DEFINING THE HUMAN VIROME IN IMMUNOCOMPROMISED CHILDREN

描述（由申请人提供）：我们正在研究发烧儿童的人类病毒。为了这些研究的目的，人类病毒组被定义为感染人类的病毒的总集合，包括引起急性、持续性或潜伏性感染的病毒，但不包括噬菌体或没有复制能力证据的整合到人类基因组中的病毒。发烧的儿童经常感染病毒，因此非常适合进行人类病毒的早期研究。在这个项目中，以前对有发烧和不发烧的正常儿童的研究将扩大到包括免疫功能低下的儿童。研究免疫功能低下儿童的原因是：1)增加我们对引起免疫功能低下儿童发烧的病毒的认识，以改善他们的医疗管理；2)了解免疫系统对人类病毒组组成的影响；3)寻找由于免疫功能低下状态可能存在于这些儿童体内的新型病毒。我们还将进行一系列的研究，以改进我们已经建立的系统，使用高通量核苷酸测序来定义人类病毒组。因此，该项目将招募400名因各种原因免疫功能低下的儿童，包括接受造血干细胞或实体器官移植，存在先天性免疫缺陷，艾滋病毒/艾滋病，以及用抑制免疫系统的药物治疗疾病。将一次性收集200名儿童的血液、鼻咽分泌物和粪便样本，以调查存在的病毒。此外，还将从100名在发热发作时以及1个月和6个月后出现发热发作的儿童中收集同一组样本。最后，为了直接研究免疫系统对病毒的影响，将从100名接受移植的儿童中收集相同的一组样本，分别是移植前和移植后1个月和6个月。将使用病毒特异性聚合酶链式反应（PCR）综合检测板和下一代高通量核苷酸测序对样本进行分析。为了完善已建立的宏基因组测序检测病毒的管道，将研究一系列新的计算方法来检测已知和新型病毒。高通量测序的新平台可能允许更长的测序读取或增加读取数量也将被评估。最后，对检测到的新型病毒进行调查，包括全基因组测序，并利用基于核苷酸序列设计的病毒特异性PCR检测方法调查其流行率和临床表现。该项目预计将提供有关免疫功能低下儿童中产生疾病的病毒范围的医学有用信息，并应大大改进研究人类病毒的方法。

DESCRIPTION (provided by applicant): We are studying the human virome in children with fever. For the purposes of these studies, the human virome is defined as the total collection of viruses infecting humans, including viruses causing acute, persistent, or latent infection, but not including bacteriophages or viruses integrated into the human genome without evidence of replicative capacity. Children with fever are frequently infected with viruses and thus are very suitable for early studies of the human virome. In this project, previous studies on normal children with and without fever will be extended to include immunocompromised children. The reasons for studying immunocompromised children are 1) to increase our knowledge of the viruses causing fever in immunocompromised children to improve their medical management, 2) to learn about the influence of the immune system on the composition of the human virome, and 3) to search for novel viruses that might be present in these children because of their immunocompromised state. A series of studies will also be performed to improve the system we have already established for using high throughput nucleotide sequencing to define the human virome. Thus, this project will enroll 400 children who are immunocompromised for varying reasons including receipt of a hematopoietic stem cell or solid organ transplant, presence of a congenital immunodeficiency, HIV/AIDS, and treatment of diseases with medications that suppress the immune system. Samples of blood, nasopharyngeal secretions, and stool will be collected from 200 children on a single occasion to survey the viruses that are present. In addition, the same set of samples will also be collected from 100 children having episodes of fever, at the time of the febrile episode and 1 and 6 months later. Finally, in order to study directly the effects of the immune system on the virome, the same set of samples will be collected from 100 children who are undergoing transplantation before the transplant and 1 and 6 months later. Samples will be analyzed using comprehensive panels of virus-specific PCR assays and by next generation high throughput nucleotide sequencing. In order to refine the established pipeline for detecting viruses by metagenomic sequencing, a series of new computational methods to detect known and novel viruses will be investigated. New platforms for high throughput sequencing that may allow longer sequencing reads or increased numbers of reads will also be evaluated. Finally investigations of novel viruses detected will be carried out, including whole genome sequencing and investigations of their prevalence and clinical manifestations using virus-specific PCR assays designed based on the nucleotide sequence. This project is expected to provide medically useful information about the range of viruses producing illness in immunocompromised children and should greatly improve methods for studying the human virome.