Next-Generation Sequencing Center for GHOSTing Hepatitis C Virus: Transforming Community Based Molecular Surveillance and Outbreak Investigation

项目总结： 美国正处于一场巨大的阿片类药物流行之中。2015年，超过5.2万名美国人死亡 由于药物过量，其中60%以上与处方或非法阿片类药物使用有关。考虑到 注射吸毒仍然是丙型肝炎病毒传播的主要危险因素，与此同时，美国观察到 2010-2013年间，丙型肝炎病毒的发病率显著增加了150%，新的丙型肝炎病毒感染增加了364% 2006年至2012年在阿巴拉契亚四个州感染，最明显的是在农村地区。因此，有 迫切需要在国家一级更具战略性地检测、预防、治疗和控制丙型肝炎病毒。 这个U24应用程序建议开发一个集中的幽灵实验室，以产生高质量、高质量的 CDC幽灵中心和相关临床研究站点的丙型肝炎病毒NGS数据吞吐量，以帮助 确定注射吸毒者之间的丙型肝炎病毒传播联系(PWID)；管理收集和 临床研究地点HIV和丙型肝炎病毒感染者的血清样本在RFA下的存储 DA-17-014；并将样本运往疾控中心进行梅毒测试和艾滋病毒和丙型肝炎病毒的系统发育图。 这项提议建立在调查人员在产生大规模桑格和NEXT- 如丙型肝炎病毒和艾滋病毒等高可变病原体的世代测序(NGS)数据，开发和 维护强大的SOP，以减少大型NGS项目中的污染和样品混淆；以及 开发强大的NGS分析平台，以实现NGS数据的实时管理和存储， 下游变种叫声，以及系统发育分析。 艾伦博士在麻省理工学院拉贡研究所和哈佛大学的实验室一直在对高度可变的 病原体艾滋病毒，丙型肝炎病毒和SIV在过去的15年里，在此期间，他发展了一种成熟的 物理实验室为实验室流程的所有阶段提供支持。他还曾担任过几部病毒的PI 在此期间对NIH/NIAID U01、U19和P01项目赠款的核心进行排序，从而提供广泛的 与经济高效地生成、管理、分析和存储病毒序列数据相关的经验 病原体。

PROJECT SUMMARY: The United States is in the midst of an enormous opioid epidemic. In 2015, more than 52,000 American's died due to a drug overdose, over 60% of which were associated with prescription or illicit opioid use. Given that injection drug use remains the major risk factor for HCV transmission, concomitantly the US has observed a striking >150% increase in the incidence of HCV between 2010-2013, and a 364% increase in new HCV infections between 2006 and 2012 in four Appalachian states, most notably in rural areas. As such, there is urgent need to more strategically detect, prevent, treat and control HCV on a national level. This U24 application proposes to develop a centralized GHOST laboratory to generate high-quality, high- throughput HCV NGS data for the CDC's GHOST center and accompanying clinical research sites to aid in the identification of HCV transmission links among persons who inject drugs (PWID); manage the collection and storage of serum samples from HIV- and HCV-infected participants from the clinical research sites under RFA- DA-17-014; and ship specimens to the CDC for syphilis testing and phylogenetic mapping for HIV and HCV. This proposal builds on the investigators' strong track record in generating large-scale Sanger and next- generation sequencing (NGS) data for highly variable pathogens such as HCV and HIV, development and maintenance of robust SOPs for reducing contamination and sample mix-up in large-scale NGS projects, and the development of robust NGS analysis platforms to enable real-time curation and storage of NGS data, downstream variant calling, and phylogenetic analysis. Dr. Allen's laboratory at the Ragon Institute of MGH, MIT and Harvard has been sequencing the highly variable pathogens HIV, HCV and SIV over the last 15 years during which time he has developed a well-established physical laboratory to support all stages of the laboratory process. He has also served as the PI of several viral sequencing cores on NIH/NIAID U01, U19 and P01 project grants during this time, thus providing extensive experience related to the cost-effective generation, curation, analysis, and deposition of sequence data for viral pathogens.