Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E
Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E
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DOI：
10.1128/jvi.74.22.10752-10765.2000
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发表时间：
2000-11-01
影响因子：
5.4
通讯作者：
Mullins, JI
中科院分区：
文献类型：
--
作者：
Anderson, JP;Rodrigo, AG;Mullins, JI
人类免疫缺陷病毒1型(HIV-1)在东南亚的流行在很大程度上是由于E分支(HIV-1E)的出现。有人认为，HIV-1E是由A亚型(HIV-1A)和E亚型的重组谱系衍生而来的，沿着E基因组有多个断裂点。我们从泰国(93TH057和93TH065)和中非共和国(90CF11697和90CF4071)获得了E分支病毒的完整基因组序列，使现有的HIV-1E全基因组序列增加到7个。全基因组的系统发育分析表明，A亚型和E亚型本身是单系进化的，尽管它们一起也形成了一个更大的单系群。以前被认为是重组证据的基因组不同区域的明显系统发育不一致在统计学上并不显著。此外，模拟表明，以前用作重组证据的引导扫描和成对距离结果可能具有误导性，特别是当不同亚型的基因组在替换或进化率方面存在差异时。综上所述，我们的分析表明，E亚型变异体来自重组谱系的假设没有得到充分支持。相比之下，许多其他声称具有重组来源的艾滋病毒毒株，包括只使用单一亲本毒株进行分析的病毒，确实满足我们提出的统计标准。因此，尽管亚型间重组HIV毒株确实在传播，但将重组来源分配给病毒结构的标准应该包括对替代假设的统计检验，以避免不适当的分配会掩盖这些病毒的真实进化特性。
The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant lineage of subtype A (HIV-1A) and subtype E, with multiple breakpoints along the E genome. We obtained complete genome sequences of clade E viruses from Thailand (93TH057 and 93TH065) and from the Central African Republic (90CF11697 and 90CF4071), increasing the total number of HIV-1E complete genome sequences available to seven. Phylogenetic analysis of complete genomes showed that subtypes A and E are themselves monophyletic, although together they also form a larger monophyletic group. The apparent phylogenetic incongruence at different regions of the genome that was previously taken as evidence of recombination is shown to be not statistically significant. Furthermore, simulations indicate that bootscanning and pairwise distance results, previously used as evidence for recombination, can be misleading, particularly when there are differences in substitution or evolutionary rates across the genomes of different subtypes. Taken jointly, our analyses suggest that there is inadequate support for the hypothesis that subtype E variants are derived from a recombinant lineage. In contrast, many other HIV strains claimed to have a recombinant origin, including viruses for which only a single parental strain was employed for analysis, do indeed satisfy the statistical criteria we propose. Thus, while intersubtype recombinant HIV strains are indeed circulating, the criteria for assigning a recombinant origin to viral structures should include statistical testing of alternative hypotheses to avoid inappropriate assignments that would obscure the true evolutionary properties of these viruses.