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

项目概要： 美国正处于阿片类药物的巨大流行之中。2015年，超过52，000名美国人死亡， 由于药物过量，其中超过60%与处方或非法阿片类药物使用有关。鉴于 注射吸毒仍然是HCV传播的主要危险因素，同时美国已经观察到， 2010-2013年间，HCV发病率显著增加>150%，新发HCV增加364%。 2006年至2012年期间，阿巴拉契亚州的四个州感染了艾滋病毒，特别是在农村地区。因此， 迫切需要在国家层面上更具战略性地检测、预防、治疗和控制HCV。 该U24应用程序建议开发一个集中的GHOST实验室，以生成高质量，高 为CDC的GHOST中心和相关临床研究中心提供HCV NGS数据， 确定注射毒品者之间的HCV传播联系（PWID）;管理收集和 储存来自RFA临床研究中心的HIV和HCV感染受试者的血清样本- DA-17-014;并将标本运送到CDC进行梅毒检测和HIV和HCV的系统发育图绘制。 这项提议建立在调查人员在产生大规模桑格和下一个- HCV和HIV等高度可变病原体的一代测序（NGS）数据， 维护稳健的SOP，以减少大规模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， 下游变异识别和系统发育分析。 博士艾伦的实验室位于麻省理工学院和哈佛大学的拉根研究所， 病原体艾滋病毒，丙型肝炎病毒和SIV在过去的15年中，在此期间，他已经制定了一个完善的 物理实验室支持实验室过程的所有阶段。他还担任了几个病毒的PI 在此期间，NIH/NIAID U 01，U19和P01项目赠款的测序核心，从而提供了广泛的 与病毒序列数据的成本效益生成、管理、分析和沉积相关的经验 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.