Project 1 Viral Genomics: surveillance, epidemiology, host response, and viral immunogenicity

确保世界安全不受微生物威胁仍然是一项紧迫的挑战。然而，仍然存在重大差距。 在我们对病毒性疾病的理解中。这项提案利用基因组学来解决这三个主要需求： 人类和媒介​中新出现的病毒威胁的基因组检测和流行病学。对于新出现的病毒， 如拉萨、埃博拉、寨卡、鲍瓦桑等NIAID A-C类重点病原体，自然 流行率、进化、遗传多样性以及人与人畜共患病宿主之间的传播 没有很好的定性，这威胁到我们准备甚至识别人类病例的能力 发生。病原体基因组学为病毒威胁的移动提供了关键的公共卫生洞察力。在……里面 与西非和非洲现有的临床、公共卫生和学术合作者建立伙伴关系 马萨诸塞州，该项目将对人类患者和人畜共患病宿主(非洲)的病毒进行测序 啮齿动物、美洲扁虱和蚊子)，公开分发基因组和元基因组数据集，并迅速 提供与这些病毒的进化、流行病学和生态相关的分析，重点是洞察 这可能为正在进行的诊断学、治疗学和其他干预策略的开发工作提供信息。 病毒出血过程中宿主反应和病毒动力学的组织特异性和单细胞特征 发烧感染​。像埃博拉和拉萨这样的病毒性出血热是高度致命的，但分子 致命性和非致命性病例的细胞宿主反应机制不同，人们对此知之甚少。在……里面 与美国国家航空航天局位于马里兰州弗雷德里克的综合研究机构(BSL-4)合作，该项目将对​进行测序 动物模型生物体中的活体​甚高频感染，同时分析宿主转录反应 和病毒在不同宿主组织中的复制和进化，并利用单细胞RNA-SEQ方法 询问单个主机PBMC类型。这将提供对细胞特异性宿主反应的新理解 VHF感染，深入了解死亡和康复背后的不同机制，并向 超高频病防治对策的研究进展。 使用数以千计合理设计的寡核苷酸​系统地发现病毒抗原。对于大多数病毒来说 对于威胁，我们的应对能力受到缺乏系统、高通量方法的阻碍，这些方法可以评估和 告知疗法和疫苗的发展。尽管细胞毒性T淋巴细胞可以提供保护 针对广泛的病毒抗原，还没有对所有可能的情况进行系统调查 免疫原肽。利用“系统病毒学”方法，我们将设计、创建、评估和测试 大型合成寡核苷酸文库，跨越数百种人类病毒病原体的大部分，并产生 疫苗设计的新候选目标。

Ensuring a world safe from microbial threats remains a pressing challenge. However, significant gaps remain in our understanding of viral diseases. This proposal employs genomics to address these three major needs: Genomic detection and epidemiology of emerging viral threats in humans and vectors​. For emerging viruses, such as Lassa, Ebola, Zika, Powassan, and other NIAID Category A-C Priority Pathogens, the natural prevalence, evolution, genetic diversity, and transmission among and between humans and zoonotic hosts are not well characterized, which threatens our ability to prepare for and even identify human cases when they occur. Pathogen genomics provides critical public health insight into the movement of viral threats. In partnership with established clinical, public health, and academic collaborators in West Africa and Massachusetts, this project will sequence viruses both human patients and zoonotic reservoirs (African rodents, American ticks and mosquitoes), publicly distribute genomic and metagenomic datasets, and rapidly deliver analyses relevant to the evolution, epidemiology and ecology of these viruses, with a focus on insights that may inform the ongoing development work of diagnostics, therapeutics, and other intervention strategies. Tissue-specific and single-cell characterizations of host response and viral dynamics during viral hemorrhagic fever infection​. Viral hemorrhagic fevers (VHFs) like Ebola and Lassa are highly fatal, but how the molecular and cellular host response mechanisms differ between fatal and non-fatal cases is poorly understood. In partnership with NIAID’s Integrated Research Facility in Frederick, MD (BSL-4), this project will sequence ​in vivo​ VHF infections in animal model organisms, simultaneously profiling both the host transcriptional response and viral replication and evolution within different host tissues, and utilizing single-cell RNA-seq approaches to interrogate individual host PBMC types. This will provide a new understanding of cell-specific host response to VHF infections, with insights into the differing mechanisms behind fatality and recovery and inform the development of countermeasures for VHFs. Systematic discovery of viral antigens using thousands of rationally designed oligonucleotides​. For most viral threats, our ability to respond is hampered by a lack of systematic, high-throughput methods that evaluate and inform the development of therapeutics and vaccines. Although cytotoxic T lymphocytes can afford protection against a wide range of viral antigens, there has not been a systematic investigation of all possible immunogenic peptides. Utilizing a “systems virology” approach, we will design, create, evaluate, and test a large synthetic library of oligos that span large portions of hundreds of human viral pathogens and produce novel candidate targets for vaccine design.