Genomic profiling of influenza infections to identify biomarkers of disease severity

该项目旨在使用综合系统级方法来发现肥胖如何影响(a)流感病毒的进化和传播，(b)特定宿主对感染的反应，以及(c)呼吸道中的微生物群落，以揭示可用于新疗法的关键特征。肥胖的人和动物会延迟病毒的清除，这可能会影响病毒、细菌和宿主之间复杂的相互作用。这些相互作用涉及许多效应机制。例如，甲型流感病毒感染可改变细菌黏附和上皮细胞上TLR的表达，增加肺部对继发性细菌性肺炎的易感性。本研究的初始阶段侧重于开发有效分析鼻咽拭子宏基因组和亚转录组的方法，以表征微生物群落的功能基因潜力和活性。我们将在肥胖雪貂模型中进行类似的分析。为了支持所提出的研究，我们之前对感染h1n1 - pdm2009的雪貂的鼻洗液进行的分析表明，呼吸道微生物组发生了显著变化。在感染前后微生物相互作用的网络分析中，我们观察到微生物动力学的明显变化。我们还将模拟病毒的进化，观察宿主内和宿主间病毒在感染过程中的遗传多样性。最近，我们的重点是缺陷病毒基因组（DVGs），因为某些缺陷基因组被认为可以调节流感感染的疾病严重程度和致病性。我们还旨在通过使用全血的转录组分析和使用血清的糖糖分析来分析宿主对感染的全身反应。在多尺度分析之后，我们将比较肥胖雪貂和肥胖人类疾病严重程度的关键驱动因素，并整合两个系统（人类和雪貂）的数据，以确定是否发现了其他驱动因素。

This project sets out to use an integrative systems-level approach to discover how obesity affects (a) the evolution and transmission of influenza virus, (b) specific host responses to infection, and (c) microbial communities in the respiratory tract, to reveal key signatures that could be targeted in novel therapeutics. Obese people and animals have delayed viral clearance, which can impact the complex interactions between virus, bacteria, and the host. These interactions involve many effector mechanisms. For example, influenza A virus infection was shown to alter bacterial adhesions and TLR expression on epithelial cells, increasing susceptibility of the lungs to secondary bacterial pneumonia. The initial phase of this study has focused on developing methods for effective analyses of the metagenome and metatranscriptome from nasopharyngeal swabs to characterize the functional gene potential and activity of the microbial community. We will perform similar analyses in the obese ferret model. In support of the proposed studies, our previous analyses of nasal washes from ferrets infected with H1N1pdm2009 demonstrated a significant change in the respiratory microbiome. In a network analysis of microbial interactions before and after infection, we observe a clear change of the microbial dynamics. We will also model the evolution of the viruslooking at intra-host and inter-host virus genetic diversityover the course of the infection. Recently our focus has been on defective virus genomes (DVGs) as certain defective genomes are thought to modulate disease severity and pathogenicity of the influenza infection. We also aim to analyze the host systemic response to infection by transcriptomic profiling using whole blood and glycomic profiling using serum. After multiscale analyses, we will compare the key drivers of disease severity in obese ferrets and obese humans, and integrate data across both systems (human and ferret) to determine if other drivers are identified.