Han Xiao-xu, Dai Di, Zhang Min, Wang Ya-nan, Jiang Yong-jun, Shang Hong
The Key Laboratoty of AIDS Immunology, the First Affiliated Hospital, China Medical University, Shenyang 110001, China.
Zhonghua Yi Xue Za Zhi. 2007 Jul 24;87(28):1966-70.
To investigate the genetic subtypes and sequence characteristics of gag-pol region of HIV-1 epidemic in Liaoning province.
99 whole blood samples of HIV-1 infected individuals of Liaoning province were collected. Provirus DNA was extracted from anti-coagulated peripheral whole blood, and then the sequences of gag-pol region were amplified through nested PCR and then sequenced. Genetic subtypes were identified by phylogenetic analysis, controlled with new version subtype reference sequences of HIV sequence database. The genetic distances of different coding regions were calculated by MEGA2.0 with Kimura 2-parameter model. The synonymous (Ks) and anonymous (Ka) as well as the ratio of Ks/Ka were analyzed by SNAP tool in HIV sequence database.
There are many HIV-1subtypes epidemic in Liaoning province. We found five subtype: A, Thai B, B, C and G, five CRFs: CRF01, CRF03, CRF06, CRF07, CRF08, and one inter CRF recombinant ICR07/08 in 99 HIV-1 infected individuals of Liaoning province. Thai B subtype was the main subtype epidemic in Liaoning, next were CRF01_AE. In gag-pol region, the genetic distances of p17, p2-p6 were higher than p24, protease and RT coding region. The genetic distance of p24 region in B subtype strains were relative high compared with other subtypes. The genetic distance and the value of Ks and Ka were rather low in each region of CRF07 and CRF08. The ratio of Ks/Ka of p2-p6 region was the lowest in each subtype, the mean value was below 1. The ratio of Ks/Ka of RT region was as high as 10.45.
The HIV-1 genetic subtypes in Liaoning province were rather complex. The p24, protease and RT coding region coding region were more conserved in gag-pol region. P24 region of B subtype strains received more positive selective pressure, while the RT region of CRF01_AE strains received more negative selective pressure. CRF07_BC and CRF08_BC were the youngest strains transmitted to Liaoning province and showed strong founder effect.
研究辽宁省HIV-1流行株gag-pol区的基因亚型及序列特征。
采集99例辽宁省HIV-1感染者的全血样本。从抗凝血外周全血中提取前病毒DNA，通过巢式PCR扩增gag-pol区序列并测序。采用系统发育分析鉴定基因亚型，以HIV序列数据库的新版亚型参考序列作为对照。用MEGA2.0软件基于Kimura 2-参数模型计算不同编码区的遗传距离。通过HIV序列数据库中的SNAP工具分析同义突变率（Ks）、非同义突变率（Ka）以及Ks/Ka比值。
辽宁省存在多种HIV-1基因亚型流行。在99例辽宁省HIV-1感染者中，发现了5种亚型：A、泰国B、B、C和G，5种CRF：CRF01、CRF03、CRF06、CRF07、CRF08，以及1种CRF间重组型ICR07/08。泰国B亚型是辽宁省主要的流行亚型，其次是CRF01_AE。在gag-pol区，p17、p2-p6的遗传距离高于p24、蛋白酶和RT编码区。B亚型毒株p24区的遗传距离相对其他亚型较高。CRF07和CRF缉的各区域遗传距离以及Ks和Ka值较低。各亚型中p2-p6区的Ks/Ka比值最低，平均值低于1。RT区的Ks/Ka比值高达10.45。
辽宁省HIV-1基因亚型较为复杂。gag-pol区中p24、蛋白酶和RT编码区较为保守。B亚型毒株的p24区受到更多的正选择压力，而CRF01_AE毒株的RT区受到更多的负选择压力。CRF07_BC和CRF08_BC是传入辽宁省的最年轻毒株，呈现出较强的奠基者效应。
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