Harris Matthew E, Serwadda David, Sewankambo Nelson, Kim Bohye, Kigozi Godfrey, Kiwanuka Noah, Phillips James B, Wabwire Fred, Meehen Mary, Lutalo Tom, Lane James R, Merling Randall, Gray Ron, Wawer Maria, Birx Deborah L, Robb Merlin L, McCutchan Francine E
Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA.
AIDS Res Hum Retroviruses. 2002 Nov 20;18(17):1281-90. doi: 10.1089/088922202320886325.
The impact of HIV-1 genetic diversity on candidate vaccines is uncertain. To minimize genetic diversity in the evaluation of HIV-1 vaccines, vaccine products must be matched to the predominant subtype in a vaccine cohort. To that end, full genome sequencing was used to detect and characterize HIV-1 subtypes and recombinant strains from individuals in Rakai District, Uganda. DNA extracted from peripheral blood mononuclear cells (PMBC) was PCR amplified using primers in the long terminal repeats (LTRs) to generate nearly full length genomes. Amplicons were directly sequenced with dye terminators and automated sequencers. Sequences were phylogenetically analyzed and recombinants were detected and mapped with distance scan and bootscan. Among 46 sequences, 54% were subtype D, 15% were subtype A, and 30% were recombinant. All recombinants were individually unique, and most combined subtypes A and D. Subtype D comprised more than 70% of all the HIV-1 genomes in Rakai when both pure subtypes and recombinants were considered. Candidate vaccines based on HIV-1 subtype D would be appropriate for evaluation in Rakai District, Uganda.
HIV-1基因多样性对候选疫苗的影响尚不确定。为了在评估HIV-1疫苗时尽量减少基因多样性，疫苗产品必须与疫苗队列中的主要亚型相匹配。为此，采用全基因组测序来检测和鉴定乌干达拉凯区个体的HIV-1亚型和重组毒株。从外周血单个核细胞（PMBC）中提取的DNA，使用长末端重复序列（LTR）中的引物进行PCR扩增，以生成近乎全长的基因组。扩增子用染料终止剂和自动测序仪直接测序。对序列进行系统发育分析，并用距离扫描和bootscan检测和定位重组体。在46个序列中，54%为D亚型，15%为A亚型，30%为重组体。所有重组体均为独特个体，且大多数为A和D亚型的组合。当同时考虑纯亚型和重组体时，D亚型占拉凯所有HIV-1基因组的70%以上。基于HIV-1 D亚型的候选疫苗适合在乌干达拉凯区进行评估。
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