Capturing the genomic variation present in Cryptosporidium and cryptosporidiosis

标题：捕获隐孢子虫和隐孢子虫病中存在的基因组变异 项目摘要 在美国，隐孢子虫属寄生虫每年导致748，000例隐孢子虫病，并且 是全球婴儿腹泻病的第二大病因。2016年，在全球范围内， 急性隐孢子虫病造成48，000人死亡，420万残疾调整生命年（DADs）损失 由于经济增长放缓，780多万丹麦人失业。隐孢子虫是真核生物 顶复门寄生虫分类为生物防御类B病原体。水媒爆发的 在美国，隐孢子虫在一次事件中导致多达40万人患病，并且是一个持续的威胁 全世界的公共卫生。疾病预防控制中心估计，自2010年以来，美国隐孢子虫病病例增加了3倍以上。 2004.为了解决这一紧迫的公共卫生问题，我们建议开发和利用新的基因组资源， 通过描述DNA变异体的分布，更好地了解感染人类的隐孢子虫物种 在地方和全球范围内。我们将从一组> 53，000个精选样本中对约1500个样本进行测序， 产生广泛适用的种群遗传数据和基因组资源的物种， 难以进行广泛的序列表征。拟议的研究和资源将采取 隐孢子虫研究社区到一个新的水平，有效地改变了问题的类型，可以 通过提供一个新的背景，以产生假设和新的工具，可以重新使用，以进一步我们的要求 了解这些病原体。具体来说，AIM 1将开发精制的混合捕获诱饵集， 新的检测方法来表征隐孢子虫。我们将开发两种用于捕获富集测序的诱饵集 (CES)，一个用于全基因组表征（侧重于最常感染人类的物种）， 用于高通量表征通常感染人类的所有隐孢子虫属物种。CES是一个 改变隐孢子虫研究的游戏规则，促进多位点和全基因组表征， 粪便DNA或隐孢子虫DNA丰度低的环境样品。AIM 2将生成 并改进C. hominis，C. tyzzeri，C.和C. 兔子这些组装完成了通常感染的物种所需的参考序列 人类（或模型），并将作为目标3中生成的数据的参考， 生物医学研究社区的资源。目的3将描述C. parvum 和C.通过调查特定背景下的基因组多样性分布，我们专注于这些 两个物种，因为它们引起>90%的隐孢子虫病病例。我们将在1152上进行高通量CES 样本，确定其中的384个加上384个额外的全基因组CES样本。我们将使用结果 数据来检验假设：隐孢子虫种群结构，混合感染，重组，和 人类菌株的进化。该项目将为隐孢子虫产生改变游戏规则的新工具 研究社区，并提供新的见解寄生虫的生物学，每天感染成千上万的儿童。

Title: Capturing the genomic variation present in Cryptosporidium and cryptosporidiosis PROJECT SUMMARY Parasites of the genus Cryptosporidium cause 748,000 cases of cryptosporidiosis annually in the U.S. and are the second-leading cause of diarrheal disease in infants worldwide. Globally in 2016, among children younger than 5, acute cryptosporidiosis caused 48,000 deaths and 4.2 million disability-adjusted life-years (DALYs) lost with 7.8 million more DALYs attributable to growth faltering. Cryptosporidium species are eukaryotic apicomplexan parasites classified as bio-defense category B pathogens. Waterborne outbreaks of Cryptosporidium have caused up to 400,000 illnesses in a single incident in the U.S., and are a constant threat to public health worldwide. The CDC estimates a >3-fold increase in cases of cryptosporidiosis in the U.S. since 2004. To address this urgent public health problem, we propose to develop and use new genomic resources to better understand Cryptosporidium species that infect humans by characterizing the distribution of DNA variants in local and global contexts. We will sequence ~1500 samples from a vast set of >53,000 curated samples to generate broadly-applicable population genetic data and genomic resources for species that have thus far been refractory to extensive sequence characterization. The proposed studies and resources will take the Cryptosporidium research community to the next level, effectively changing the types of questions that can be asked by providing a new context to generate hypotheses and new tools that can be re-used to further our knowledge of these pathogens. Specifically, AIM 1 will develop refined hybrid capture bait sets for powerful new assays to characterize Cryptosporidium. We will develop two bait sets for capture enriched sequencing (CES), one for whole genome characterization (focusing on species that most frequently infect humans) and one for high-throughput characterization of all Cryptosporidium species that commonly infect humans. CES is a game-changer for Cryptosporidium research, facilitating multi-locus and whole genome characterization from fecal DNA or environmental samples where Cryptosporidium DNA is low in abundance. AIM 2 will generate and improve genome assemblies and annotation for C. hominis, C. tyzzeri, C. meleagridis, and C. cuniculus. These assemblies complete the reference sequences needed for species that commonly infect humans (or are a model) and will serve as a reference for the data that will be generated in Aim 3 and as a resource for the biomedical research community. AIM 3 will characterize the genetic diversity of C. parvum and C. hominis through surveys of the distribution of genomic diversity in specific contexts. We focus on these two species because they cause >90% cryptosporidiosis cases. We will conduct high-throughput CES on 1152 samples, identifying 384 of those plus 384 additional samples for full genome CES. We will use the resulting data to test hypotheses on: Cryptosporidium population structure, mixed infections, recombination, and the evolution of anthroponotic strains. This project will generate game-changing new tools for the Cryptosporidium research community and provide new insight into the biology of parasites that sicken thousands of children daily.