A single genomic assay for HIV incidence and transmitted drug resistance mutation screening

 说明(申请人提供)：本建议书为上级R01项目(AI095066)的续展申请。这项应用建立在我们在母体时期取得的开创性成就的基础上，在这些成就中，我们成功地证明了宿主内HIV序列群体中的基因组签名是区分事件和慢性感染的精确和可靠的标记。这些基因组生物标记物，测量密切相关菌株的存在作为发病的标志，显示出超过95%的准确性。我们通过应用尖端技术来设计高通量的下一代测序平台，进一步完善了发病率分析。目前，这项检测正在600多个突发事件和慢性病例样本上进行积极测试，并与具有良好队列的卓越中心合作。在目前的应用中，我们建议开发一种高精度和低成本的基因组检测方法，它可以同时确定HIV发病率和在横断面调查中从单一测量中分析传播的耐药突变(TDRM)。该方案的主要创新包括i)将高通量下一代测序平台与生物信息学管道相结合，统计测试和数学建模，ii)设计 新的统计方法，以客观地确定假近期率(FRR)和最近感染的平均持续时间(MDRI)--标准发病率分析评估标准--和iii)分发易于访问的基于网络的软件，全球艾滋病毒社区可以与之互动，进行发病率和TDRM监测。我们的基因组分析将首先产生下一代包膜基因片段的测序读数，以报告感染阶段。使用我们新的统计分层贝叶斯模型，我们将分析基因组生物标记物随时间的动态变化，以计算MDRI和FRR。然后，我们将监测与卫生与公众服务部推荐和替代治疗方案有关的82个世卫组织列出的常见TDRM的存在。我们的单一检测方法满足了随着TDRM在全球的存在增加而精确识别TDRM的日益增长的需求。建议的检测方法的有效性将用来自不同人群的大量HIV序列进行广泛测试，包括i)来自著名中心(WIHS、CDC、CHAVI和CEPHIA)的成熟队列，ii)我们在南加州大学和洛杉矶同性恋中心的Rand Schrader诊所的队列，以及iii)来自艾滋病临床试验小组的病毒学失败队列(A5202)。该项目的最终产品是基于网络的软件，它将系统地产生和组织重要信息，为个人提供最佳治疗方案，并在地理上跟踪全人群的发病率和TDRM趋势。拟议的工作将通过提供可直接用于横断面疫情监测的有效发病率和TDRM监测分析来推进艾滋病毒预防工作。

 DESCRIPTION (provided by applicant): This proposal is a renewal application of the parent R01 project (AI095066). This application builds upon our pioneering accomplishments made during the parent period wherein we successfully demonstrated that genomic signatures within the intrahost HIV sequence population are precise and robust markers to distinguish incident from chronic infections. These genomic biomarkers, measuring the presence of closely related strains as a signature of incidence, showed over 95% accuracy. We further refined the incidence assay by implementing cutting-edge technology to design a high-throughput, next-generation sequencing platform. This assay is currently being actively tested on over 600 incident and chronic specimens in collaboration with preeminent centers with well-established cohorts. In the present application, we propose to develop a highly accurate and low cost genomic assay which concurrently determines HIV incidence and profiles transmitted drug resistance mutations (TDRMs) from a single measure in cross-sectional surveys. Major innovations of the proposal include i) integrating a high-throughput next-generation sequencing platform with a bioinformatics pipeline, statistical tests and mathematical modeling, ii) designing novel statistical methods to objectively determine the False Recency Rate (FRR) and mean duration of recent infection (MDRI) - the standard incidence assay evaluation criteria - and iii) distributing easily accessible web-based software with which the global HIV community can interact for incidence and TDRM surveillance. Our genomic assay will first produce next-generation sequencing reads of envelope gene segments to report the stage of infection. Using our new statistical hierarchical Bayesian models, we will analyze the genomic biomarker dynamics over time to calculate the MDRI and FRR. We will then monitor the presence of 82 WHO-listed commonly occurring TDRMs associated with the Department of Health and Human Services' recommended and alternative therapy regimens. Our single assay approach responds to the growing need to precisely identify TDRMs as their global presence increases. The validity of the proposed assay will be extensively tested with a large volume of HIV sequences from diverse populations, including i) well-established cohorts from preeminent centers (WIHS, CDC, CHAVI, and CEPHIA), ii) our own cohorts at the Rand Schrader Clinic at USC and Los Angeles Gay and Lesbian center, and iii) the virologic failure cohort (A5202) from the Clinical AIDS Trial Group. This project's end-product, web-based software, will systematically produce and organize vital information to inform optimal therapy regimens for individuals and geographically trace population-wide incidence and TDRM trends. The proposed work will advance HIV prevention efforts by providing a working incidence and TDRM surveillance assay ready for direct use in cross-sectional epidemic monitoring.