Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India
Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India
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DOI：
10.1128/jcm.42.6.2742-2751.2004
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发表时间：
2004-06-01
影响因子：
9.4
通讯作者：
Ranga, U
中科院分区：
文献类型：
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作者：
Siddappa, NB;Dash, PK;Ranga, U
人类免疫缺陷病毒1型（HIV-1） C亚型病毒与全世界近一半的HIV-1感染有关，在印度以及非洲南部和东部地区最为突出。来自印度的早期报告确定了C型病毒的优势和一小部分a型病毒。随后的报告确定了多种亚型，建议通过扩大筛查进行新引入和/或检测。印度南部地区是该流行病的新兴地区，但尚不清楚这些地区的艾滋病毒-1感染是否与C亚型病毒有关，还是由于潜在的新引入的非C亚型病毒。在这里，我们描述了一种特异性和敏感的基于pcr的策略来识别c型病毒（C-PCR）的发展。该策略基于在第一轮扩增包含长末端重复和gag的区域，随后是两组嵌套引物；一种扩增多种亚型，而另一种扩增c亚型。通过琼脂糖凝胶的长度差异和c亚型特异性片段中编码的NF-kappaB位点的数量差异，可以区分普通HIV和c亚型特异性片段。我们采用该方法对来自南部4个州和东部1个城市的35个城镇的256名bw -1感染者进行了筛查。除了A和B亚型的单个样本和B/C重组样本外，我们发现所有样本都感染了C亚型病毒，并且通过异双工迁移试验和序列系统发育分析确认了亚型归属。我们建议使用C-PCR来促进快速分子流行病学表征，以帮助疫苗和治疗策略。
Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-kappaB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 BW-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.