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

确保世界免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， 我们对病毒性疾病的理解。该提案利用基因组学来解决这三个主要需求： 人类和病媒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， 如拉沙、埃博拉、寨卡、波瓦桑和其他NIAID A-C类优先病原体， 流行、进化、遗传多样性以及人与人畜共患病宿主之间的传播， 没有很好地描述，这威胁到我们准备甚至识别人类病例的能力， 发生.病原体基因组学提供了关键的公共卫生洞察病毒威胁的运动。在 与西非的临床、公共卫生和学术合作者建立伙伴关系， 在马萨诸塞州，该项目将对人类患者和人畜共患病宿主（非洲 啮齿动物、美洲蜱和蚊子），公开分发基因组和宏基因组数据集，并迅速 提供与这些病毒的进化、流行病学和生态学相关的分析，重点关注见解 这可能会为正在进行的诊断、治疗和其他干预策略的开发工作提供信息。 病毒性出血症中宿主反应和病毒动力学的组织特异性和单细胞表征 发烧感染像埃博拉和拉沙这样的病毒性出血热（VHF）是高度致命的，但分子如何 并且细胞宿主应答机制在致命和非致命病例之间的差异知之甚少。在 与NIAID在马里兰州弗雷德里克的综合研究设施（BSL-4）合作，该项目将于 在动物模型生物体中的体内VHF感染，同时分析宿主转录应答 以及病毒在不同宿主组织内的复制和进化，并利用单细胞RNA-seq方法， 询问个体宿主PBMC类型。这将提供一个新的理解细胞特异性宿主反应， VHF感染，深入了解死亡和恢复背后的不同机制，并为 制定针对特高频的对策。 使用数千种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 威胁，我们的反应能力受到缺乏系统的，高通量的方法，评估和 为治疗和疫苗的发展提供信息。虽然细胞毒性T淋巴细胞可以提供保护， 针对广泛的病毒抗原，尚未对所有可能的病毒抗原进行系统研究。 免疫原性肽。利用“系统病毒学”的方法，我们将设计，创建，评估和测试一个 跨越数百种人类病毒病原体大部分的寡核苷酸的大型合成文库， 疫苗设计的新候选靶点。

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.