Feng Yue, Gao Qinghua, Gao Li, Zhang Mi, Liu Yang, Xiao Meng, Dong Xingqi, Xia Xueshan
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
Infect Genet Evol. 2021 Nov;95:105053. doi: 10.1016/j.meegid.2021.105053. Epub 2021 Aug 26.
New human immunodeficiency virus (HIV)-1 circulating recombinant forms (CRFs) have recently emerged and disseminated rapidly in China; in total 38 CRFs have been identified thus far. Yunnan province shares its border with Myanmar, and is regarded as a "hotspot" for the occurrence of new HIV-1 recombinations; more than half of novel CRFs reported in China have been first documented in Yunnan province. In the present study, based on the information available on four existing near-full-length genome (NFLG) sequences, combined with data on four other closely related sequences obtained via Basic Local Alignment Search Tool (BLAST) analysis, NFLG/subregion phylogenetic, bootscanning, and time to the most recent common ancestor (TMRCA) analyses were performed. Phylogenetic analysis revealed that the eight strains demonstrated the formation of a distinct monophyletic branch with a bootstrap value of 100%. Strains in this branch were distantly related to all known HIV-1 CRFs; it was temporarily named CRF111_01C. Bootscanning analysis revealed that CRF111_01C consisted of a CRF01_AE backbone and four inserted subtype C segments. Remarkably, CRF111_01C shared six mosaic fragment identities with the previously identified CRF100_01C. Furthermore, CRF111_01C may be deemed a potential second-generation CRF consisting of CRF100_01C and C. Coalescent Bayesian analyses revealed that the TMRCA of CRF111_01C was approximately the period 1999-2002. The emergence of such second-generation recombinants highlights that continuous molecular screening is necessary to carefully monitor the evolutionary dynamics of HIV-1 epidemics.
新型人类免疫缺陷病毒1型（HIV-1）循环重组型（CRF）最近在中国出现并迅速传播；迄今为止共鉴定出38种CRF。云南省与缅甸接壤，被视为新HIV-1重组发生的“热点地区”；在中国报告的新型CRF中，超过半数首先在云南省被记录。在本研究中，基于四条现有近全长基因组（NFLG）序列的可用信息，结合通过基本局部比对搜索工具（BLAST）分析获得的另外四条密切相关序列的数据，进行了NFLG/子区域系统发育分析、步移扫描分析以及最近共同祖先时间（TMRCA）分析。系统发育分析显示，这八株毒株形成了一个独特的单系分支，自展值为100%。该分支中的毒株与所有已知HIV-1 CRF的亲缘关系较远；暂时将其命名为CRF111_01C。步移扫描分析显示，CRF111_01C由CRF01_AE主干和四个插入的C亚型片段组成。值得注意的是，CRF111_01C与先前鉴定的CRF100_01C共有六个镶嵌片段特征。此外，CRF111_01C可被视为由CRF100_01C和C型组成的潜在第二代CRF。贝叶斯合并分析显示，CRF111_01C的TMRCA约为1999 - 20 years ago。这种第二代重组体的出现凸显了持续进行分子筛查对于密切监测HIV-1流行的进化动态的必要性。 2年期间。此类第二代重组体的出现突出表明，持续的分子筛查对于密切监测HIV-1流行的进化动态是必要的。
