Genomic Characterization and Surveillance of Microbial Threats in West Africa

项目概要-总体 西非最近的病毒爆发，特别是2013-16年的埃博拉病毒爆发， 目前该地区公共卫生监测和诊断的许多局限性， 系统.用于快速、准确诊断和患者样本基因组分析的工具， 在受这种疾病影响最严重的地区， 在流行病期间降低发病率和死亡率更加困难。有必要 非洲人更多地参与当地使用广泛的基因组技术和数据， 以改善患者治疗。.该提案旨在表征和调查微生物 西非各地的威胁，如埃博拉病毒，拉沙热和疟疾，通过建立一个长期的 在尼日利亚建立的学术、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），沿着美国的其他合作伙伴， 布罗德研究所和杜兰大学。拟议的合作中心将（1）利用下一个 代测序和微生物宏基因组学技术， 研究中心循环病毒病原体的性质和程度;（2）制定稳健的 具有成本效益的现场诊断，使用分子和免疫测定， 准确地捕捉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，沿着对这些疾病的临床表现的研究， 疾病，以表征病原体-宿主相互作用和加强临床护理。此外 拟议的项目将大大提高非洲科学家在以下领域的能力建设： 基因组学领域，既通过改善项目地点的技术资源， 在非洲和美国进行基因组学和生物信息学的强化培训。具体地说， 使用目前在尼日利亚和塞内加尔现场的Illumina MiSeq仪器（即将在 塞拉利昂），我们将进一步扩大下一代测序的能力， 计算机分析这些活动服务于我们的总体战略目标， 研究业务到非洲的网站，并授权非洲科学家进行尖端的 基因组传染病的研究和发现完全在非洲大陆。

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.