Abstract This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork (Ciconia boyciana) and other was found in the genome of spine-bellied sea snake (Hydrophis hardwickii), designated ERV-Spuma.N-Cbo (where 'N' runs from one to thirteen) and ERV-Spuma.1-Hha, respectively. This discovery of avian and serpentine endogenous FVs adds snakes, and perhaps more crucially, birds to the list of currently known hosts of FVs, in addition to mammals, reptiles, amphibians, and fish. This indicates that FVs are, or at least were, capable of infecting all major lineages of vertebrates. Moreover, together with other FVs, phylogenetic analyses showed that both of them are most closely related to mammalian FVs. Further examination revealed that reptilian FVs form a deep paraphyletic group that is basal to mammalian and avian FVs, suggesting that there were multiple ancient FV cross-class transmissions among their hosts. Evolutionary timescales of various FV lineages were estimated in this study, in particular, the timescales of reptilian FVs and that of the clade of mammalian, avian, and serpentine FVs. This was accomplished by using the recently established time-dependent rate phenomenon models, inferred using mainly the knowledge of the co-speciation history between FVs and mammals. It was found that the estimated timescales matched very well with those of reptiles. Combined with the observed phylogenetic patterns, these results suggested that FVs likely co-speciated with ancient reptilian animals, but later jumped to a protomammal and/or a bird, which ultimately gave rise to mammalian and avian FVs. These results contribute to our understanding of FV emergence, specifically the emergence of mammalian and avian FVs, and provide new insights into how FVs co-evolved with their non-mammalian vertebrate hosts in the distant past.

中文翻译：

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鸟类和蛇形内源性泡沫病毒，以及对泡沫病毒宏观进化史的新见解

摘要 本研究报告并表征了内源性逆转录病毒 (ERV) 形式的两种新型泡沫病毒 (FV) 谱系。在东方鹳 (Ciconia boyciana) 的基因组中发现了几个密切相关的元素，在脊腹海蛇 (Hydrophis hardwickii) 的基因组中发现了其他元素，命名为 ERV-Spuma.N-Cbo（其中“N”从一个至十三）和 ERV-Spuma.1-Hha。除了哺乳动物、爬行动物、两栖动物和鱼类之外，鸟类和蛇纹石内源性 FV 的这一发现将蛇，也许更重要的是，鸟类添加到了目前已知的 FV 宿主列表中。这表明 FV 能够或至少能够感染脊椎动物的所有主要谱系。此外，与其他 FV 一起，系统发育分析表明，它们都与哺乳动物的 FV 最密切相关。进一步的检查表明，爬行动物 FV 形成了一个深层并系群，它是哺乳动物和鸟类 FV 的基础，这表明它们的宿主之间存在多个古老的 FV 跨类传播。本研究估计了各种 FV 谱系的进化时间尺度，特别是爬行动物 FV 和哺乳动物、鸟类和蛇形 FV 进化枝的时间尺度。这是通过使用最近建立的时间相关速率现象模型来完成的，主要使用 FV 和哺乳动物之间的共同物种形成历史的知识来推断。结果发现，估计的时间尺度与爬行动物的时间尺度非常吻合。结合观察到的系统发育模式，这些结果表明 FV 可能与古代爬行动物共同物种，但后来跳到了原始哺乳动物和/或鸟类，最终产生了哺乳动物和鸟类 FV。这些结果有助于我们理解 FV 的出现，特别是哺乳动物和鸟类 FV 的出现，并提供了关于 FV 在遥远的过去如何与其非哺乳动物脊椎动物宿主共同进化的新见解。