HIV Evolution Defines Virus-Host/Drug Interactions In Viremic and Aviremic People

HIV进化定义了病毒血症和无病毒血症人群中病毒-宿主/药物的相互作用

• 批准号: 10412103
• 负责人: Ronald I Swanstrom
• 金额: $ 64.79万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-06-25 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10412103
• 关键词: Address; Adoption; Age; Anti-Retroviral Agents; Area; Automobile Driving; Bar Codes; Biological; Biological Assay; Biological Process; Biology; CD4 Positive T Lymphocytes; CXCR4 gene; Case-Control Studies; Cell Count; Cells; China; Conflict (Psychology); DNA; DNA amplification; Data; Data Set; Dideoxy Chain Termination DNA Sequencing; Disease; Disease Management; Drug Interactions; Drug Monitoring; Drug resistance; Early treatment; Environment; Epitopes; Evolution; Failure; Foundations; Frequencies; Genetic Recombination; Genome; Genomics; Genotype; Goals; HIV; HIV Genome; HIV-1; Haplotypes; Infection; Lead; Length; Link; Malawi; Measurable; Measures; Mediating; Menopausal Status; Methods; Minor; Mutation; Natural History; Nature; Neurons; Noise; Participant; Pathogenicity; Persons; Pharmaceutical Preparations; Phenotype; Plasma; Population; Population Analysis; Population Dynamics; Population Heterogeneity; Problem Solving; Process; Property; Research; Research Design; Role; Sampling; Screening procedure; Sequence Analysis; Site; Source; Structure; Techniques; Technology; Testing; Time; Treatment Failure; Variant; Viral; Viral Genes; Viral Genome; Viral reservoir; Virus; Virus Replication; Woman; Work; base; case control; cohort; comparative; deep sequencing; design; drug testing; genome sequencing; improved; in vivo; inflammatory marker; insight; neutralizing antibody; new technology; next generation sequencing; pathogen; pressure; quantum; resistance mutation; response; sequencing platform; success; tool; viral rebound; whole genome

Viral gene sequences represent a rich and valuable source of information about biological processes. Advances in next generation sequencing (NGS) technology over the past decade now provide the opportunity to probe viral population diversity and evolution in unprecedented ways. We developed specialized sequencing strategies to overcome several serious limitations of conventional NGS in analyzing viral populations, including greatly reducing the mis- incorporation and recombination introduced by the preceding PCR step, reducing the errors of the sequencing platform, and revealing sampling depth of the initial viral genomes/templates that are actually represented in the final data set. In this application we will use state-of-the-art NGS to address long-standing issues in HIV-1 population analysis in the context of viral evolution in the absence of therapy, the role of minor variants in predicting failed therapy, and whether the latent reservoir on therapy is replicating. In addition, we will link our sequence data to state-of-the-art evolutionary analysis, and confirm key aspects of our inferences with measures of changing viral phenotypes and host environment. In Aim 1, we will analyze longitudinal plasma samples from 27 HIV-infected women (from the WIHS cohort) starting with high CD4+ T cell counts until they progress to CD4+ T cell counts of less than 100 cells/µL. We will perform multiplexed NGS sequencing to obtain near full length HIV-1 genome sequences. We predict that X4 variants in viral populations first emerge at low abundance and that we will be able to detect them much earlier than previously observed and follow their evolution. In addition, we will investigate longitudinal viral diversity changes in all sequenced regions to assess population dynamics and link these changes to markers of inflammation, CNS damage, CTL response, and the breadth and potency of neutralizing antibodies. In Aim 2, we will apply multiplexed NGS sequencing as a screening tool for minor drug resistance variants that predict therapy failure. We hypothesize that the potential for drug resistance mutations to mediate escape can occur from minor variants, too minor to be reliably detected with the methods that have been used to date. We will analyze samples from four cohorts (Malawi and China) to determine how often minor variants are missed by using Sanger sequencing. We will then link resistance mutations leading to therapy failure with their pretherapy abundance in a case- control design. In Aim 3, we will use near full length genome sequencing of reservoir virus (either outgrowth or rebound) in 13 participants who were infected with a single variant and started therapy early. Potential evolution on therapy will include a focus on extant CTL responses. In this way we will provide a critical test of sequence evolution as a signature of viral replication during years of successful suppressive therapy. With this application we are examining questions that are central to understanding HIV-1 in the absence of therapy, when faced with the selection of antiretroviral drugs, and on successful therapy. Insights into each of these questions can be first approached with the appropriate use of NGS sequencing but in ways that account for the strengths and weaknesses of these platforms. High quality sequence information then leads the way to insights in viral evolution in response to a changing host, in response to drug selection, and in response to apparently suppressive therapy.

病毒基因序列代表了有关生物的丰富而有价值的信息来源 流程。过去十年下一代测序 (NGS) 技术的进展 现在提供了以前所未有的方式探索病毒种群多样性和进化的机会 方式。我们开发了专门的测序策略来克服一些严重的限制 传统NGS在分析病毒种群方面的优势，包括大大减少错误 前面的PCR步骤引入的掺入和重组，减少了错误 测序平台，并揭示初始病毒基因组/模板的采样深度 实际上在最终数据集中表示。在此应用程序中，我们将使用最先进的 NGS 将解决病毒背景下 HIV-1 群体分析中长期存在的问题 在没有治疗的情况下的进化，微小变异在预测治疗失败中的作用，以及 治疗中的潜在储存库是否正在复制。此外，我们将链接我们的序列数据 最先进的进化分析，并确认我们推论的关键方面 改变病毒表型和宿主环境的措施。在目标 1 中，我们将分析 来自 27 名 HIV 感染女性（来自 WIHS 队列）的纵向血浆样本 高 CD4+ T 细胞计数，直至 CD4+ T 细胞计数低于 100 个细胞/μL。我们 将进行多重 NGS 测序以获得接近全长的 HIV-1 基因组序列。 我们预测病毒群体中的 X4 变体首先以低丰度出现，并且我们将 能够比以前观察到的更早地发现它们并跟踪它们的演变。在 此外，我们将调查所有测序区域的纵向病毒多样性变化，以 评估群体动态并将这些变化与炎症、中枢神经系统损伤标志物联系起来， CTL 反应以及中和抗体的广度和效力。在目标 2 中，我们将应用 多重 NGS 测序作为预测微小耐药变异的筛选工具 治疗失败。我们假设耐药突变可能介导 较小的变体可能会发生逃逸，这些变体太小而无法用以下方法可靠地检测到： 至今已被使用。我们将分析四个队列（马拉维和中国）的样本，以 确定使用桑格测序遗漏微小变异的频率。然后我们将链接 在某种情况下，耐药突变会因其治疗前的丰度而导致治疗失败- 控制设计。在目标 3 中，我们将使用储存病毒的近全长基因组测序 （增长或反弹）在 13 名感染单一变异的参与者中，并且 很早就开始治疗。治疗的潜在发展将包括关注现有的 CTL 回应。通过这种方式，我们将提供序列进化的关键测试作为病毒的特征 在多年成功的抑制治疗期间复制。有了这个应用程序，我们 检查对于在没有治疗的情况下了解 HIV-1 至关重要的问题，当 面临着抗逆转录病毒药物的选择以及成功的治疗。深入了解每一个 这些问题可以首先通过适当使用 NGS 测序来解决，但在 解释这些平台的优点和缺点的方法。高质量序列 然后，信息将引导我们深入了解病毒进化以应对不断变化的宿主， 对药物选择的反应，以及对明显抑制治疗的反应。

项目成果

Selection of HIV-1 for resistance to fifth-generation protease inhibitors reveals two independent pathways to high-level resistance.

• DOI: 10.7554/elife.80328
• 发表时间: 2023-03-15
• 期刊: eLife
• 影响因子: 7.7
• 作者: Spielvogel E;Lee SK;Zhou S;Lockbaum GJ;Henes M;Sondgeroth A;Kosovrasti K;Nalivaika EA;Ali A;Yilmaz NK;Schiffer CA;Swanstrom R
• 通讯作者: Swanstrom R

HIV-1 drug resistance and genetic diversity in a cohort of people with HIV-1 in Nigeria.

• DOI: 10.1097/qad.0000000000003098
• 发表时间: 2022-01-01
• 期刊: AIDS (London, England)
• 作者: Oluniyi PE;Ajogbasile FV;Zhou S;Fred-Akintunwa I;Polyak CS;Ake JA;Tovanabutra S;Iroezindu M;Rolland M;Happi CT
• 通讯作者: Happi CT