Real Time Phylogeny and Contact Tracing to Disrupt HIV Transmission

真实的时间系统发育和接触者追踪以阻断HIV传播Kantor，Rami MD 总结 预防艾滋病毒传播仍然是一个重大的全球挑战，需要创新的方法来实现这一目标。 破坏虽然实际的传播网络是未知的，但其特征是社会和系统发育 网络可以指导预防干预措施。接触者追踪是目前的公共卫生工具， 网络和识别，通知，测试和连接到新诊断的艾滋病毒病例的护理伙伴。系统发育 对现有序列的分析被用于研究流行病的特征，并促进了疫情的爆发 调查事务所然而，真实的时间整合的遗传学与接触追踪的公共卫生，国家- 水平还没有得到评估。我们建议将系统发育分析与接触 追踪真实的时间，并评估这种整合对罗得岛艾滋病毒感染的影响。我们 假设来自系统发育推断信息的真实的时间使用可以增强接触者追踪， 改进艾滋病毒检测、诊断和与护理的联系，阻断传播。具体目标是：（1） 对患者水平的序列数据进行真实的实时系统发育分析;（2）增强系统发育推断 通过增加抽样和更全面的测试;和（3）评估真实的时间积分的好处， 遗传学与接触追踪的努力。我们将开发和自动化的工具，将系统发育和 将动态推理引入联系人跟踪，探索其增强功能，并评估其真实的时间影响， 对男男性行为者、静脉注射毒品使用者和 艾滋病病毒抗药性。我们希望这种方法将改善识别和联系，以照顾 未被感染的个体，未被感染的个体与护理无关，未被感染的个体 感染的风险很高这个建议的主要前提是，系统发育网络包含 这些信息可以扩大社交网络并影响艾滋病毒的传播。如果我们的假设正确， 这项研究将对艾滋病毒预防和护理连续性产生重大影响，并阻断艾滋病毒的传播， 罗得岛。我们的多学科临床医生团队加强了我们研究方法的严谨性， 公共卫生官员，统计学家，生物信息学家，进化和分子生物学家，结合我们的 相关的现有数据和专业知识，国家的小规模和强大和密切的学术公众 健康伙伴关系。此外，还直接涉及重要和基本的道德操守考虑， 贯穿始终。这种方法将使成果具有普遍性和可持续性， 资源分配和持续执行以及结论的推广。2013年， 国际扶轮卫生部宣布在2020年内在该州实现“零”新艾滋病毒感染的愿景 然而，五年来，高风险网络之间的传播明显增加，阻碍了进展。这 该提案将有助于使小国际扶轮更接近其目标，即成为第一个实现零新感染的州， 展示如何集中努力可以防止艾滋病毒在国际扶轮及其他地区传播。

Real Time Phylogeny and Contact Tracing to Disrupt HIV Transmission Kantor, Rami MD SUMMARY Prevention of HIV transmission is still a major global challenge, and innovative methods are needed for its disruption. Though actual transmission networks are unknown, characterizing social and phylogenetic networks can guide prevention interventions. Contact tracing is the current public health tool to derive social networks and identify, notify, test and link to care partners of newly-diagnosed HIV cases. Phylogenetic analysis of available sequences is used in research to characterize epidemics and has facilitated outbreak investigations. However, real time integration of phylogenetics with contact tracing on a public health, state- wide level has not been evaluated. We propose to prospectively integrate phylogenetic analysis with contact tracing in real time, and evaluate the impact of such integration on HIV infection in Rhode Island (RI). We hypothesize that real time use of information from phylogenetic inference can enhance contact tracing, improve HIV testing, diagnoses and linkage to care, and disrupt transmission. The Specific Aims are to: (1) Conduct real time phylogenetic analyses of patient-level sequence data; (2) Augment phylogenetic inference by increased sampling and more comprehensive testing; and (3) Evaluate the benefit of real time integration of phylogenetics with contact tracing efforts. We will develop and automate tools to incorporate phylogenetic and phylodynamic inference into contact tracing, explore its enhancement, and evaluate its real time impact, with special consideration of key populations like men who have sex with men, intravenous drug users and persons with HIV drug resistance. We expect that this approach will improve identification and linkage to care of infected-unaware individuals, infected-aware individuals not linked to care, and uninfected individuals that are at high risk of infection. The main premise of this proposal is that phylogenetic networks contain information which can expand social networks and impact HIV transmission. If our hypothesis is correct, this research will have high impact on HIV prevention and the care continuum and disrupt HIV transmission in Rhode Island. The rigor of our research approach is strengthened by our multidisciplinary team of clinicians, public health officials, statisticians, bioinformaticians, evolutionary and molecular biologists, combined with our relevant existing data and expertise, the small size of the state and the strong and close academic-public health partnership. Furthermore, important and essential ethics considerations are directly addressed and incorporated throughout. Such an approach will make results generalizable and sustainable, allowing focused resource allocation and continuous implementation and generalization of findings. In 2013 the Director of the RI Department of Health declared the vision of ‘Getting to Zero’ new HIV infections in the state within the next five years, however apparent increases in transmission among high risk networks has impeded progress. This proposal will help bring small RI closer to its goal of being the first state to get to zero new infections and demonstrate how focusing efforts can prevent HIV transmission in RI and beyond.