Papio cynocephalus Endogenous Retrovirus among Old World Monkeys: Evidence for Coevolution and Ancient Cross-Species Transmissions

To study the evolutionary history of Papio cynocephalus endogenous retrovirus (PcEV), we analyzed the distribution and genetic characteristics of PcEV among 17 different species of primates. The viral pol-env and long terminal repeat and untranslated region (LTR-UTR) sequences could be recovered from all Old World species of the papionin tribe, which includes baboons, macaques, geladas, and mangabeys, but not from the New World monkeys and hominoids we tested. The Old World genera Cercopithecus and Miopithecus hosted either a PcEV variant with an incomplete genome or a virus with substantial mismatches in the LTR-UTR. A complete PcEV was found in the genome of Colobus guereza—but not in Colobus badius—with a copy number of 44 to 61 per diploid genome, comparable to that seen in papionins, and with a sequence most closely related to a virus of the papionin tribe. Analysis of evolutionary distances among PcEV sequences for synonymous and nonsynonymous sites indicated that purifying selection was operational during PcEV evolution. Phylogenetic analysis suggested that possibly two subtypes of PcEV entered the germ line of a common ancestor of the papionins and subsequently coevolved with their hosts. One strain of PcEV was apparently transmitted from a papionin ancestor to an ancestor of the central African lowland C. guereza.

为研究黄狒狒内源性逆转录病毒（Papio cynocephalus endogenous retrovirus, PcEV）的进化历史，我们对17种不同灵长类动物中PcEV的分布与遗传特征展开了分析。该病毒的pol-env基因、长末端重复序列与非翻译区（long terminal repeat and untranslated region, LTR-UTR）序列可从狒狒族（papionin tribe）的所有旧世界猴类中获取，此类群涵盖狒狒、猕猴、狮尾狒以及白眉猴；但在我们检测的新世界猴与类人猿中未检测到该序列。旧世界猴属的长尾猴属（Cercopithecus）和小长尾猴属（Miopithecus）中，要么存在基因组不完整的PcEV变体，要么携带LTR-UTR区域存在大量错配的病毒。我们在黑白疣猴（Colobus guereza）的基因组中发现了完整的PcEV，但未在红疣猴（Colobus badius）中检测到该病毒；该病毒在每个二倍体基因组中的拷贝数为44至61，与狒狒族中的拷贝数相当，且其序列与狒狒族病毒的亲缘关系最为密切。通过对PcEV序列同义位点与非同义位点的进化距离进行分析，结果表明纯化选择在PcEV的进化过程中发挥了作用。系统发育分析显示，PcEV可能存在两种亚型，它们先后进入了狒狒族共同祖先的生殖细胞系，并随后与其宿主发生协同进化。有一株PcEV显然是从狒狒族祖先传递给了中非低地黑白疣猴的祖先。