Genomic Characterization and Surveillance of Microbial Threats in West Africa

项目摘要--总体 西非最近爆发的病毒疫情，特别是2013-16年的埃博拉病毒疫情，揭示了 关于当前监测和诊断在该区域公共卫生方面的许多局限性 系统。用于对患者样本进行快速、准确诊断和基因组分析的工具 在受疾病影响最严重的地区往往不容易获得，使 在疫情期间，降低发病率和死亡率变得更加困难。有必要 非洲人利用广泛的基因组技术和数据在当地更多地参与其中 以提高患者的治疗水平。。该提案旨在对微生物进行表征和调查 西非的威胁，如埃博拉、拉沙热和疟疾，通过长期的 尼日利亚现有的学术、研究和临床中心之间的合作努力(Run， ISTH)、塞内加尔(UCAD)和塞拉利昂(KGH)，以及在美国的其他合作伙伴 布罗德学院和杜兰大学。提议的协作中心将(1)利用NEXT 世代测序和微生物元基因组学技术用于鉴定和表征 研究地点传播的病毒病原体的性质和范围；(2)发展强大的和 经济高效的现场诊断，使用分子和免疫分析来快速和 准确捕获这些病原体在人群中的流行情况，以及(3)使用此 基因组和免疫学数据，以及对这些疾病的临床表现的研究 疾病，以确定病原体与宿主的相互作用并加强临床护理。此外 拟议中的项目将大幅提高非洲科学家在 基因组学领域，通过改善项目现场的技术资源和通过 在非洲和美国的地点进行基因组学和生物信息学方面的强化培训。具体来说， 使用目前在尼日利亚和塞内加尔现场的Illumina MiSeq仪器(不久将 塞拉利昂)，我们将进一步扩大下一代测序和 计算分析..这些活动服务于我们行动更多的总体战略目标 对非洲站点的研究操作，并使非洲科学家能够执行尖端技术 基因组传染病的研究和发现完全在大陆范围内。

Project Summary – Overall Recent viral outbreaks in West Africa, specifically the 2013-16 Ebola Virus Outbreak, shed light on the many limitations of current surveillance and diagnostics in the region's public health systems. Tools for rapid, accurate diagnostics and genomic analysis of patient samples were often not readily available in the areas that were most severely affected by the disease, making it more difficult to reduce morbidity and mortality during the epidemic. There is a need for Africans to get more engaged in locally using the wide array of genomic techniques and data in order to improve patient treatment. . This proposal aims to characterize and survey microbial threats across West Africa, such as Ebola, Lassa fever, and malaria, by building on a long-term collaborative effort among established academic, research and clinical centers in Nigeria (RUN, ISTH), Senegal (UCAD), and Sierra Leone (KGH), along with additional partners in the US at the Broad Institute and Tulane University. The proposed collaborative center will (1) utilize next generation sequencing and microbial metagenomics technologies to identify and characterize the nature and extent of circulating viral pathogens at the study sites; (2) develop robust and cost-effective field diagnostics, using both molecular and immunoassays to swiftly and accurately capture the prevalence of these pathogens in the population, and (3) use this genomic and immunological data, along with studies on the clinical manifestations of these diseases, to characterize the pathogen-host interaction and enhance clinical care. In addition the proposed project will substantially increase the building capacity for African scientists in the field of genomics, both by improving the technical resources at the project sites and through intensive training in genomics and bioinformatics at both the African and US sites. Specifically, using Illumina MiSeq instruments currently on site in Nigeria and Senegal (and coming soon to Sierra Leone), we will further expand capacity for next generation sequencing and computational analysis.. These activities serve our overall strategic goals of moving more research operations to African sites and empowering African scientists to perform cutting-edge genomic infectious disease research and discovery fully within the continent.