启动子多样性的增加揭示了印度人类免疫缺陷病毒1型C亚型的复杂系统发育。

Journal of human virology Pub Date : 2000-01-01
S Choudhury, M A Montano, C Womack, J T Blackard, J K Maniar, D G Saple, S Tripathy, S Sahni, S Shah, G P Babu, M Essex
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引用次数: 0

摘要

目的:评估人类免疫缺陷病毒1型(HIV-1)长末端重复序列(LTR)序列在印度不同人群中的多样性,并确定其流行亚型。研究设计/方法:在1992-1993年(浦那、新德里)和1995-1996年(浦那、孟买和维洛尔)对28个hiv -1阳性样本进行了3'LTR分析。从共培养的外周血单个核细胞(PBMCs)中提取基因组DNA,利用染料终止化学进行聚合酶链反应(PCR)扩增和测序。序列被编辑、对齐,并利用间隙剥离和自举参数进行系统发育分析。迁移率转移试验用于确认结合活性。结果:基于系统发育分析,所有核苷酸序列均为HWV-1亚型C。来自浦那/德里的分离株在单独分析时形成亚簇,而不考虑时间或样本来源。然而,在对来自孟买或韦洛尔的分离株或整个样本集进行集体分析时,未观察到显著的亚聚类。亚型特异性增强子分析揭示了预期的第三个NF-kappaB位点,但也揭示了六个分离株具有先前未描述的插入和缺失,其中一个类似于AP-1结合位点。结论:研究结果证实了HIV-1C的流行,并表明印度HIV-1C的系统发育日益复杂,因此先前观察到的亚聚类可能不再充分反映目前在印度流行的分离株的多样性。
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Increased promoter diversity reveals a complex phylogeny of human immunodeficiency virus type 1 subtype C in India.

Objective: To evaluate human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) sequence diversity among distinct populations within India and to determine the prevalent subtype.

Study design/methods: Analysis of the 3'LTR was conducted from 28 HIV-1-positive samples: 1992-1993 (Pune, New Delhi) and 1995-1996 (Pune, Mumbai and Vellore). Genomic DNA was extracted from cocultivated peripheral blood mononuclear cells (PBMCs) and used for polymerase chain reaction (PCR) amplification and sequencing using dye terminator chemistry. Sequences were edited, aligned, and analyzed phylogenetically utilizing gap-stripped and bootstrapping parameters. Mobility shift assays were used to confirm binding activity.

Results: All nucleotide sequences were HWV-1 subtype C based on phylogenetic analysis. The isolates from Pune/Delhi formed subclusters when analyzed separately, irrespective of time or sample source. However, no significant subclustering was observed with isolates from Mumbai or Vellore or with the entire sample set when analyzed collectively. Subtype-specific enhancer analysis revealed an expected third NF-kappaB site but also revealed six isolates with insertions and deletions not previously described, one of which resembles an AP-1 binding site.

Conclusions: The results confirm the prevalence of HIV-1C and suggest increasingly complex phylogeny of HIV-1C within India, such that the previously observed subclustering may no longer adequately reflect the diversity of isolates currently circulating throughout India.

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