发的。因此，我的目标是通过输入目前代表性不足的地区的数据来扩大条形码的地理范围。这种条形码在预测来自东非的样本时效率也较低，这些样本偶尔会被误认为是来自西非的寄生虫，这被认为是由于东非疟原虫的遗传多样性很高。我将通过使用更多来自东非的样本来解决这个问题，以了解该地区高度的遗传多样性。疾病控制的另一个并发症是对青蒿素联合疗法（ACT）的耐药性的出现，青蒿素联合疗法是目前治疗无并发症恶性疟原虫疟疾的一线疗法。已知与act耐药性相关的特定遗传区域可能被纳入条形码中，以允许检测耐药寄生虫。结合条形码中的地理信息，可以追踪耐药寄生虫的传播，这可能有助于在不久的将来作为一种革命性的疟疾控制工具。在这个项目的过程中，我将获得较强的生物信息学技能来分析大量的基因序列数据，这将培养我的定量技能，符合MRC“大数据集的定量技能”的研究主题。许多疟原虫样本将使用全基因组测序进行遗传多样性研究；这将在基因组学领域训练我，提高我在整个有机体生理学方面的技能。最后，该项目的目标是开发一个被称为分子条形码的平台，它可以跟踪疟原虫在全球的运动和传播。我的目标是将条形码纳入一种可用于评估复杂疟疾干预和控制规划的诊断工具。

Malaria is an important disease caused by parasites of the Plasmodium genus. Whilst theincidence of malaria has decreased in recent years, the burden still remains significant,with approximately 212 million new cases of malaria in 2015. Imported malaria canjeopardise disease control and elimination, and its prevalence is likely to increase due togreater travel. When assessing whether a country has successfully eliminated malaria,there is a need to distinguish imported cases from the cases transmitted locally. Amolecular barcode has been developed for P. falciparum parasites to predict thegeographical region of parasite origin, to high (>90%) accuracy. The barcode wasdeveloped by investigating the genetic variation within two parasite organelles, themitochondrion and the apicoplast. These organelles are present within all Plasmodiumparasite species, and both contain specific sequences of DNA. There is regional geneticdiversity within these genomes, and this diversity can be used within the barcode topredict the origin of the parasite.The barcode developed could prove to be an important tool for malaria control, but thereare limitations, which if overcome would improve its performance. P. falciparum parasitesare the main cause of malaria-related deaths worldwide, however there are many otherhuman-infective Plasmodium species, including P. vivax, P. malariae, P. knowlesi, P.ovale wallikeri and P. ovale curtisi. I propose to broaden the scope of the barcode byincluding additional genetic markers to profile multiple Plasmodium species. In addition,the previous barcode was developed using parasite samples from West Africa, EastAfrica, Southeast Asia and a limited set of countries in South America and Oceania.Therefore, I will aim to broaden the geographical scope of the barcode by inputting datafrom currently underrepresented regions. The barcode was also less efficient at predictingsamples from East Africa which were occasionally mistaken for parasites from WestAfrica, this is thought to be due to the high levels of genetic diversity within East AfricanPlasmodium parasites. I will address this issue by using more samples from East Africa toappreciate the high levels of genetic diversity within this region.2A further complication in disease control is the emergence of drug resistance toArtemisinin Combination Therapy (ACT), which is the current first line of treatment foruncomplicated P. falciparum malaria. Specific genetic regions known to be associated withACT resistance may be incorporated into the barcode to allow for the detection of drugresistant parasites. Combined with the geographical information within the barcode, thisallows for tracking the spread of drug resistant parasites, which may aid as a revolutionarytool for malaria control in the near future.During the process of this project, strong bioinformatics skills will be gained to analyselarge sets of genetic sequence data, this will develop my quantitative skills, fitting in withthe 'Quantitative Skills for Large Data Sets' MRC research theme. Many Plasmodiumsamples will be investigated for genetic diversity using whole genome sequencing; this willtrain me within the field of genomics, enhancing my skills on whole organism physiology.Finally, the aim of the project is to develop a platform known as a molecular barcode,which can track the movement and spread of Plasmodium parasites globally. I will aim toincorporate the barcode into a diagnostic tool that can be used in the evaluation ofcomplex malaria interventions and control programmes.