The prevalence of HIV-1 drug resistance is increasing worldwide and monitoring its emergence is important for the successful management of populations receiving combination antiretroviral therapy. It is likely that pre-existing drug resistance mutations linked on the same viral genomes are predictive of treatment failure. Because of the large number of sequences generated by ultrasensitive single-genome sequencing (uSGS) and other similar next-generation sequencing methods, it is difficult to assess each sequence individually for linked drug resistance mutations. Several software/programs exist to report the frequencies of individual mutations in large data sets, but they provide no information on linkage of resistance mutations. In this study, we report the HIV-DRLink program, a research tool that provides resistance mutation frequencies as well as their genetic linkage by parsing and summarizing the Sierra output from the Stanford HIV Database. The HIV-DRLink program should only be used on data sets generated by methods that eliminate artifacts due to polymerase chain reaction recombination, for example, standard single-genome sequencing or uSGS. HIV-DRLink is exclusively a research tool and is not intended to inform clinical decisions.

中文翻译：

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HIV-DRLink：使用斯坦福 HIV 数据库在大型单基因组数据集中报告相关 HIV-1 耐药突变的工具。

HIV-1 耐药性的流行在世界范围内不断增加，监测其出现对于成功管理接受联合抗逆转录病毒治疗的人群很重要。连接在相同病毒基因组上的预先存在的耐药性突变很可能预示着治疗失败。由于超灵敏单基因组测序 (uSGS) 和其他类似的下一代测序方法产生的大量序列，很难单独评估每个序列的连锁耐药突变。有几种软件/程序可以报告大型数据集中单个突变的频率，但它们没有提供有关耐药突变连锁的信息。在这项研究中，我们报告了 HIV-DRLink 计划，一种研究工具，通过解析和总结斯坦福 HIV 数据库的 Sierra 输出，提供抗性突变频率及其遗传联系。HIV-DRLink 程序应仅用于通过消除聚合酶链反应重组造成的伪影的方法生成的数据集，例如标准单基因组测序或 uSGS。HIV-DRLink 仅是一种研究工具，并非旨在为临床决策提供信息。