Wilkinson Eduan, Holzmayer Vera, Jacobs Graeme B, de Oliveira Tulio, Brennan Catherine A, Hackett John, van Rensburg Estrelita Janse, Engelbrecht Susan
1 Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University , Tygerberg Academic Hospital, Tygerberg, Cape Town, South Africa .
AIDS Res Hum Retroviruses. 2015 Apr;31(4):412-20. doi: 10.1089/AID.2014.0230. Epub 2015 Jan 21.
By the end of 2012, more than 6.1 million people were infected with HIV-1 in South Africa. Subtype C was responsible for the majority of these infections and more than 300 near full-length genomes (NFLGs) have been published. Currently very few non-subtype C isolates have been identified and characterized within the country, particularly full genome non-C isolates. Seven patients from the Tygerberg Virology (TV) cohort were previously identified as possible non-C subtypes and were selected for further analyses. RNA was isolated from five individuals (TV047, TV096, TV101, TV218, and TV546) and DNA from TV016 and TV1057. The NFLGs of these samples were amplified in overlapping fragments and sequenced. Online subtyping tools REGA version 3 and jpHMM were used to screen for subtypes and recombinants. Maximum likelihood (ML) phylogenetic analysis (phyML) was used to infer subtypes and SimPlot was used to confirm possible intersubtype recombinants. We identified three subtype B (TV016, TV047, and TV1057) isolates, one subtype A1 (TV096), one subtype G (TV546), one unique AD (TV101), and one unique AC (TV218) recombinant form. This is the first NFLG of subtype G that has been described in South Africa. The subtype B sequences described also increased the NFLG subtype B sequences in Africa from three to six. There is a need for more NFLG sequences, as partial HIV-1 sequences may underrepresent viral recombinant forms. It is also necessary to continue monitoring the evolution and spread of HIV-1 in South Africa, because understanding viral diversity may play an important role in HIV-1 prevention strategies.
截至2012年底，南非有超过610万人感染了HIV-1。C亚型是这些感染中的主要类型，并且已有300多个近乎全长的基因组（NFLGs）被发表。目前，该国境内鉴定和表征的非C亚型分离株非常少，尤其是全基因组非C分离株。先前从泰格堡病毒学（TV）队列中的7名患者被鉴定为可能的非C亚型，并被选作进一步分析。从5名个体（TV047、TV096、TV101、TV218和TV546）中分离出RNA，从TV016和TV1057中分离出DNA。这些样本的NFLGs通过重叠片段进行扩增并测序。使用在线亚型分析工具REGA 3版和jpHMM筛选亚型和重组体。使用最大似然（ML）系统发育分析（phyML）推断亚型，并使用SimPlot确认可能的亚型间重组体。我们鉴定出3株B亚型（TV016、TV047和TV1057）分离株、1株A1亚型（TV096）、1株G亚型（TV546）、1种独特的AD（TV101）和1种独特的AC（TV218）重组形式。这是在南非描述的第一例G亚型NFLG。所描述的B亚型序列也使非洲的NFLG B亚型序列从3个增加到6个。需要更多的NFLG序列，因为部分HIV-1序列可能无法充分代表病毒重组形式。继续监测南非HIV-1的演变和传播也很有必要，因为了解病毒多样性可能在HIV-1预防策略中发挥重要作用。
