Automation and Evaluation of Real-Time Transmission Network-Based HIV Prevention Services in New York City

纽约市基于实时传输网络的艾滋病毒预防服务的自动化和评估

• 批准号: 10308047
• 负责人: Joel Okrent Wertheim
• 金额: $ 66.69万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-24 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10308047
• 关键词: AIDS prevention; Address; Automation; California; Caring; Centers for Disease Control and Prevention (U.S.); Cities; Clinic; Collaborations; Country; County; Data; Demography; Diagnosis; Drug resistance; Epidemic; Epidemiology; Evaluation; Future; Genetic; Genotype; Geography; Goals; Growth; Guide prevention; HIV; HIV Infections; HIV Seronegativity; HIV Seropositivity; HIV diagnosis; HIV-1; Health; Health Resources; Individual; Infection; Infrastructure; Intervention; Laboratories; Lead; Link; Location; Mental Health; Methods; Molecular; Monitor; Names; Network-based; New York City; Newly Diagnosed; Observational Study; Outcome; Partner Notification; Persons; Physicians; Plant Roots; Prevention; Protocols documentation; Provider; Public Health; Reporting; Research Design; Risk Factors; Scheme; Secure; Sequence Analysis; Services; Specific qualifier value; System; Testing; Time; United States; United States Public Health Service; Universities; Viral; Work; antiretroviral therapy; base; burden of illness; care systems; high risk; improved; indexing; pre-exposure prophylaxis; prevent; prevention service; programs; rapid growth; screening; standard of care; therapy adherence; transmission process; trend; virus genetics; web app

ABSTRACT Introduction. The HIV epidemic in the United States persists. Public health departments across the country are exploring how to better use viral genetic sequence data to reconstruct transmission networks and guide prevention efforts. In 2017, the Centers for Disease Control and Prevention (CDC) and University of California, San Diego (UCSD) unveiled a nationwide initiative, Secure HIV-TRACE, to allow public health departments to construct genetic transmission networks in near-real time. Concurrently, the New York City (NYC) Public Health Labs (PHL) began sequencing viral genotypes themselves (i.e., point-of-diagnosis genotyping) for people diagnosed by select providers, in order to reduce the time between diagnosis and sequence analysis. The goal of this these programs are to direct standard pubic health resources in near real-time to cases, clusters, and locations of greatest concern (i.e., greatest potential for future cases). The underlying assumption of this strategy is that prioritization based on cluster growth dynamics inferred from genetic sequence data will disproportionately reduce future disease burden. Therefore, the important question is not whether real-time time targeting can prevent incident infections; rather, the important question is: Can real-time targeting prevent more incident infections than current, network-agnostic public health strategies? Methods. Here, we propose an observational study designed to evaluate the impact of these real-time strategies, which are currently implemented in NYC. We will automate Secure HIV-TRACE to construct genetic transmission clusters in real- time to guide standard public health services in NYC. Using these clusters, we will identify Index Cases (i.e., HIV-infected people diagnosed by select provides who receive point-of-diagnosis genotyping by PHL) and then to identify Priority Partners (i.e., in-care viremic or out-of-care HIV-infected partners, genetically linked to the Index Case). Standard public health services will then be offered to these Priority Partners [e.g., return to care, antiretroviral therapy (ART) adherence support, partner elicitation services]. Using data routinely reported to NYC Department of Health and Mental Hygiene, we will assess whether these services provided to Priority Partners lead to (i) increased rates of viral suppression in the Priority Partners, (ii) less than predicted incident HIV cases in their transmission cluster, (iii) an interaction with past cluster growth to result in even less than predicted incident HIV cases in their transmission cluster, and (iv) an interaction with past cluster growth to identify more than predicted prevalent, undiagnosed HIV cases in their transmission cluster. Conclusions. If we observe an interaction between past cluster growth and public health outcomes resulting from standard prevention services, this will suggest that real-time network based prevention should become standard of care in NYC and beyond. Through Secure HIV-TRACE, we can expand this scope approach nationwide.

抽象的 介绍。美国的艾滋病毒流行仍然存在。全国公共卫生部门 正在探索如何更好地使用病毒遗传序列数据来重建传输网络并指导 预防努力。 2017年，疾病控制与预防中心（CDC）和加利福尼亚大学 圣地亚哥（UCSD）揭示了一项全国性的倡议，即安全的HIV-trace，允许公共卫生部门到达公共卫生部门 在近场时构建遗传传播网络。同时，纽约市（纽约市）公众 健康实验室（PHL）开始对病毒基因型本身进行测序（即，诊断基因分型） 由选定提供者诊断的人，以减少诊断和序列分析之间的时间。 这些计划的目的是将近乎实时的标准耻骨医疗资源指导到案件中， 集群和最关心的位置（即未来病例的最大潜力）。基础假设 该策略的是，基于遗传序列数据推断的基于群集增长动力学的优先级将 不成比例地减轻未来的疾病负担。因此，重要的问题不是实时 定位时间可以预防事件感染；相反，重要的问题是：实时定位可以防止 事件感染比当前的网络不足的公共卫生策略更多？方法。在这里，我们建议 一项旨在评估这些实时策略的影响的观察性研究，目前是 在纽约实施。我们将自动化安全的HIV跟踪，以在实地中构建遗传传播簇 是时候指导纽约市的标准公共卫生服务了。使用这些集群，我们将确定索引案例（即 由Select诊断出的HIV感染者提供了由PHL接受诊断点基因分型的人，然后 要确定优先伴侣（即，在遗传性艾滋病毒感染的伴侣中，与该伙伴有关 索引案例）。然后，标准公共卫生服务将提供给这些优先合作伙伴[例如，恢复护理， 抗逆转录病毒疗法（ART）依从性支持，合作伙伴启发服务]。使用常规报告的数据 纽约市卫生与精神卫生部，我们将评估这些服务是否优先 合作伙伴导致（i）优先伴侣中病毒抑制率的提高，（ii）比预测的事件少 HIV病例在其传输集群中，（iii）与过去簇增长的相互作用，甚至少于 预测其传播集群中的事件HIV病例，以及（iv）与过去簇增长的相互作用 在其传播集群中识别超过预测的普遍，未诊断的HIV病例。结论。如果 我们观察到过去的群集增长与标准产生的公共卫生结果之间的互动 预防服务，这将表明基于实时网络的预防应成为护理标准 在纽约市及其他地区。通过安全的HIV痕迹，我们可以在全国范围内扩展这种范围。

项目成果

The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.

• DOI: 10.1126/science.abp8715
• 发表时间: 2022-08-26
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Worobey, Michael;Levy, Joshua, I;Serrano, Lorena Malpica;Crits-Christoph, Alexander;Pekar, Jonathan E.;Goldstein, Stephen A.;Rasmussen, Angela L.;Kraemer, Moritz U. G.;Newman, Chris;Koopmans, Marion P. G.;Suchard, Marc A.;Wertheim, Joel O.;Lemey, Philippe;Robertson, David L.;Garry, Robert F.;Holmes, Edward C.;Rambaut, Andrew;Andersen, Kristian G.
• 通讯作者: Andersen, Kristian G.

The emergence of SARS-CoV-2 in Europe and the US.

• DOI: 10.1101/2020.05.21.109322
• 发表时间: 2020-05-23
• 期刊: bioRxiv : the preprint server for biology
• 作者: Worobey, Michael;Pekar, Jonathan;Lemey, Philippe
• 通讯作者: Lemey, Philippe

Increasing Capacity to Detect Clusters of Rapid HIV Transmission in Varied Populations-United States.

• DOI: 10.3390/v13040577
• 发表时间: 2021-03-30
• 期刊: Viruses
• 作者: Oster AM;Panneer N;Lyss SB;McClung RP;Watson M;Saduvala N;Ocfemia MCB;Linley L;Switzer WM;Wertheim JO;Campbell E;Hernandez AL;France AM
• 通讯作者: France AM

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.

• DOI: 10.1038/s41467-022-31247-x
• 发表时间: 2022-06-25
• 期刊: Nature communications
• 影响因子: 16.6

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York.

• DOI: 10.1038/s41467-021-25168-4
• 发表时间: 2021-08-09
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: West AP Jr;Wertheim JO;Wang JC;Vasylyeva TI;Havens JL;Chowdhury MA;Gonzalez E;Fang CE;Di Lonardo SS;Hughes S;Rakeman JL;Lee HH;Barnes CO;Gnanapragasam PNP;Yang Z;Gaebler C;Caskey M;Nussenzweig MC;Keeffe JR;Bjorkman PJ
• 通讯作者: Bjorkman PJ