Abstract Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

中文翻译：

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感染动物的分段RNA病毒的新谱系

摘要 宏基因组测序彻底改变了我们对病毒多样性的认识，新病毒序列的报道速度比以往任何时候都快。然而，从宏基因组测序中发现病毒通常取决于可检测的同源性：如果没有足够近的亲属，所谓的“暗”病毒序列仍然无法识别。另一种方法是使用不依赖检测同源性的病毒识别方法，例如通过宿主抗病毒免疫来识别病毒。例如，病毒衍生的小 RNA 以前曾被用于提出与果蝇科（双翅目）相关的“暗”病毒序列。这里，我们将已发表的果蝇数据与对转录组序列和选定的元转录组数据集的全面搜索相结合，以确定一个全新的分段正链单链 RNA 病毒谱系，我们暂时将其称为昆雅病毒。这五个片段中的每一个都包含一个开放阅读框，大多数编码蛋白与特征病毒没有可检测到的相似性，一个与单链和双链 RNA 病毒的 RNA 依赖性 RNA 聚合酶共享少量残基。使用这些序列，我们确定了大约 20 种节肢动物的近亲，包括昆虫、甲壳类动物、蜘蛛和多足类动物。使用来自假定聚合酶的更保守的序列，我们进一步鉴定了来自肠道、鳃、脊椎动物的肺组织，反映脊椎动物或其相关寄生虫的感染。我们的数据说明了小 RNA 在检测序列保守性有限的病毒方面的效用，并为新的深度分歧和系统发育不同的 RNA 病毒谱系提供了有力的证据。