HIV-1 subtype C is the predominant circulating virus in South Africa. There are reports of non-C subtypes emerging in different regions of the country, however, very little information exists on the genetic diversity of HIV in the Eastern Cape Province, despite having the third largest HIV epidemic in the country. In the current study, a near full-length genomic sequence obtained from a heterosexual woman in the Eastern Cape (ADE/CMH/0032), was analyzed using two rapid online subtyping tools; REGA and the jumping Profile Hidden Markov Model (jpHMM). There was agreement between the two tools in the assignment of the pol, Vif, and vpr regions, identified as a C/D recombinant (pol) and subtype C (vif and vpr). Some degree of agreement existed in the assignment of the Gag region, as recombinant: A1/C/B/D by REGA, and A1/C/D by jPHMM, respectively. There was disparity between the two online tools in the subtype assignment of the remaining gene regions. Phylogenetic analysis with pure subtype reference sequences showed that the query sequence clustered with a subtype C reference strain, with a low bootstrap value of 43%. This is the first report from South Africa of a putative unique recombinant as classified by rapid online subtyping tools, involving subtype A1, C, D, B, and K. However, the clinical and epidemiological implications of this variant remain unclear. Further studies are needed to fully understand the genetic diversity of HIV in the Eastern Cape.

中文翻译：

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来自南非东开普省的 HIV-1 亚型 A1/C/D/B/K 独特重组形式的遗传特征

HIV-1 C 亚型是南非主要的流行病毒。有报道称该国不同地区出现了非 C 亚型，然而，尽管东开普省是该国第三大艾滋病毒流行地区，但关于艾滋病毒遗传多样性的信息很少。在目前的研究中，从东开普省一名异性恋女性身上获得的近全长基因组序列 (ADE/CMH/0032) 使用两种快速在线子分型工具进行了分析；REGA 和跳跃轮廓隐马尔可夫模型 (jpHMM)。两种工具在pol、Vif 和 vpr区域的分配方面达成一致，确定为 C/D 重组 ( pol ) 和 C 亚型（vif和vpr）. Gag区域的分配存在一定程度的一致性，作为重组： REGA 的 A1/C/B/D 和 jPHMM 的 A1/C/D，分别。在剩余基因区域的亚型分配中，两种在线工具之间存在差异。使用纯亚型参考序列的系统发育分析表明，查询序列与 C 亚型参考菌株聚类，引导值较低，为 43%。这是南非的第一份关于通过快速在线亚型工具分类的推定独特重组体的报告，涉及亚型 A1、C、D、B 和 K。然而，这种变异的临床和流行病学意义仍不清楚。需要进一步研究以充分了解东开普省艾滋病毒的遗传多样性。