Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000, South Africa.
National Health Laboratory Services (NHLS), Western Cape Region, Tygerberg Hospital, Cape Town, South Africa.
Sci Rep. 2019 Apr 17;9(1):6227. doi: 10.1038/s41598-019-42417-1.
HIV-1 subtype C is the most prevalent subtype in South Africa. Although subtype B was previously detected in South Africa, there is limited sequence information available. We characterized near full-length HIV-1 subtype B sequences from samples collected at the start of the South African HIV-1 epidemic, in the 1980s. Five samples were analysed by PCR amplification, Sanger DNA sequencing and phylogenetic analyses. The viral genomes were amplified in two overlapping fragments of 5.5 kb and 3.7 kb. The sequences were subtyped using REGA version 3.0, RIP version 3.0 and jpHMM. Maximum Likelihood phylogenetic trees were inferred with MEGA version 6. Four HIV-1 patient sequences were subtyped as pure HIV-1 subtype B. One sequence was characterized as a novel HIV-1 subtype B and D recombinant. The sequences clustered phylogenetically with other HIV-1 subtype B sequences from South Africa, Europe and the USA. We report the presence of an HIV-1 subtype B and D recombinant strain detected in the beginning of the epidemic. This indicates that viral recombination events were already happening in 1985, but could have been missed as sequence analyses were often limited to small genomic regions of HIV-1.
HIV-1 亚型 C 是南非最流行的亚型。虽然以前在南非检测到过 HIV-1 亚型 B，但可用的序列信息有限。我们对 20 世纪 80 年代南非 HIV-1 流行初期采集的样本中近全长的 HIV-1 亚型 B 序列进行了特征描述。通过 PCR 扩增、Sanger DNA 测序和系统发育分析对 5 个样本进行了分析。病毒基因组在 5.5kb 和 3.7kb 的两个重叠片段中扩增。使用 REGA 版本 3.0、RIP 版本 3.0 和 jpHMM 进行亚型分类。使用 MEGA 版本 6 推断最大似然系统发育树。4 个 HIV-1 患者序列被分类为纯 HIV-1 亚型 B。一个序列被鉴定为新型 HIV-1 亚型 B 和 D 重组体。这些序列与南非、欧洲和美国的其他 HIV-1 亚型 B 序列在系统发育上聚类。我们报告了在疫情初期检测到的 HIV-1 亚型 B 和 D 重组株的存在。这表明病毒重组事件早在 1985 年就已经发生，但由于序列分析通常仅限于 HIV-1 的小基因组区域，因此可能被忽略了。
