Analysis of the nearly full-length genome of a novel HIV-1 CRF01_AE/B/C recombinant strain isolated in Yunnan Province

Q4 Immunology and Microbiology

中华微生物学和免疫学杂志 Pub Date : 2019-08-31 DOI:10.3760/CMA.J.ISSN.0254-5101.2019.08.007

Jia-fa Liu, Mi Zhang, Bihui Yang, Xuemei Deng, A. Sun, Suyun Lei

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引用次数: 0

Abstract

Objective To analyze the genetic structure and recombination characteristics of a newly discovered HIV-1 unique recombinant strain in Yunnan Province. Methods During a test for drug-resistant HIV genotypes in Yunnan Province in 2016, a recombinant fragment was found in the pol region of a HIV-1 strain isolated from a patient. Two overlapping segments of the HIV-1 genome were amplified by RT-PCR, and then the products were sequenced. Recombination analysis was performed using RIP, jpHMM and SimPlot3.5 software. A phylogenetic tree was constructed for homology analysis by Neighbor-joining method using MEGA6.06 software. Results A nearly full-length HIV-1 gene sequence with 8 590 bp in length was obtained. Breakpoint analysis indicated that the sequence consisted of CRF01_AE and fragments of B and C subtypes. CRF01_AE was used as the backbone with B and C subtype fragments inserted. The positions were 791 to 1 171 for CRF01_AE, 1 172 to 2 652 for C subtype fragment, 2 653 to 2 977 for B subtype fragment, and 2 978 to 9 380 for CRF01_AE using HIV-1 HXB2 as the reference strain. Conclusions Some new strains formed by cross-recombination of CRF01_AE and B and C subtypes were discovered in Yunnan Province in recent years. It was found that the recombination pattern of the newly discovered strain was complex, suggesting that close attention should be paid to the changes in epidemic trends, which was of great importance to understand the current prevalence and epidemic trends of HIV-1. Key words: Human immunodeficiency virus type 1; Unique recombinant form; Near-full-length gene sequence analysis

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云南分离的一株新的HIV-1 CRF01_AE/B/C重组株的近全长基因组分析

目的分析云南省新发现的HIV-1独特重组株的遗传结构和重组特性。方法在云南省2016年的一次HIV耐药基因型检测中，从一名患者身上分离到一株HIV-1毒株的pol区发现一个重组片段。通过RT-PCR扩增HIV-1基因组的两个重叠片段，然后对产物进行测序。使用RIP、jpHMM和SimPlot3.5软件进行重组分析。使用MEGA6.06软件，通过邻居连接法构建系统发育树进行同源性分析。结果获得了全长8 590 bp的HIV-1基因序列。断点分析表明，该序列由CRF01_AE和B、C亚型片段组成。以CRF01_AE为骨架，插入B和C亚型片段。使用HIV-1HXB2作为参考菌株，CRF01_AE的位置为791-1 171，C亚型片段的位置为1 172-2 652，B亚型片段为2 653-2 977，CRF01TE的位置为2 978-9 380。结论云南省近年来发现了一些由CRF01_AE与B、C亚型交叉重组形成的新菌株。研究发现，新发现的毒株重组模式复杂，提示应密切关注流行趋势的变化，这对了解当前HIV-1的流行情况和流行趋势具有重要意义。关键词：人类免疫缺陷病毒1型；独特的重组形式；近全长基因序列分析

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来源期刊

中华微生物学和免疫学杂志 Immunology and Microbiology-Virology

CiteScore

0.50

自引率

0.00%

发文量

6906

期刊介绍： Chinese Journal of Microbiology and Immunology established in 1981. It is one of the series of journal sponsored by Chinese Medical Association. The aim of this journal is to spread and exchange the scientific achievements and practical experience in order to promote the development of medical microbiology and immunology. Its main contents comprise academic thesis, brief reports, reviews, summaries, news of meetings, book reviews and trends of home and abroad in this field. The distinguishing feature of the journal is to give the priority to the reports on the research of basic theory, and take account of the reports on clinical and practical skills.