Core 3: Genomic Sequencing and Population Genetics Core

摘要-基因组测序和群体遗传学核心-核心3 基因组测序和群体遗传学核心（核心3）支持该计划的两个项目， 评估和了解cCMV遗传变异、传播和免疫之间的关系 反应核心对疱疹病毒和人类巨细胞病毒 特别地，巨细胞病毒（HCMV）是表现出令人惊讶的序列多样性水平的大DNA病毒： 来自患者的样本在一致性和群体水平上通常具有1，000的多态性。这 常设遗传变异的水平在生物学上是重要的，因为它已被证明在一个重要的作用， 一系列临床传染病挑战。例如，在HCMV中，遗传多样性有助于时间上的改变。 和先天性胎儿感染中等位基因频率的区室变化。支持调查 在我们的RhCMV模型中，基因组测序核心将对RhCMV群体进行测序 由项目1-2（目标1）提供的动物、接种物和培养的病毒样品的基因组。序列 通过参考介导比对的迭代过程，将读段映射为RhCMV序列 and de de novo从头contig重叠builds建造. RhCMV序列数据集将用于定义注释的共有序列（即，的 最常见的）序列，并提供病毒群体的汇总统计。总结 统计数据包括序列读数总数、映射读数/效率、平均覆盖度、多态性 在相对于亲本病毒和种群多样性的共识中。结果将提供给 项目此外，核心将通过编目RhCMV饱和度数据集来改进工作流程， 处理协议，并将与病毒病原体和分析资源（ViPR）合作， RhCMV序列数据和相关的体内数据，其简单，可搜索的格式（目的2）。批量序列 数据将提交到公开可用的NCBI序列阅读档案馆。最后，核心将采用 群体遗传学策略，以研究先天性RhCMV模型中RhCMV进化的模式， 询问病毒载量和病毒群体序列空间以确定多样性和趋异机制 在母婴病毒人群中（目标3）。影响感染、传播的其他参数 和疾病，包括病毒基因缺失株（项目2）和免疫状态改变（项目1）， 分析它们对病毒群体多样性、创始者大小和与病毒感染相关的房室效应的影响。 传播和疾病。总之，核心将提供重要的理解，如何在体内 进化过程，如瓶颈和选择压力，影响病毒传播和胎儿 疾病

ABSTRACT – Genomic Sequencing and Population Genetics Core – Core 3 The Genomic Sequencing and Population Genetics Core (Core 3) supports the Program’s two projects in evaluating and understanding the relationship between cCMV genetic variation, transmission, and immune response. The Core is responsive to the understanding that herpes viruses, and human cytomegalovirus (HCMV) in particular, are large DNA viruses that exhibit surprising levels of sequence diversity: HCMV samples from patients often have 1,000’s polymorphisms at both the consensus and population levels. This level of standing genetic variation is biologically important, as it has been shown to play a significant role in a range of clinical infectious disease challenges. For example, in HCMV, genetic diversity contributes to temporal and compartmental changes in allele frequencies in congenital fetal infections. To support investigations of such dynamics in our RhCMV model, the Genomic Sequencing Core will sequence populations of RhCMV genomes from animals, inoculum, and cultured virus samples provided by Projects 1-2 (Aim 1). Sequence reads will be mapped as RhCMV sequences through an iterative process of reference mediated alignments and de novo contig builds. RhCMV sequence datasets will be used to define an annotated consensus (i.e., the most common) sequence of each sample and provide summary statistics of viral populations. Summary statistics include total number of sequences reads, mapped reads/efficiency, mean coverage, polymorphisms in the consensus relative to the parental virus and population diversity. Results will be made available to the Projects. In addition, the Core will improve workflow by cataloguing an RhCMV saturation dataset, improve processing protocols, and will collaborate with the Viral Pathogen and Analysis Resource (ViPR) to provide RhCMV sequence data and related in vivo data for their simple, searchable format (Aim 2). Bulk sequence data will be submitted to the publicly available NCBI Sequence Read Archive. Finally, the Core will employ population genetics strategies to investigate the patterns of RhCMV evolution in congenital RhCMV models by interrogating viral loads and viral population sequence space to define diversity and mechanisms of divergence amongst maternal and infant viral populations (Aim 3). Other parameters that influence infection, transmission and disease including viral gene deletion strains (Project 2) and altered immunological states (Project 1) will be analyzed for their influence on viral population diversity, founder size and compartmental effects in relation to transmission and disease. Taken together, the Core will provide important understanding of how in vivo evolutionary processes, such as bottlenecks and selective pressure, influence viral transmission and fetal disease.