Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.
Department of Immunology, Nara Medical University, Kashihara, Nara 634-8521, Japan.
Bioinformatics. 2021 Jun 16;37(10):1465-1467. doi: 10.1093/bioinformatics/btaa859.
The possibility that RNA transcripts from clinical samples contain plenty of virus RNAs has not been pursued actively so far. We here developed a new tool for analyzing virus-transcribed mRNAs, not virus copy numbers, in the data of bulk and single-cell RNA-sequencing of human cells. Our pipeline, named VIRTUS (VIRal Transcript Usage Sensor), was able to detect 762 viruses including herpesviruses, retroviruses and even SARS-CoV-2 (COVID-19), and quantify their transcripts in the sequence data. This tool thus enabled simultaneously detecting infected cells, the composition of multiple viruses within the cell, and the endogenous host-gene expression profile of the cell. This bioinformatics method would be instrumental in addressing the possible effects of covertly infecting viruses on certain diseases and developing new treatments to target such viruses.
: VIRTUS is implemented using Common Workflow Language and Docker under a CC-NC license. VIRTUS is freely available at https://github.com/yyoshiaki/VIRTUS.
Supplementary data are available at Bioinformatics online.
迄今为止，人们尚未积极探索临床样本中的 RNA 转录本是否含有大量病毒 RNA。在这里，我们开发了一种新的工具，用于分析人类细胞批量和单细胞 RNA 测序数据中病毒转录的 mRNA，而不是病毒拷贝数。我们的管道名为 VIRTUS（病毒转录物使用传感器），能够检测包括疱疹病毒、逆转录病毒甚至 SARS-CoV-2（COVID-19）在内的 762 种病毒，并对序列数据中的病毒转录本进行定量。因此，该工具能够同时检测感染细胞、细胞内多种病毒的组成以及细胞内的内源性宿主基因表达谱。这种生物信息学方法将有助于解决隐匿性感染病毒对某些疾病的可能影响，并开发针对这些病毒的新治疗方法。
VIRTUS 使用 Common Workflow Language 和 Docker 以 CC-NC 许可证实现。VIRTUS 可在 https://github.com/yyoshiaki/VIRTUS 上免费获得。
补充数据可在生物信息学在线获得。
