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是消除艾滋病毒流行的关键。实时系统动力学是 关键，因为只有实时监测艾滋病毒传播动态和识别新出现的艾滋病毒亚 流行病可以指导实时的公共政策决策。这项研究的结果将证明现实的可行性。 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，新诊断出的携带可检测到的艾滋病毒rna的个体存在不成比例的关联。 对于活跃的艾滋病毒亚流行病，即具有有效生殖数量Re&gt；1.0的集群。我们将表演 使用新的纳米孔基因分型技术实时进行艾滋病毒基因分型。这将使我们能够评估系统发育 携带可检测到的艾滋病毒RNA的个人与活跃的艾滋病毒亚流行病之间的实时联系。一种模型 对艾滋病毒集群动态的实时监测将是研究的结果。 具体目标1.实时艾滋病毒基因分型：现场实时艾滋病毒基因分型的可行性，以及 结果验证。我们将招募750名参与者新诊断的个人和发起ART的人 通过转介。我们将对病毒载量进行现场检测，测试实时艾滋病毒检测的可行性 在现场进行基因分型，使用新的纳米孔进行HIV远程扩增、条形码和测序 Minion技术，并使用纳米孔生成近667(高达750)个全长艾滋病毒基因组 技术在该领域的实时。为了验证结果，我们将比较使用纳米孔minion获得的数据 在现场和由Illumina HiSeq生成的下一代测序数据中。 具体目标2.实时系统发育聚类分析：监测艾滋病毒传播的可行性 实时监测群集性和活跃的艾滋病毒亚流行病。为了实时评估艾滋病毒聚集性动态，我们将 推断新产生的艾滋病毒序列的系统发育(n=667；最多750个)。我们将列举艾滋病毒的传播情况 通过识别在系统发育上不同的艾滋病毒亚流行来形成聚集群。我们将重建过时的进化史和 确定活跃的艾滋病毒亚流行--即有效繁殖数为Re1.0的那些。我们会估计 新诊断的病毒载量可检测到的个体与活跃的艾滋病毒亚流行之间的联系。我们会 进行HIV耐药性分析，并将结果实时返回给临床医生和参与者。 这项拟议的研究有可能开发一种实时监测艾滋病毒传播集群的模型， 并用于实时识别新出现的艾滋病毒亚流行。这项研究将证明，实时 对艾滋病毒传播集群的监测是可行的，将验证结果，并将确定是否真正- 时间耐药性测试是现实的，可以在现场进行。我们将测试是否将成本 现场的实时HIV基因分型可能会降至每个样本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.