Utilize Microbial Metagenomics for Viral Pathogen Characterization

利用微生物宏基因组学进行病毒病原体表征

• 批准号: 10207710
• 负责人: Christian T. Happi
• 金额: $ 14.73万
• 依托单位: REDEEMER'S UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-23 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10207710
• 关键词: Address; Africa; Africa South of the Sahara; African; Area; Biological; Clinical; Collaborations; Communicable Diseases; Communities; Country; Development; Diagnostic; Diagnostic tests; Disease; Disease Outbreaks; Ebola; Epidemic; Fever; Future; Genome; Genomic approach; Genomics; Geographic Locations; Health system; Individual; Infection; Infectious Diseases Research; Infrastructure; Lassa Fever; Metagenomics; Methods; Microbe; Nigeria; Pathogen detection; Patients; Population Genetics; Positioning Attribute; Property; Public Health; Public Health Applications Research; Recording of previous events; Research Personnel; Resolution; Sampling; Senegal; Sierra Leone; Symptoms; Technology; Viral; Viral Genome; Virus; Virus Assembly; Virus Diseases; chikungunya; cohort; cost; cost effective; improved; insight; metagenomic sequencing; microbial; multidisciplinary; next generation sequencing; novel; novel virus; pathogen; pathogenic virus; prevent; public health emergency; sustainability framework; tool; transmission process; virology; virome

Project Summary – Project 1 Recent public health emergencies, most notably the 2014-2016 Ebola epidemic, have exposed the vulnerabilities in West African health systems and the urgent need for improved global surveillance of infectious disease threats. Despite the burden of infectious disease in this region, the spectrum of circulating microbes, especially viruses, in West Africa is poorly understood. This owes, in part, to the lack of diagnostic capacity to detect known pathogens in many areas, and the nonspecific symptoms caused by many of these microbes, making it difficult to clinically determine the cause of infection. In this context, genomic approaches, including next-generation sequencing, have recently emerged as powerful tools for pathogen detection and discovery, as well as enabling valuable insight into the origins, transmission and biological properties of these pathogens. In this Project, we propose to use cutting edge next-generation sequencing capacity established at the three West African Collaborative Centers to identify known and novel viruses in patients with a fever and healthy controls. We will use computational approaches to assemble full viral genomes and understand the evolutionary dynamics and population genetics of the most important viral threats identified through metagenomic sequencing. Lastly, we will implement novel tools to enhance the efficiency and sensitivity of pathogen sequencing. This project will establish a framework for the sustainable application of powerful sequencing technologies in public health contexts and identify the most pressing viral threats in this region, informing the development of relevant diagnostic tests in Project 2. Furthermore, working across three West African countries, the sequencing efforts of our collaborative center will yield broad insights into the virome across a wide geographic region and allow for the sharing of approaches to enhance biosurveillance across West Africa. Not only will this continue to advance the genomics of infectious disease in West Africa, it will provide immediate, actionable insights to protect local communities and prevent future outbreaks.

项目摘要-项目1 最近的公共卫生突发事件，特别是2014 - 2016年的埃博拉疫情，暴露了 认识到西非卫生系统的脆弱性，迫切需要改善全球卫生系统， 监测传染病威胁。尽管这个地区有传染病的负担， 对西非的微生物，特别是病毒的传播谱知之甚少。 部分原因是许多地区缺乏检测已知病原体的诊断能力， 以及许多这些微生物引起的非特异性症状，使得临床上很难 确定感染的原因。在这方面，基因组方法，包括下一代 测序，最近已经成为病原体检测和发现的有力工具， 并使有价值的洞察这些起源，传播和生物特性， 病原体在本项目中，我们建议使用尖端的下一代测序能力 在三个西非合作中心建立，以识别已知和新型病毒 在发烧患者和健康对照组中。我们将使用计算方法来组装 完整的病毒基因组，并了解进化动力学和人口遗传学的 通过宏基因组测序确定最重要的病毒威胁。最后，我们将 实施新的工具，以提高病原体测序的效率和灵敏度。 该项目将为强大测序的可持续应用建立框架 在公共卫生方面的技术，并确定该地区最紧迫的病毒威胁， 为项目2中相关诊断测试的开发提供信息。此外，在跨 三个西非国家，我们的合作中心的测序工作将产生广泛的 深入了解广泛地理区域的病毒组，并允许共享 加强整个西非的生物监测。这不仅将继续 在西非推进传染病的基因组学，它将提供即时的，可操作的 保护当地社区和防止未来爆发的见解。