State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Sun Yat-sen University, Shenzhen, China.
Mol Biol Evol. 2024 Oct 4;41(10). doi: 10.1093/molbev/msae202.
RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.
RNA 病毒表现出广泛的系统发育多样性，会对公共卫生和农业产生重大影响。然而，目前用于从宏基因组数据中发现病毒的生物信息学工具经常产生假阳性的病毒结果，高估病毒多样性，并错误分类病毒序列。此外，目前的工具通常无法确定病毒-宿主的关联，这阻碍了对新发现病毒的潜在威胁的调查。为了解决这些问题，我们开发了 VirID，这是一种专门用于从宏基因组数据中发现和描述 RNA 病毒的软件工具。VirID 的基础是一个全面的 RNA 依赖性 RNA 聚合酶数据库，以增强包括 RNA 病毒发现、系统发育分析和基于系统发育的病毒特征描述在内的工作流程。在模拟数据集上的基准测试表明，VirID 在分析病毒和估计病毒丰富度方面具有很高的准确性。在使用实际样本进行的评估中，VirID 能够识别所有类型的 RNA 病毒，但也能够准确估计病毒的遗传多样性和病毒分类，以及全面了解病毒与人类、动物和植物的关联。因此，VirID 提供了一种强大的病毒发现工具，并成为基础病毒学研究、病原体监测以及传染病爆发的早期预警系统的宝贵资源。
