Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia.
Viruses. 2020 Jun 4;12(6):613. doi: 10.3390/v12060613.
The discovery of highly divergent RNA viruses is compromised by their limited sequence similarity to known viruses. Evolutionary information obtained from protein structural modelling offers a powerful approach to detect distantly related viruses based on the conservation of tertiary structures in key proteins such as the RNA-dependent RNA polymerase (RdRp). We utilised a template-based approach for protein structure prediction from amino acid sequences to identify distant evolutionary relationships among viruses detected in meta-transcriptomic sequencing data from Australian wildlife. The best predicted protein structural model was compared with the results of similarity searches against protein databases. Using this combination of meta-transcriptomics and protein structure prediction we identified the (PB1) gene segment of a divergent negative-sense RNA virus, denoted (LTAV), in a native Australian gecko (). The presence of this virus was confirmed by PCR and Sanger sequencing. Phylogenetic analysis revealed that likely represents a newly described genus within the family order , that is most closely related to the fish virus (TiLV). These findings provide important insights into the evolution of negative-sense RNA viruses and structural conservation of the viral replicase among members of the order .
高度分化的 RNA 病毒的发现受到其与已知病毒有限的序列相似性的限制。从蛋白质结构建模中获得的进化信息提供了一种强大的方法，可以基于关键蛋白质（如 RNA 依赖性 RNA 聚合酶（RdRp））的三级结构保守性来检测远距离相关的病毒。我们利用基于模板的方法从氨基酸序列预测蛋白质结构，以确定从澳大利亚野生动物的元转录组测序数据中检测到的病毒之间的远缘进化关系。将最佳预测的蛋白质结构模型与针对蛋白质数据库的相似性搜索结果进行比较。通过这种元转录组学和蛋白质结构预测的组合，我们在一种澳大利亚原生壁虎（）中鉴定出了一种分化的负义 RNA 病毒的 PB1 基因片段，命名为 （LTAV）。通过 PCR 和 Sanger 测序证实了该病毒的存在。系统发育分析表明， 可能代表了家族 目 中的一个新描述的属，与鱼类病毒 （TiLV）最为密切相关。这些发现为负义 RNA 病毒的进化以及该目中病毒复制酶的结构保守性提供了重要的见解。
