Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil
Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in Sao Paulo, Brazil
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DOI：
10.1186/1743-422x-6-78
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发表时间：
2009-06-16
期刊：
影响因子：
4.8
通讯作者：
Sabino, Ester Cerdeira
中科院分区：
文献类型：
--
作者：
Sanabani, Sabri Saeed;de Souza Pastena, Evelyn Regina;Sabino, Ester Cerdeira
背景：人类免疫缺陷病毒1型（HIV-1）的遗传多样性对成功设计药物或疫苗至关重要。在这项研究中，我们旨在描述和定义目前在巴西圣保罗流行的HIV-1亚分支F1的分子流行率。方法：从888名居住在圣保罗的成年患者中选取36份样本，这些患者之前在我们实验室的两项独立研究中被诊断为基于pol亚基因组片段测序的F1亚分支感染。用5段重叠PCR法从纯化的36份血样基因组DNA中扩增出原病毒DNA，然后直接测序。从纯亚枝F1的5个片段中获得序列数据，构建系统发育树并与先前发表的序列进行比较。结果：我们的片段扩增和测序方法证实，从pol区推断出的F1亚枝序列中只有5个序列在整个基因组中也是正确的，因此，估计其真实患病率为0.56%。结果还显示，在亚基因组和全长基因组分析中，巴西亚枝F1和非巴西南美分离株存在单一的系统发育集群，总体亚型内核苷酸差异为6.9%。南美洲和中非F1菌株在C2-C3环境中的核苷酸差异分别为8.5%和12.3%。结论：总之，我们的研究结果显示F1亚枝在巴西的流行率低得惊人，表明这些分离株起源于中非，随后被引入南美洲。
Background: The genetic diversity of the human immunodeficiency virus type 1 (HIV-1) is critical to lay the groundwork for the design of successful drugs or vaccine. In this study we aimed to characterize and define the molecular prevalence of HIV-1 subclade F1 currently circulating in Sao Paulo, Brazil.Methods: A total of 36 samples were selected from 888 adult patients residing in Sao Paulo who had previously been diagnosed in two independent studies in our laboratory as being infected with subclade F1 based on pol subgenomic fragment sequencing. Proviral DNA was amplified from the purified genomic DNA of all 36 blood samples by 5 fragments overlapping PCR followed by direct sequencing. Sequence data were obtained from the 5 fragments of pure subclade F1 and phylogenetic trees were constructed and compared with previously published sequences. Subclades F1 that exhibited mosaic structure with other subtypes were omitted from any further analysisResults: Our methods of fragment amplification and sequencing confirmed that only 5 sequences inferred from pol region as subclade F1 also holds true for the genome as a whole and, thus, estimated the true prevalence at 0.56%. The results also showed a single phylogenetic cluster of the Brazilian subclade F1 along with non-Brazilian South American isolates in both subgenomic and the full-length genomes analysis with an overall intrasubtype nucleotide divergence of 6.9%. The nucleotide differences within the South American and Central African F1 strains, in the C2-C3 env, were 8.5% and 12.3%, respectively.Conclusion: All together, our findings showed a surprisingly low prevalence rate of subclade F1 in Brazil and suggest that these isolates originated in Central Africa and subsequently introduced to South America.