The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examined a subset (n = 275) of sequences from Rakai, Uganda, collected between August 2011 and January 2015. Sequences were initially screened with COMET for subtyping and then evaluated using bootscanning and phylogenetic inference. Among 275 sequences, 38.6% were subtype D, 19.3% were subtype A, 2.9% were subtype C, and 39.3% were recombinant. The recombinants were structurally diverse in the number of breakpoints observed, the location of recombinant segments, and represented subtypes, with AD recombinants accounting for the majority of all recombinants (29.8%). Within the AD subpopulation, we identified a potential new circulating recombinant form in five individuals where the polymerase gene was subtype D and most of env was subtype A (D-A junctures at HXB2 6760 and 8709). While the breakpoints were identical for the viruses from these individuals, the viral fragments did not cluster together. These results suggest selection for a viral strain where properties of the subtype A and subtype D portions of the virus confer a survival advantage. The continued study of recombinants will increase our breadth of knowledge for the genetic diversity and evolution of HIV-1, which can further contribute to our understanding toward a universal HIV-1 vaccine.

中文翻译：

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乌干达拉凯近全长 HIV-1 序列的重组分析和潜在新循环重组形式的鉴定。

非洲普遍 HIV 流行病的系统发育学和网络 (PANGEA-HIV) 联盟在生成和检查从撒哈拉以南非洲产生的近乎全长的 HIV-1 序列方面至关重要。在这项研究中，我们检查了一个子集（n = 275) 来自乌干达 Rakai 的序列，收集于 2011 年 8 月至 2015 年 1 月之间。最初使用 COMET 筛选序列进行亚型分类，然后使用引导扫描和系统发育推断进行评估。275个序列中，38.6%为D亚型，19.3%为A亚型，2.9%为C亚型，39.3%为重组序列。重组体在观察到的断点数量、重组片段的位置和所代表的亚型方面存在结构差异，其中 AD 重组体占所有重组体的大部分 (29.8%)。在 AD 亚群中，我们在 5 个个体中发现了一种潜在的新循环重组形式，其中聚合酶基因是 D 亚型，大部分是env是 A 亚型（在 HXB2 6760 和 8709 处的 DA 接合点）。虽然来自这些个体的病毒的断点相同，但病毒片段并没有聚集在一起。这些结果表明选择了一种病毒株，其中病毒的 A 亚型和 D 亚型部分的特性赋予了生存优势。对重组体的持续研究将增加我们对 HIV-1 遗传多样性和进化的知识广度，这可以进一步促进我们对通用 HIV-1 疫苗的理解。