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RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes

文献类型： 外文期刊

作者： Chen, Guowei 1 ; Jiang, Jingzhe 2 ; Sun, Yanni 1 ;

作者机构： 1.City Univ Hong Kong, Dept Elect Engn, Kowloon, 83 Tat Chee Ave, Hong Kong, Peoples R China

2.Chinese Acad Fishery Sci, South China Sea Fisheries Res Inst, Key Lab South China Sea Fishery Resources Exploita, Minist Agr & Rural Affairs, Guangzhou 510300, Peoples R China

关键词： RNA virus; host prediction; machine learning; metagenomics

期刊名称：GIGASCIENCE （ 影响因子：11.8； 五年影响因子：9.4 ）

ISSN： 2047-217X

年卷期： 2024 年 13 卷

页码：

收录情况： SCI

摘要： Background The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity.Results In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%.Conclusions The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.

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