High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS.

中文翻译：

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高通量测序产生的 HIV-1 半基因组序列的简化亚群、亚型和重组分析

高通量测序 (HTS) 已被广泛用于表征 HIV-1 基因组序列。目前没有算法可以使用从长基因组序列生成的短 HTS 读数直接确定基因型和准种种群，而无需额外的软件。为了建立强大的亚群、亚型和重组分析工作流程，我们从 65 个 HIV-1 感染者的血浆样本中扩增了 HIV-1 3'-半基因组，并通过 HTS 对整个扩增子（~4,500 bp）进行了测序。通过使用 HIVE-六面体直接分析原始读数，我们发现 48% 的样本包含 2 到 13 个亚群。我们鉴定了各种亚型（17 个 A1、4 个 B、27 个 C、6 个 CRF02_AG 和 11 个独特的重组形式）并定义了 10 个重组体的重组断点。这些结果通过单基因组测序 (SGS) 或 HTS 读数的共有序列分析生成的病毒基因组序列进行了验证。HIVE-六面体工作流程比仅评估共有序列更灵敏和准确，并且比 SGS 更具成本效益。