Combined phylogenetic and epidemiological analysis to identify HIV transmission sources in Seattle WA

结合系统发育和流行病学分析来确定华盛顿州西雅图的艾滋病毒传播源

• 批准号: 9305837
• 负责人: Joshua T Herbeck
• 金额: $ 49.04万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9305837
• 关键词: AIDS prevention; Acquired Immunodeficiency Syndrome; Adolescent; Affect; Africa South of the Sahara; African; Age; American; Automobile Driving; Behavioral; Big Data; Caring; Clinical; Clinical Data; Clinical Research; Collaborations; Communities; Continuity of Patient Care; County; Data; Data Set; Data Sources; Databases; Decentralization; Diagnosis; Education and Outreach; Epidemic; Epidemiology; Ethnic Origin; Generations; Genotype; Goals; Government; Guide prevention; HIV; HIV Infections; HIV diagnosis; HIV-1; Health Resources; Heterosexuals; Hispanics; Human immunodeficiency virus test; Incidence; Individual; Infection; Information Systems; Interview; Latin America; Latino; Link; Location; London; Methodology; Modeling; Molecular; Molecular Epidemiology; Netherlands; Newly Diagnosed; Patients; Pattern; Pediatric Hospitals; Persons; Phylogenetic Analysis; Play; Population; Prevention; Primary Infection; Process; Public Health; Risk; Risk Factors; Role; Services; Sexual Partners; Source; Subgroup; Suggestion; System; Testing; United States; Universities; Washington; adolescent men who have sex with men; behavioral study; cohort; college; epidemiologic data; epidemiology study; expectation; experience; genetic analysis; genetic linkage analysis; high risk; innovation; men who have sex with men; methamphetamine use; novel; novel strategies; pre-exposure prophylaxis; research and development; sex; success; surveillance data; trait; transmission process; young men who have sex with men

ABSTRACT Despite substantial progress in education, outreach, diagnosis, ART and PrEP use, HIV incidence among MSM in the U.S. has not decreased substantially in the last decade, with increases in new infections seen in younger MSM. There is an urgent need for novel approaches to identify the main sources of ongoing transmission. Our project leverages the existence of multiple, decentralized, HIV databases in Seattle that contain HIV pol genotypes from, in total, >4,000 individuals (>50% of the HIV-infected population), each linked to a range of behavioral, clinical, and epidemiological data (the databases are from Public Health–Seattle and King County, PHSKC; University of Washington HIV Information System, UWHIS; UW Primary Infection Cohort, PIC; and Seattle Children’s Hospital, SCH). From these databases, we will create a single, combined pol dataset, which will facilitate novel molecular epidemiological analyses with diverse HIV data types. Our creation of this combined dataset (via processes of de-identification, anonymization, record linkage and genetic analysis) will serve as a model for communities that have comparable decentralized HIV data sources and available HIV genotypes. Subsequently, we will use this dataset for innovative “second generation” phylogenetic studies. First, we will describe HIV transmission patterns among key affected populations, including foreign-born Seattle residents and adolescent MSM. We hypothesize that phylogenetic linkage analyses will indicate that more than 80% of African- born cases, but less than 50% of Latino cases, are imported, with important public health implications. We also hypothesize that phylogenetic analysis of our combined dataset will reveal that adolescent MSM are frequently found in clusters with older MSM, at rates elevated above baseline expectations, indicating that age-discrepant pairs may play a role in driving transmission in this population in Seattle. Second, we will, in collaboration with Christophe Fraser and Oliver Ratmann (Imperial College London), estimate the proportion of transmissions in Seattle arising from each stage of the infection and care continuum. For this cutting edge analysis of the Seattle dataset, we will extend a data-driven clinical and phylogenetic methodology that was originally used to study MSM transmission in the Netherlands. We hypothesize that >50% of transmissions in Seattle arise from undiagnosed individuals, while transmission from patients not retained in care is less than previously estimated. Seattle is an ideal location to perform this project, as even with abundant public health resources, active and strong collaborations between academic and governmental communities, and great successes in the HIV care cascade, the epidemic persists.

抽象的 尽管在教育，外展，诊断，艺术和准备使用方面取得了长足进展，但MSM的艾滋病毒发病率 在美国 MSM迫切需要新的方法来识别我们的主要源 项目利用西雅图的多个，分散的HIV数据库的存在 来自> 4,000个个体（>感染HIV的人群的50％）的基因型，每种 行为，临床和流行病学数据（数据库来自公共卫生！ phskc; 西雅图儿童医院，SCH）。 将促进具有不同HIV数据类型的新分子流行病分析。 数据集（通过去识别，匿名，记录联系和遗传分析的过程）将作为一个 为可比较的分散艾滋病毒数据来源和可用的HIV基因型的社区模型。 随后，我们将使用数据集进行创新的“第二代”系统发育研究 描述关键受影响人群的艾滋病毒传播模式，包括外国出生的西雅图居民和 青少年MSM。 出生的卡斯（Casses），但不到50％的拉丁裔卡斯（Casses）进口了重要的公共卫生 假设对我们组合的数据集的企业发育分析，青春期的MSM经常是 在具有较旧MSM的群集中发现，以基线期望升高，表明IS-Discreppepant 对座位的驱动传播可能会发挥作用。 克里斯托夫·弗雷泽（Christophe Fraser）和奥利弗·拉特曼（Oliver Ratmann）（伦敦帝国学院），估计了传播的比例 西雅图来自感染的每个阶段和护理连续性。 数据集，我们将扩展一个由数据驱动的临床和系统发育方法，该方法最初是用过的。 荷兰的MSM传播。 未诊断的个体，而未保留护理的患者的传播则不足以估计。 西雅图是执行该项目的伦理当地地点，即使拥有大量的公共卫生资源，也有活跃和 学术和政府社区之间的强大合作，以及HIB护理中的巨大成功 级联，流行病仍然存在。