Powell Rebecca L R, Lezeau Lynchy, Kinge Thompson, Nyambi Phillipe N
Department of Microbiology, New York University School of Medicine, New York, New York 10010, USA.
AIDS Res Hum Retroviruses. 2010 Mar;26(3):253-64. doi: 10.1089/aid.2009.0174.
Little is known regarding the likelihood of recombination between any given pair of nonidentical HIV-1 viruses in vivo. The present study analyzes the HIV-1 quasispecies in the C1C2 region of env, the vif-vpr-vpu accessory gene region, and the reverse transcriptase region of pol. These sequences were amplified from samples obtained sequentially over a 12- to 33-month period from five dually HIV-1-infected subjects. Analysis of an average of 248 clones amplified from each subject revealed no recombinants within the three loci studied of the subtype-discordant infecting strains, whose genetic diversity was >11% in env. In contrast, two subjects who were initially coinfected by two subtype-concordant variants with genetic diversity of 7.4% in env were found to harbor 10 unique recombinants of these strains, as exhibited by analysis of the env gene. The frequent recombination observed among the subtype-concordant strains studied herein correlates with prior sequence analyses that have commonly found higher rates of recombination at loci bearing the most conserved sequences, demonstrating an important role for sequence identity in HIV-1 recombination. Viral load analysis revealed that the samples studied contained an average of 8125 virus copies/ml (range, 882-31,626 copies/ml), signifying that the amount of viral RNA in the samples was not limiting for studying virus diversity. These data reveal that recombination between genetically distant strains may not be an immediate or common outcome to dual infection in vivo and suggest critical roles for viral and host factors such as viral fitness, virus diversity, and host immune responses that may contribute to limiting the frequency of intersubtype recombination during in vivo dual infection.
关于体内任意一对非同一HIV-1病毒之间发生重组的可能性,目前所知甚少。本研究分析了env基因的C1C2区域、vif-vpr-vpu辅助基因区域以及pol基因的逆转录酶区域中的HIV-1准种。这些序列是从5名双重感染HIV-1的受试者在12至33个月期间连续获取的样本中扩增得到的。对每个受试者平均扩增出的248个克隆进行分析,结果显示在研究的三个基因座中,亚型不一致的感染毒株未出现重组体,其env基因的遗传多样性>11%。相比之下,对env基因的分析表明,最初由两个env基因遗传多样性为7.4%的亚型一致变体共同感染的两名受试者,体内存在这两种毒株的10种独特重组体。本文研究的亚型一致毒株中频繁出现的重组现象与先前的序列分析结果相关,先前的分析通常发现在具有最保守序列的基因座处重组率更高,这表明序列同一性在HIV-1重组中起重要作用。病毒载量分析显示,所研究的样本平均每毫升含有8125个病毒拷贝(范围为882 - 31,626个拷贝/毫升),这表明样本中的病毒RNA量并不限制对病毒多样性的研究。这些数据表明,基因距离较远的毒株之间的重组可能不是体内双重感染的直接或常见结果,并提示病毒适应性、病毒多样性和宿主免疫反应等病毒和宿主因素在限制体内双重感染期间亚型间重组频率方面可能发挥关键作用。