Real-time Analysis for the Phylogenetic Investigation of Drug-resistant HIV clusters (RAPID-HIV)

项目摘要 该项目的总体目标是实现对艾滋病毒-1耐药性和传播的实时监测 使用集成计算流水线和我们开发的新的扩增方法的集群 用于纳米孔测序。这个项目很重要，因为在全球范围内，对艺术的抵触情绪的兴起 威胁在抑制病毒方面取得的重大进展。在非洲，这种威胁尤其严重。 有几个国家报告了治疗前艾滋病毒耐药性超过10%的情况 标准的一线治疗。便携式测序技术的出现意味着病毒基因组测序 现在已经做好准备，对公共卫生应对高涨的耐药性产生更大的影响。在……里面 这项建议我们将使用Minion测序仪并评估其性能特征 (准确度、特异度、灵敏度)的新的基于扩增子的方法，以便准确地表征 使用全长POL扩增的HIV-1多样性。由于HIV-1的核苷酸组成存在偏见 基因组和原始纳米孔数据的复杂性，我们将确定如何提高原始读数 非生物信息学专家对纳米孔测序数据的准确性和简化分析。基于 乌干达渔业社区内艾滋病毒-1风险的上升我们假设病毒集群来自 渔民经常存在耐药突变，并成为抗药性的储备者。因此，我们需要 了解HIV-1感染者中传播耐药的传播动态和演变 维多利亚湖周围的渔业社区。该提案将整合测序、基准化和 使用集成工作流实现近乎实时的分析，以实现艾滋病毒-1耐药性监测和 传输簇的检测。为了实现这些目标，我们将使用一组HIV-1样本 包括局部循环菌株，以评估我们的扩增子的性能特征 使用全长POL扩增准确表征HIV-1多样性的测序方法。我们会 开发针对HIV-1的定制培训基本呼叫模型，以准确量化耐药性和 实施用于实时基因分型和耐药性报告的集成分析管道，以简化 非生物信息学专家对纳米孔测序数据的分析。最后，我们将使用我们最近的 开发的扩增子测序方法与我们的实时分析流水线相结合，以了解 HIV-1感染者中传播耐药的传播动态和进化 维多利亚湖周围的渔业社区。综上所述，这些结果将促进我们对 HIV-1在渔业社区中的传播动态及对渔民的抗性负担 这些高危人群。

Project Abstract The overall aim of this project is to enable real-time surveillance of HIV-1 drug resistance and transmission clusters using an integrated computational pipeline and novel amplicon approach that we have developed for nanopore sequencing. This project is important because globally the rise of resistance to ART is threating the significant progress made in suppressing the virus. In Africa, this threat is particularly acute where several countries have reported levels of pre-treatment HIV resistance exceeding 10% to the standard first-line therapy. The advent of portable sequencing technology means viral genomic sequencing is now positioned to exert a greater impact on the public health response to the upsurge in resistance. In this proposal we will use the MinION sequencing device and assess the performance characteristics (accuracy, specificity, sensitivity) of a novel amplicon-based approach in order to accurately characterize HIV-1 diversity using full-length pol amplicons. Owing to the biased nucleotide composition of the HIV-1 genome and the complexity of the raw nanopore data we will identify how we can improve raw read accuracy and simplify the analysis of nanopore sequencing data by non-bioinformatics experts. Based on the elevated HIV-1 risks within Ugandan fishing communities we hypothesize that viral clusters from fisherfolk frequently harbor drug-resistance mutations and act as reservoirs of resistance. Thus, we need to understand the transmission dynamics and evolution of transmitted drug resistance within HIV-1 infected fishing communities around Lake Victoria. This proposal will integrate sequencing, basecalling, and analysis in near real-time using an integrated workflow to enable HIV-1 drug resistance surveillance and the detection of transmission clusters. To achieve these objectives, we will use a panel of HIV-1 samples comprising locally circulating strains in order to evaluate the performance characteristics of our amplicon sequencing approach to accurately characterize HIV-1 diversity using full-length pol amplicons. We will develop custom trained basecalling models specific to HIV-1 to accurately quantify drug resistance and implement an integrated analysis pipeline for real-time genotyping and drug resistance reporting to simplify the analysis of nanopore sequencing data by non-bioinformatics experts. Lastly, we will use our recently developed amplicon sequencing approach coupled with our real-time analysis pipeline to understand the transmission dynamics and evolution of transmitted drug resistance within HIV-1 infected individuals from fishing communities around Lake Victoria. Together, these results will advance our understanding of the transmission dynamics of HIV-1 among fishing communities and evaluate the burden of resistance among this high-risk sub-population.