Within-host and between-host evolutionary rates across the HIV-1 genome.
Within-host and between-host evolutionary rates across the HIV-1 genome.
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DOI：
10.1186/1742-4690-10-49
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发表时间：
2013-05-02
期刊：
影响因子：
3.3
通讯作者：
Fraser C
中科院分区：
文献类型：
--
作者：
Alizon S;Fraser C
HIV 在流行病学层面以及在宿主体内的层面上都迅速演变。人们认为该病毒的宿主内进化率远高于宿主间进化率。然而，这一结论依赖于对病毒包膜基因的一小部分的分析。在这里，我们详细研究了艾滋病毒基因组的这些进化速率。我们使用宽松的分子钟假设来构建系统发育，以估计 HIV 基因组不同区域的进化速率。我们发现这些比率在整个基因组中差异很大，包膜基因 (env) 中的比率更高。在整个艾滋病毒基因组中，宿主内进化率始终高于宿主间进化率。这种差异在 env 中更为明显。最后，我们发现重叠区域和非重叠区域之间存在微弱差异。我们对宿主内和宿主间水平的 HIV 分子进化速率差异进行了全基因组概述。与丙型肝炎病毒相反，差异仅位于包膜基因中，整个艾滋病毒基因组的宿主内进化率高于宿主间进化率。这支持了这样的假设：不太适应宿主的艾滋病毒株在传播过程中具有优势。最可能的机制是病毒在潜伏 T 细胞中储存，然后优先传播。这些结果为传播瓶颈在艾滋病毒进化动力学中的作用提供了新的线索。
HIV evolves rapidly at the epidemiological level but also at the within-host level. The virus’ within-host evolutionary rates have been argued to be much higher than its between-host evolutionary rates. However, this conclusion relies on analyses of a short portion of the virus envelope gene. Here, we study in detail these evolutionary rates across the HIV genome. We build phylogenies using a relaxed molecular clock assumption to estimate evolutionary rates in different regions of the HIV genome. We find that these rates vary strongly across the genome, with higher rates in the envelope gene (env). Within-host evolutionary rates are consistently higher than between-host rates throughout the HIV genome. This difference is significantly more pronounced in env. Finally, we find weak differences between overlapping and non-overlapping regions. We provide a genome-wide overview of the differences in the HIV rates of molecular evolution at the within- and between-host levels. Contrary to hepatitis C virus, where differences are only located in the envelope gene, within-host evolutionary rates are higher than between-host evolutionary rates across the whole HIV genome. This supports the hypothesis that HIV strains that are less adapted to the host have an advantage during transmission. The most likely mechanism for this is storage and then preferential transmission of viruses in latent T-cells. These results shed a new light on the role of the transmission bottleneck in the evolutionary dynamics of HIV.
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