DEFINING THE HUMAN VIROME IN IMMUNOCOMPROMISED CHILDREN

描述(申请人提供)：我们正在研究发烧儿童的人类病毒。在这些研究中，人类病毒体被定义为感染人类的病毒的总集合，包括引起急性、持续或潜伏感染的病毒，但不包括整合到人类基因组中但没有复制能力的病毒。发烧的儿童经常感染病毒，因此非常适合人类病毒体的早期研究。在这个项目中，以前对有发烧和没有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。研究免疫低下儿童的原因是1)增加我们对免疫低下儿童引起发烧的病毒的知识，以改善他们的医疗管理；2)了解免疫系统对人类病毒组成的影响；3)寻找可能存在于这些儿童中的新病毒，因为他们的免疫低下状态。还将进行一系列研究，以改进我们已经建立的使用高通量核苷酸测序来定义人类病毒体的系统。因此，该项目将招募400名因各种原因而免疫受损的儿童，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，以及使用抑制免疫系统的药物治疗疾病。将一次从200名儿童身上采集血液、鼻咽分泌物和粪便样本，以调查存在的病毒。此外，还将从100名发烧时以及发烧后1个月和6个月后出现发烧症状的儿童身上收集相同的样本。最后，为了直接研究免疫系统对病毒的影响，在移植前以及移植后1个月和6个月后，将从100名正在接受移植的儿童中收集相同的样本。样本将使用全面的病毒特异性聚合酶链式反应分析小组和下一代高通量核苷酸测序进行分析。为了完善已建立的通过元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的病毒。还将评估用于高通量测序的新平台，这些平台可能允许更长的测序读数或增加的读数。最后，将对检测到的新病毒进行调查，包括全基因组测序，并使用根据核苷酸序列设计的病毒特异性聚合酶链式反应分析方法调查其流行情况和临床表现。该项目预计将提供有关免疫受损儿童致病病毒范围的医学有用信息，并将极大地改进研究人类病毒体的方法。

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.