Sadiq Sabrina, Holmes Edward C, Mahar Jackie E
Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Laboratory of Data Discovery for Health Limited, Hong Kong, SAR, China.
Virus Evol. 2024 Apr 22;10(1):veae033. doi: 10.1093/ve/veae033. eCollection 2024.
The RNA virus family has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing genera that we tentatively name 'Alpha-', 'Beta-', 'Gamma-', 'Delta-', 'Epsilon-', 'Zeta-', and 'Etapicobirnavirus'. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in genomes than in the two groups of established RNA bacteriophage-the and . Overall, our findings support the hypothesis that the have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.
RNA病毒家族传统上与陆地哺乳动物和鸟类的胃肠道系统相关联,大多数病毒是在动物粪便样本中检测到的。对脊椎动物、无脊椎动物、微生物群落和环境样本的宏转录组学研究极大地扩展了该病毒家族的基因组和系统发育多样性。然而,微小双股RNA病毒的分类仍然很差,只有一个属和三个种得到了国际病毒分类委员会的正式认可。此外,由于无法在实验室环境中培养微小双股RNA病毒或在动物组织样本中分离它们,再加上其基因组中存在细菌遗传基序,这表明这些病毒可能代表RNA噬菌体,而不是与动物感染有关。利用一个包含2286种来自哺乳动物、鸟类、爬行动物、鱼类、无脊椎动物、微生物群落和环境样本的微小双股RNA病毒数据集,我们确定了七个一致的系统发育簇,可能代表我们暂定命名为“α-”、“β-”、“γ-”、“δ-”、“ε-”、“ζ-”和“埃塔微小双股RNA病毒”的属。对病毒-宿主系统发育之间拓扑一致性的统计分析表明,与任何其他RNA病毒家族相比,跨物种传播更为频繁。此外,细菌核糖体结合位点基序在该病毒家族的基因组中比在两组已确定的RNA噬菌体(即 和 )中更为丰富。总体而言,我们的研究结果支持了该病毒家族以细菌为宿主的假设,并为这个高度多样化和普遍存在的RNA病毒家族提供了一个较低级别的分类。
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