Harding Emma F, Russo Alice G, Yan Grace J H, Waters Paul D, White Peter A
School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia.
Virus Evol. 2021 Sep 2;7(2):veab076. doi: 10.1093/ve/veab076. eCollection 2021.
Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed 'endogenous viral elements' (EVEs), could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing data sets ( = 35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either , or EVEs. The other twelve transcripts were from putative active infections from members of the and , and . EVE transcripts ( = 188) were mapped to marsupial genomes (where available, = 5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum, and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts = 71). Every marsupial has , and EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American-Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence data sets, we detected replicase and nucleoprotein produced small RNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.
与有胎盘哺乳动物的病毒相比，有袋类动物的病毒研究较少，尽管它们可能对脆弱的有袋类动物种群构成严重威胁。基因组病毒整合，即所谓的“内源性病毒元件”（EVE），可以保护宿主免受感染。众所周知，过去的病毒感染和EVE在无脊椎动物和植物的抗病毒防御中发挥着积极作用。本研究旨在表征澳大利亚有袋类物种中活跃转录的EVE，因为它们可能在细胞对病毒的防御中发挥不可或缺的作用。本研究筛选了公开可用的RNA测序数据集（n = 35），并对来自13种澳大利亚有袋类物种的200个病毒转录本进行了表征。在这200个转录本中，188个起源于逆转录病毒、乳头瘤病毒或多瘤病毒EVE。另外12个转录本来自γ逆转录病毒、星状病毒和圆环病毒成员的推定活跃感染。将EVE转录本（n = 188）映射到有袋类动物基因组（如有可用数据，n = 5/13）以确定基因组插入位点。在188个转录本中，117个映射到考拉、裸鼻袋熊、袋狸、帚尾袋貂和袋獾基因组内的39个EVE。其余8种动物没有可用的基因组（转录本n = 71）。每种有袋类动物都有逆转录病毒、乳头瘤病毒和多瘤病毒EVE，这是在有胎盘哺乳动物中广泛观察到的一种趋势。虽然有胎盘哺乳动物的博尔纳病毒EVE主要来源于核蛋白，但有袋类动物的博尔纳病毒EVE表现出惊人的复制酶基因偏向性。我们预测这些广泛分布的EVE在古代种系整合后在有袋类动物中是保守的，因为其中许多超过6500万年历史。一个存在于6个有袋类动物基因组中的博尔纳病毒复制酶EVE估计有1.6亿年历史，早于美洲-澳大利亚有袋类动物的分化。我们认为这些EVE通过小非编码RNA的转录是一种古老的病毒防御机制。与此一致的是，在考拉小RNA序列数据集中，我们检测到复制酶和核蛋白产生的小RNA。这些在睾丸组织中富集，表明它们可以保护有袋类动物免受垂直传播的病毒整合。
