HIV Incidence and Drug Resistance Surveillance using Microdrop HIV Sequencing

90-90-90运动：人人享有治疗的目标是到2030年结束艾滋病流行;然而， 1.7 2019年全球新增艾滋病毒感染者100万人，强调需要改善现有的艾滋病毒系统 流行病监测和有针对性的预防和干预。作为父R 01的续期申请 项目（AI 095066），该提案建立在我们发明微滴HIV的开创性成就之上 测序用于高分辨率和低成本的艾滋病毒发病率和耐药性同步监测。我们 单次抽血检测方法，希达（HIV发病率和耐药性检测），响应于不断增长的 需要精确地确定艾滋病毒的发病率，并确定耐药突变，包括少数变异， 在单个基因组中连接的跨类耐药突变。我们的主要创新是放大艾滋病毒的完整- 微滴内长度包膜和pol基因序列以及这种隔室扩增， 通过长读高通量测序，我们可以在一个特定的基因组中提取发病率和耐药性特征。 非常精确的方式。该应用程序的中心目标是提供一个端到端的实时艾滋病毒检测平台 发病率和耐药性横断面监测。在目标1中，我们建议进行一次横向调查， 通过获取来自尼日利亚的2，658份艾滋病毒阳性血浆样本进行监测 调查（NAIIS），与尼日利亚疾病预防控制中心合作。通过产生大量的HIV全长包膜和pol基因 序列，我们将报告尼日利亚的区域艾滋病毒发病率概况和93世卫组织监测耐药性 在群体和个体水平上的突变流行率。本申请的目的2致力于设计一种低成本的 开源实验室自动化平台。在自助式自动化平台方面的最新进展将 促进希达的微滴艾滋病毒测序部署到低收入和中等收入国家， 艾滋病毒的永久监测。这种标准化的高通量自动化平台非常适合执行交叉 在资源有限的情况下进行分区调查。Aim 3将希达与基于云的平台集成， 将发病率和耐药性监测算法自动化为软件即服务。标准化 高通量测序数据分析是常规监测的核心要求。希达的软件- 即服务将直接向用户输出标准化的高质量监测结果， 调查人员需要投资于高成本的硬件，以进行自己耗时的分析。这个云 该平台将报告特定人群和个体水平的发病率和耐药性特征， 地理区域。通过微滴HIV测序的希达将促进全球实时监测， 一个精确的和高通量的横断面调查工具的发病率和耐药性。

The movement of 90-90-90: Treatment for All aims to end the AIDS epidemic by 2030; however, there were still 1.7 million new HIV infections in 2019 worldwide, emphasizing the need to improve current systems of HIV epidemic monitoring and targeted preventions and interventions. As a renewal application of the parent R01 project (AI095066), this proposal builds upon our pioneering accomplishments of inventing microdrop HIV sequencing for high-resolution and low-cost simultaneous HIV incidence and drug resistance surveillance. Our single blood draw assay approach, HIDA (HIV Incidence and Drug Resistance Assay), responds to the growing need to precisely determine HIV incidence and identify drug resistance mutations, including minority variants and cross-class drug resistance mutations linked in a single genome. Our major innovation is to amplify HIV full- length envelope and pol gene sequences within micro-droplets and this compartmental amplification alongside with long-read high-throughput sequencing allows us to extract incidence and drug resistance signatures in a highly precise manner. The central goal of this application is to deliver an end-to-end platform for real-time HIV incidence and drug resistance cross-sectional surveillance. In Aim 1, we propose to conduct a cross-sectional surveillance by accessing 2,658 HIV positive plasma specimens from the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS), in partnership with Nigeria CDC. By producing massive HIV full-length envelope and pol gene sequences, we will report Nigeria’s regional HIV incidence profiles and 93 WHO surveillance drug resistance mutation prevalence at the population and individual levels. Aim 2 of this application is devoted to devise a low- cost, open-source laboratory automation platform. Recent advances in do-it-yourself automation platforms will facilitate the deployment of HIDA’s microdrop HIV sequencing into low- and middle- income countries for their perpetual HIV surveillance. This standardized, high-throughput automation platform is ideal for performing cross- sectional surveys in resource-limited settings. Aim 3 will integrate HIDA with a cloud-based platform that fully automates incidence and drug resistance surveillance algorithms as a software-as-a-service. The standardization of high-throughput sequencing data analysis is a central requirement for routine surveillance. HIDA’s software- as-a-service will output standardized, high-quality surveillance outcomes directly to users, circumventing the need for investigators to invest in high-cost hardware to perform their own time-consuming analyses. This cloud platform will report both population-level and individual-level incidence and drug resistance profiles in a given geographic region. HIDA via microdrop HIV sequencing will promote global real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool for incidence and drug resistance.