CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
J Virol. 2021 Jun 24;95(14):e0048421. doi: 10.1128/JVI.00484-21.
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a coevolutionary pattern with their hosts that could be dated back to the Paleozoic era, while in contrast, frog FVs were much more likely acquired from cross-species (class-level) transmission in the Cenozoic era. In addition, we found that three distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, we identified a lineage of endogenous FVs in caecilians that expressed all complete major genes, demonstrating the potential existence of an exogenous form of FV outside of mammals. Our discovery of rare phenomena in amphibian FVs has significantly increased our understanding of the macroevolution of the complex retrovirus. Foamy viruses (FVs) represent, more so than other viruses, the best model of coevolution between a virus and a host. This study represents the largest investigation so far of amphibian FVs and reveals 412 FVs of 6 distinct lineages from three major orders of amphibians. Besides a coevolutionary pattern, cross-species and repeated infections were also observed during the evolution of amphibian FVs. Remarkably, expressed FVs including a potential exogenous form were discovered, suggesting that active FVs might be underestimated in nature. These findings revealed that the multiple origins and complex evolution of amphibian FVs started from the Paleozoic era.
泡沫病毒（Foamy viruses，FVs）是一种复杂的逆转录病毒，能够感染人类和其他动物。在这项研究中，我们通过整合转录组和基因组数据，从两栖动物中发现了 6 个谱系的 412 种 FVs，这显著增加了已知的两栖动物 FV 种类。在这些谱系中，蝾螈 FVs 与其宿主保持着共同进化的模式，可以追溯到古生代，而相比之下，蛙 FVs 更有可能是在新生代从跨物种（类级）传播中获得的。此外，我们发现有 3 个不同的 FV 谱系已经整合到了一种蝾螈的基因组中。出乎意料的是，我们在蚓螈中鉴定出了一种内源性 FV 谱系，它表达了所有完整的主要基因，这表明在哺乳动物之外可能存在外源性 FV 的存在。我们对两栖动物 FV 中罕见现象的发现，极大地提高了我们对复杂逆转录病毒宏观进化的理解。泡沫病毒（FVs）比其他病毒更能代表病毒和宿主之间共同进化的最佳模型。这项研究是迄今为止对两栖动物 FV 最大规模的调查，揭示了来自三大主要两栖动物目 6 个不同谱系的 412 种 FV。除了共同进化模式外，在两栖动物 FV 的进化过程中还观察到了跨物种和重复感染。值得注意的是，我们发现了表达的 FVs，包括一种潜在的外源性形式，这表明活跃的 FVs 在自然界中可能被低估了。这些发现表明，两栖动物 FV 的多起源和复杂进化始于古生代。
