Gao F, Robertson D L, Morrison S G, Hui H, Craig S, Decker J, Fultz P N, Girard M, Shaw G M, Hahn B H, Sharp P M
Department of Medicine, University of Alabama at Birmingham 35294, USA.
J Virol. 1996 Oct;70(10):7013-29. doi: 10.1128/JVI.70.10.7013-7029.1996.
Since 1989, human immunodeficiency virus type 1 (HIV-1) has spread explosively through the heterosexual population in Thailand. This epidemic is caused primarily by viruses classified as "subtype E", which, on the basis of limited sequence comparisons, appear to represent hybrids of subtypes A (gag) and E (env). However, the true evolutionary origins of "subtype E" viruses are still obscure since no complete genomes have been analyzed, and only one full-length subtype A sequence has been available for phylogenetic comparison. In this study, we determined full-length proviral sequences for "subtype E" viruses from Thailand (93TH253) and the Central African Republic (90CR402) and for a subtype A virus from Uganda (92UG037). We also sequenced the long terminal repeat (LTR) regions from 16 virus strains representing clades A, C, E, F, and G. Detailed phylogenetic analyses of these sequences indicated that "subtype E" viruses do indeed represent A/E recombinants with multiple points of crossover along their genomes. The extracellular portion of env, parts of vif and vpr, as well as most of the LTR are of subtype E origin, whereas the remainder of the genome is of subtype A origin. The possibility that the discordant phylogenetic positions of "subtype E" viruses in gag- and env-derived trees are the result of unusual rates or patterns of evolution was also considered but was ruled out on the basis of two lines of evidence: (i) phylogenetic trees constructed for synonymous and nonsynonymous substitutions yielded the same discordant branching orders for "subtype E" gag and env gene sequences, thus excluding selection-driven evolution, and (ii) multiple crossovers in the viral genome are most consistent with the copy choice model of recombination and have been observed in other documented examples of HIV-1 intersubtype recombination. Thai and CAR "subtype E" viruses exhibited the same pattern of A/E mosaicism, indicating that the recombination event occurred in Africa prior to the spread of virus to Asia. Finally, all "subtype E" viruses were found to contain a distinctive two-nucleotide bulge in their transactivation response (TAR) elements. This feature was present only in viruses which also contained a subtype A 5' pol region (i.e., subtype A viruses or A/D and A/E recombinants), raising the possibility of a functional linkage between the TAR region and the polymerase. The implications of epidemic spread of a recombinant HIV-1 strain to viral natural history and vaccine development are discussed.
自1989年以来，人类免疫缺陷病毒1型（HIV-1）在泰国的异性恋人群中呈爆发式传播。这一疫情主要由被归类为“E亚型”的病毒引起，基于有限的序列比较，这些病毒似乎是A亚型（gag）和E亚型（env）的杂交体。然而，“E亚型”病毒的真正进化起源仍然不明，因为尚未对完整基因组进行分析，且仅有一个全长A亚型序列可用于系统发育比较。在本研究中，我们测定了来自泰国（93TH253）和中非共和国（90CR402）的“E亚型”病毒以及来自乌干达（92UG037）的一个A亚型病毒的全长前病毒序列。我们还对代表A、C、E、F和G分支的16个病毒株的长末端重复序列（LTR）区域进行了测序。对这些序列的详细系统发育分析表明，“E亚型”病毒确实代表了A/E重组体，其基因组上有多个交叉点。env的细胞外部分、vif和vpr的部分以及大部分LTR源自E亚型，而基因组的其余部分源自A亚型。“E亚型”病毒在基于gag和env构建的系统发育树中不一致的系统发育位置是由异常的进化速率或模式导致的这种可能性也被考虑过，但基于两条证据被排除：（i）为同义替换和非同义替换构建的系统发育树对于“E亚型”gag和env基因序列产生了相同的不一致分支顺序，从而排除了选择驱动的进化，以及（ii）病毒基因组中的多个交叉点与重组的拷贝选择模型最为一致，并且在其他已记录的HIV-1亚型间重组例子中也有观察到。泰国和中非共和国的“E亚型”病毒表现出相同的A/E镶嵌模式，表明重组事件发生在非洲，在病毒传播到亚洲之前。最后，发现所有“E亚型”病毒在其反式激活应答（TAR）元件中都含有一个独特的两核苷酸凸起。这一特征仅存在于也含有A亚型5' pol区域的病毒中（即A亚型病毒或A/D和A/E重组体），这增加了TAR区域与聚合酶之间存在功能联系的可能性。讨论了重组HIV-1毒株的流行传播对病毒自然史和疫苗开发的影响。
