Reis Mônica N G, Guimarães Monick L, Bello Gonzalo, Stefani Mariane M A
Laboratório de Imunologia da Aids e da Hanseníase, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil.
Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
Front Microbiol. 2019 Feb 11;10:97. doi: 10.3389/fmicb.2019.00097. eCollection 2019.
Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous region studies (2003-2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B ( = 629), 6.4% subtype C ( = 53), 4.2% subtype F1 ( = 35), 13.4% intersubtype recombinants: 10.5% BF1 ( = 87), 2.3% BC ( = 19), 0.4% F1CB ( = 3), and 0.2% CF1 ( = 2). Two full and one partial BF1C genomes allowed the characterization of the CRF81_cpx that has 9 breakpoints dividing the genome into 10 subregions. Basic Local Alignment Search Tool searches (Los Alamos HIV Sequence Database) identified six other sequences with the same recombination profile in , five from Brazil, and one from Italy. The estimated median TMRCA of CRF81_cpx was 1999 (1992-2003). CRF60_BC-like sequences, originally described in Italy, were also found. Two full and one near full-length BF1 genomes led to the characterization of the new CRF99_BF1 that has six recombination breakpoints dividing the genome into seven subregions. Two new URFs BF1, with six recombination breakpoints and seven subregions were also characterized. The description of the first Brazilian BF1C CRF81_cpx and of the new CRF99_BF1 corroborate the important role of CRFs in the HIV/AIDS epidemic throughout Brazil. Our data also highlight the value of HIV-1 full-genome sequence studies in order to fully reveal the complexity of the epidemic in a huge country as Brazil.
被归类为循环重组形式（CRF）或独特重组形式（URF）的亚型间重组体已被证明在复杂且动态变化的巴西艾滋病毒/艾滋病疫情中发挥着重要作用。此前对巴西中西部、北部和东北部六个州的828名患者进行的区域研究（2003年至2013年）报告了BF1、F1CB、BC和CF1嵌合体的不同发生率。在本研究中，对艾滋病毒-1亚型多样性中的BF1、F1CB、BC和CF1重组体进行了分析。从F1CB和BF1重组体中生成了全基因组/近全基因组/部分基因组序列。从全血中提取的基因组DNA用于巢式PCR，以扩增涵盖整个艾滋病毒-1基因组的四个重叠片段。使用邻接法/NJ方法（MEGA 6.0）生成系统发育树。使用贝叶斯马尔可夫链蒙特卡罗方法（BEAST v1.8；BEAGLE）估计F1CB和BF1分支的最近共同祖先时间（TMRCA）。使用Bootscanning进行重组分析（Simplot v3.5.1）；对片段进行单独的NJ系统发育分析以确认亚型。对828名患者的蛋白酶/逆转录酶序列进行的系统发育分析显示，76%为B亚型（n = 629），6.4%为C亚型（n = 53），4.2%为F1亚型（n = 35），13.4%为亚型间重组体：10.5%为BF1（n = 87），2.3%为BC（n = 19），0.4%为F1CB（n = 3），0.2%为CF1（n = 2）。两个完整和一个部分BF1C基因组使得能够对CRF81_cpx进行特征描述，该重组体有9个断点，将基因组分为10个区域。基本局部比对搜索工具搜索（洛斯阿拉莫斯艾滋病毒序列数据库）在巴西发现了另外六个具有相同重组图谱的序列，五个来自巴西，一个来自意大利。CRF81_cpx的估计中位TMRCA为1999年（1992年至2003年）。还发现了最初在意大利描述的CRF60_BC样序列。两个完整和一个近全长BF1基因组使得能够对新的CRF99_BF1进行特征描述，该重组体有六个重组断点，将基因组分为七个区域。还对两个新的具有六个重组断点和七个区域的URF BF1进行了特征描述。对巴西首个BF1C CRF81_cpx和新的CRF99_BF1的描述证实了CRF在巴西全国艾滋病毒/艾滋病疫情中的重要作用。我们的数据还强调了艾滋病毒-1全基因组序列研究的价值，以便充分揭示像巴西这样的大国疫情的复杂性。
