DEFINING THE HUMAN VIROME IN IMMUNOCOMPROMISED CHILDREN

描述（由申请人提供）：我们正在研究发热儿童中的人类病毒组。出于这些研究的目的，人类病毒组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，但不包括噬菌体或整合到人类基因组中而没有复制能力证据的病毒。发烧的儿童经常感染病毒，因此非常适合人类病毒组的早期研究。在这个项目中，以前对正常儿童发烧和不发烧的研究将扩展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）增加我们对导致免疫功能低下儿童发热的病毒的了解，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而可能存在于这些儿童中的新型病毒。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组的系统。因此，该项目将招募400名因各种原因而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、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。将一次性从200名儿童中采集血液、鼻咽分泌物和粪便样本，以调查存在的病毒。此外，还将从100名发热儿童中采集同一组样本，分别在发热发作时以及1个月和6个月后采集。最后，为了直接研究免疫系统对病毒组的影响，将从100名正在接受移植的儿童中收集移植前和移植后1个月和6个月的同一组样本。将使用全面的病毒特异性PCR检测试剂盒和下一代高通量核苷酸测序对样本进行分析。为了完善已建立的通过宏基因组测序检测病毒的管道，将研究一系列检测已知和新型病毒的新计算方法。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数量。最后，将对检测到的新型病毒进行调查，包括全基因组测序，并使用基于核苷酸序列设计的病毒特异性PCR检测方法对其流行率和临床表现进行调查。该项目预计将提供有关免疫功能低下儿童致病病毒范围的医学有用信息，并将大大改进研究人类病毒组的方法。

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.