HCV Ghost Sequencing Center

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。 在母公司的奖励下，我们建立了一个高质量、高通量的丙型肝炎病毒下一代测序(NGS)平台 这使得能够从来自8个农村研究的1000多个患者样本中产生丙型肝炎病毒hvr1序列 站点，以及内部信息学管道，能够验证由 疾控中心幽灵实验室。对NGS数据的传输网络分析表明，聚类率 (可能是直接传播)在不同的研究地点差异很大，从10%到42%不等。横跨所有 地理分布以1a型最常见(57%)，其次为3a型(30%)、2b型(9%)、1b型(4%)。 混合基因型在病例中所占比例不到5%。幽灵丙型肝炎病毒分子的实现 监测技术表明，在农村社区进行丙型肝炎病毒基因组监测是可行的，并建议 潜在因素可能正在影响跨站点传输网络的规模。在家长奖下 我们还研究了使用干血斑(DBS)采集这一应用的可行性。一项初步研究 由14个血清样本组成，显示DBS内的病毒群体在遗传上与 来自血浆的病毒种群，表明DBS可以捕获类似的传播网络 以及从传统的血清样本收集中观察到的病毒多样性。因此，星展银行可以增强传统的 在资源有限的地区，丙型肝炎病毒监测方法是替代冷冻血浆的一种实用且经济有效的方法 环境，如农村人口。 由于SARS-CoV-2大流行对我们在拉贡研究所的实验室工作产生了重大影响， 在我们的UH3合作者为我们的工作提供了样本之后，我们应用程序的许多初始目标 都没有完成。我们的U24应用程序的这一行政副刊建议支持生成 以及为疾控中心幽灵中心分析额外的丙型肝炎病毒NGS数据，以识别丙型肝炎病毒在 注射毒品者(PWID)；验证用于采集和生成的干血斑的应用 通过NGS数据管理传播链路；管理艾滋病毒和丙型肝炎病毒血清样本的收集和存储- 来自RFA-DA-17-014临床研究地点的受感染参与者；并将样本运往疾病预防控制中心 梅毒检测和艾滋病毒和丙型肝炎病毒的系统发育图。 我们计划在第六年使用这些资金来支付额外的工作量，以实现我们项目的原始目标。这 包括处理和分析数百个新的患者样本，这些样本最近从 我们的临床站点通过合并NGS数据和特定站点的RDS来确定推动高聚集率的因素 数据，并完成我们星展银行的研究以供发表。

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. Under the parent award we built a high-quality, high-throughput HCV next-generation sequencing (NGS) platform that enabled the generation of HCV HVR1 sequences from over 1,000 patient samples derived from 8 rural study sites, along with an in-house informatics pipeline capable of validating phylogenetic clustering identified by the CDC GHOST laboratory. Transmission network analysis of the NGS data showed that the rate of clustering (likely direct transmission) varied considerably across study sites ranging from 10% to 42%. Across all geographical sites, genotype 1a (57%) was the most common followed by genotype 3a (30%), 2b (9%), 1b (4%) and mixed genotypes represented less than 5% of cases. The implementation of the GHOST HCV molecular surveillance technology illustrates that genomic surveillance of HCV in rural communities is feasible and suggest underlying factors may be influencing the size of transmission networks across sites. Under the parent award we also examined the feasibility of using dried blood spot (DBS) collection for this application. A pilot study comprising 14 serum samples revealed that viral populations within DBS were genetically indistinguishable from viral populations derived from plasma, demonstrating that DBS can capture comparable transmission networks and viral diversity observed from the traditional collection of serum samples. Thus, DBS can augment traditional HCV surveillance approaches as a practical and cost-effective alternative to frozen plasma in resource-limited settings such as rural populations. Due to the substantial impact of the SARS-CoV-2 pandemic upon both our laboratory work at the Ragon Institute, and upon our UH3 collaborators providing specimens for our work, many of the initial goals of our application were not completed. This Administrative Supplement to our U24 application proposes to support the generation and analysis of additional HCV NGS data for the CDC’s GHOST center to identify HCV transmission links among persons who inject drugs (PWID); validate the application of dried blood spots for the collection and generation of transmission links by NGS data; 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. We plan to use these funds to cover additional workload in Year 6 to meet the original goals of our project. This includes, the processing and analysis of several hundred new patient samples that have recently arrived from our clinical sites, identify factors driving high rates of clustering by merging NGS data with site-specific RDS data, and completing our DBS study for publication.