Pilot Study to Monitor HIV Cluster Dynamics and Active HIV sub-Epidemics in Real Time

了解当地的艾滋病毒亚流行病是消除艾滋病毒流行病的关键。实时动态分析是 至关重要，因为只有实时监测艾滋病毒传播动态和确定新出现的艾滋病毒亚群， 流行病可以指导实时的公共决策。本研究的结果将证明真实的- 在资源有限的情况下对艾滋病毒传播集群进行时间监测。 我们假设，新诊断的艾滋病毒RNA检测的个人不成比例地与 活跃的HIV亚流行，即有效繁殖数Re > 1.0的簇。我们将执行 使用新型纳米孔MinION技术进行真实的HIV基因分型。这将使我们能够评估系统发育 在真实的时间内，检测到HIV RNA的个体与活跃的HIV亚流行之间的联系。的典范 实时监测艾滋病毒集群动态将是研究成果。 具体目标1。实时HIV基因分型：现场实时HIV基因分型的可行性，以及 结果验证我们将招募750名参与者，包括新诊断的个人和开始抗逆转录病毒治疗的人。 通过转介。我们将对病毒载量进行即时检测，测试实时艾滋病毒检测的可行性， 基因分型领域，执行远程艾滋病毒扩增，条形码，并使用新的纳米孔测序 MinION技术在该领域的应用，并使用纳米孔生成667个（最多750个）接近全长的HIV基因组 真实的现场技术。为了验证结果，我们将比较使用纳米孔MinION获得的数据， 和由Illumina HiSeq生成的下一代测序数据。 具体目标2。实时系统发育聚类分析：监测HIV传播的可行性 集群和活跃的艾滋病毒亚流行的真实的时间。为了真实的评估艾滋病毒集群动态，我们将 推断新生成的HIV序列的同源性（n=667;高达750）。我们将列举艾滋病毒传播 通过识别遗传学上不同的艾滋病毒亚流行病来聚类。我们将重建过时的古希腊建筑， 确定活跃的艾滋病毒亚流行病，有效繁殖数Re ≥ 1.0的。我们估计 新诊断的具有可检测病毒载量的个体与活跃的艾滋病毒亚流行之间的联系。我们将 进行艾滋病病毒耐药性分析，并将结果真实的反馈给临床医生和参与者。 这项拟议的研究有可能开发一个实时监测艾滋病毒传播集群的模型， 并用于真实的识别新出现的艾滋病毒亚流行病。研究表明，实时 监测艾滋病毒传播集群是可行的，将验证结果，并将确定是否真实的- 时间耐药性测试是现实的，可以在现场进行。我们将测试 现场实时HIV基因分型可降至每份样本34美元。

Understanding local HIV sub-epidemics is key to eliminating the HIV epidemic. Real-time phylodynamics is critical, as only real-time monitoring of HIV transmission dynamics and identification of emerging HIV sub- epidemics could guide real-time public policy decisions. Results of this study will prove the feasibility of real- time monitoring of HIV transmission clusters in limited-resource settings. We hypothesize that newly diagnosed individuals with detectable HIV RNA are disproportionately linked to active HIV sub-epidemics, i.e. clusters with effective reproductive number Re > 1.0. We will perform HIV genotyping in real time using novel nanopore MinION technology. This will allow us to assess phylogenetic linkages between individuals with detectable HIV RNA and active HIV sub-epidemics in real time. A model for real-time monitoring of HIV cluster dynamics will be the study outcome. Specific Aim 1. Real-time HIV genotyping: Feasibility of real-time HIV genotyping in the field, and results validation. We will enroll 750 participantsnewly diagnosed individuals and people initiating ART through referrals. We will perform point-of-care testing of viral load, test the feasibility of real-time HIV genotyping in the field, perform long-range HIV amplification, barcoding, and sequencing using novel nanopore MinION technology in the field, and generate 667 (up to 750) near full-length HIV genomes using nanopore technology in the field in real time. To validate results, we will compare data obtained using nanopore MinION in the field and next-generation sequencing data generated by Illumina HiSeq. Specific Aim 2. Real-time phylogenetic cluster analysis: Feasibility of monitoring HIV transmission clusters and active HIV sub-epidemics in real time. To assess HIV cluster dynamics in real time, we will infer phylogenies of newly generated HIV sequences (n=667; up to 750). We will enumerate HIV transmission clusters by identifying phylogenetically distinct HIV sub-epidemics. We will reconstruct dated phylogenies and identify active HIV sub-epidemics—i.e., those with an effective reproduction number Re  1.0. We will estimate linkages between newly diagnosed individuals with detectable viral load and active HIV sub-epidemics. We will perform HIV drug-resistance analysis and return the results to clinicians and participants in real time. The proposed study has the potential to develop a model for real-time monitoring of HIV transmission clusters, and for identifying emerging HIV sub-epidemics in real time. The study will demonstrate that real-time monitoring of HIV transmission clusters is feasible, will validate the results, and will determine whether real- time drug-resistance testing is realistic and could be performed in the field. We will test whether the cost of real-time HIV genotyping in the field could be dropped to $34 per sample.