Accurately measuring recombination between closely related HIV-1 genomes.
Accurately measuring recombination between closely related HIV-1 genomes.
复制标题
DOI：
10.1371/journal.pcbi.1000766
复制
发表时间：
2010-04-29
影响因子：
4.3
通讯作者：
Davenport MP
中科院分区：
文献类型：
--
作者：
Schlub TE;Smyth RP;Grimm AJ;Mak J;Davenport MP
逆转录病毒重组被认为通过改组病毒群体中预先存在的突变在免疫逃逸和多重耐药性的产生中起重要作用。目前对HIV-1重组率的估计来自报告基因序列或遗传上不同的HIV序列内的测量。这些测量不能模拟体内密切相关的基因组之间发生的重组。此外，用于测量重组的方法对潜在过程进行了各种假设，并且通常无法充分考虑诸如细胞共感染或重组位点之间多个模板转换的可能性等问题。我们通过在gag中进行少量密码子修饰，开发了一种HIV-1标记系统，该系统允许在密切相关的病毒基因组之间的各种长度上测量重组。我们已经开发了统计工具来测量重组率，可以补偿多个模板开关的可能性。我们的研究结果表明，当多个模板开关被忽略的错误是相当大的，特别是当重组率高，或基因组距离大。我们证明，该系统是适用于其他研究，以准确地测量重组率，并表明重组不会随机发生在HIV基因组内。艾滋病毒产生和维持高遗传多样性的能力导致多重耐药性和逃避免疫系统，最终导致免疫失败和发展为艾滋病。HIV通过突变（病毒复制中遗传信息的错误复制）和重组（在病毒后代的产生中混合两种病毒基因组）的过程来保持这种多样性。通常通过插入编码非病毒荧光蛋白的基因来研究荧光。然而，在这种修饰的HIV基因组中的重组可能不能准确地反映感染HIV的患者体内发生的重组水平。此外，在亲本基因组相同的区域中，重组将无法检测到，并且这种效应通常被忽略。我们开发了一种新的实验系统，可以测量两个非常密切相关的HIV基因组之间的重组。我们还开发了统计工具来精确计算重组率，以补偿亲本基因组相同区域中无法检测到的重组。我们表明，我们的实验系统绕过了荧光重组实验的一些陷阱，我们的工具为这一领域的未来研究提供了强有力的定量基础。
Retroviral recombination is thought to play an important role in the generation of immune escape and multiple drug resistance by shuffling pre-existing mutations in the viral population. Current estimates of HIV-1 recombination rates are derived from measurements within reporter gene sequences or genetically divergent HIV sequences. These measurements do not mimic the recombination occurring in vivo, between closely related genomes. Additionally, the methods used to measure recombination make a variety of assumptions about the underlying process, and often fail to account adequately for issues such as co-infection of cells or the possibility of multiple template switches between recombination sites. We have developed a HIV-1 marker system by making a small number of codon modifications in gag which allow recombination to be measured over various lengths between closely related viral genomes. We have developed statistical tools to measure recombination rates that can compensate for the possibility of multiple template switches. Our results show that when multiple template switches are ignored the error is substantial, particularly when recombination rates are high, or the genomic distance is large. We demonstrate that this system is applicable to other studies to accurately measure the recombination rate and show that recombination does not occur randomly within the HIV genome. HIV's ability to generate and maintain high genetic diversity leads to multiple drug resistances and evasion from the immune system, eventually leading to immune failure and progression to AIDS. HIV maintains this diversity with a process of mutation (incorrect copying of genetic information in viral replication) and recombination (mixing two viral genomes in the creation of viral offspring). Recombination is generally studied by inserting genes encoding non-viral fluorescent proteins. However, recombination in such modified HIV genomes may not accurately reflect the level of recombination occurring within a patient infected with HIV. Additionally, recombination will go undetected in regions where the parental genomes are identical, and this effect is often ignored. We have developed a novel experimental system which allows recombination to be measured between two very closely related HIV genomes. We have also developed statistical tools to accurately calculate the recombination rate, compensating for undetectable recombination in identical regions of the parental genomes. We show that our experimental system bypasses some of the pitfalls of fluorescent recombination experiments and our tools provide a strong quantitative foundation for future studies in this area.
登录
查看更多内容
影响因子：
56.9
作者：
COFFIN, JM
通讯作者：
COFFIN, JM
影响因子：
4
作者：
Bretscher, MT;Althaus, CL;Bonhoeffer, S
通讯作者：
Bonhoeffer, S
HIV-1跨型重组期间断点位置的序列决定因素。
影响因子：
14.9
作者：
Baird HA;Galetto R;Gao Y;Simon-Loriere E;Abreha M;Archer J;Fan J;Robertson DL;Arts EJ;Negroni M
通讯作者：
Negroni M
影响因子：
5.4
作者：
ADACHI, A;GENDELMAN, HE;MARTIN, MA
通讯作者：
MARTIN, MA
影响因子：
5.4
作者：
Hill, MK;Shehu-Xhilaga, M;Mak, J
通讯作者：
Mak, J