Xin Ruo-Lei, Ma Ze-Qin, Cheng Chun-Lin, Xing Hui, Hong Kun-Xue, Ruan Yu-Hua, Li Jia, Lu Hong-Yan, Shao Yi-Ming, He Xiang
Beijing Centers for Preventive Medical Research, Beijing 100013, China.
Bing Du Xue Bao. 2013 May;29(3):316-22.
To explore the genetic characteristics of viral quasispecies in HIV-1 CRF07_BC infections among intravenous drug users (IDU), the gp120 fragments of HIV-1 env gene were amplified from plasma samples collected from 6 CRF07_BC infected persons using single genome amplification and sequencing (SGA/ SGS) method, and 11 to 28 sequences were obtained from these samples, respectively, A neighbor-joining phylogenetic tree was reconstructed to describe the genetic characteristics of viral quasispecies. The Simplot, segments' phylogenetic trees and diversity plots based on average pairwise distance (APD) were used to identify the recombination events between quasispecies. The SGA sequences derived from single specimen formed a large monophyletic cluster in the neighbor-joining phylogenetic tree and showed the complex topologic structures of viral quasispecies. Of the 6 CRF07_BC infected patients, only one possessed the high genetic homogeneity, whereas the other five individuals showed high heterogeneity, with two to four subclusters inside the monophyletic cluster for each specimen. In addition, the recombinant events were identified among viral quasispecies from 3 cases. The results show SGA technique and phylogenetic analyses are useful tool to investigate the intrahost CRF07_BC gp120 complex quasispecies variation and high genetic diversity.
为探索静脉吸毒者（IDU）中HIV-1 CRF07_BC感染的病毒准种的遗传特征，采用单基因组扩增和测序（SGA/SGS）方法从6例CRF07_BC感染者的血浆样本中扩增HIV-1 env基因的gp120片段，分别从这些样本中获得11至28个序列，重建邻接法系统发育树以描述病毒准种的遗传特征。基于平均成对距离（APD）的Simplot、片段系统发育树和多样性图用于识别准种之间的重组事件。来自单个样本的SGA序列在邻接法系统发育树中形成一个大的单系簇，并显示出病毒准种复杂的拓扑结构。在6例CRF07_BC感染患者中，只有1例具有高遗传同质性，而其他5例表现出高异质性，每个样本的单系簇内有2至4个亚簇。此外，在3例患者的病毒准种中鉴定出重组事件。结果表明，SGA技术和系统发育分析是研究宿主内CRF07_BC gp120复杂准种变异和高遗传多样性的有用工具。
