Using artificial intelligence to document the hidden RNA virosphere.
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| Autori principali: | , , , , , , , , , , , , , , , , , , , , , , , , |
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| Natura: | Artículo científico |
| Lingua: | en |
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Cell
2024
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| _version_ | 1868266292651229185 |
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| author | Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang |
| author_facet | Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang |
| collection | PubMed - marine biology |
| contents | Using artificial intelligence to document the hidden RNA virosphere. Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang RNA Viruses RNA-Dependent RNA Polymerase RNA, Viral Genome, Viral Artificial Intelligence Virome Phylogeny Metagenomics Algorithms Deep Learning Hot Springs Hydrothermal Vents Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome. |
| format | Artículo científico |
| id | pubmed_39389057 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | Cell |
| record_format | pubmed |
| spellingShingle | Using artificial intelligence to document the hidden RNA virosphere. Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang RNA Viruses RNA-Dependent RNA Polymerase RNA, Viral Genome, Viral Artificial Intelligence Virome Phylogeny Metagenomics Algorithms Deep Learning Hot Springs Hydrothermal Vents Using artificial intelligence to document the hidden RNA virosphere. Hou, Xin He, Yong Fang, Pan Mei, Shi-Qiang Xu, Zan Wu, Wei-Chen Tian, Jun-Hua Zhang, Shun Zeng, Zhen-Yu Gou, Qin-Yu Xin, Gen-Yang Le, Shi-Jia Xia, Yin-Yue Zhou, Yu-Lan Hui, Feng-Ming Pan, Yuan-Fei Eden, John-Sebastian Yang, Zhao-Hui Han, Chong Shu, Yue-Long Guo, Deyin Li, Jun Holmes, Edward C Li, Zhao-Rong Shi, Mang RNA Viruses RNA-Dependent RNA Polymerase RNA, Viral Genome, Viral Artificial Intelligence Virome Phylogeny Metagenomics Algorithms Deep Learning Hot Springs Hydrothermal Vents Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome. |
| title | Using artificial intelligence to document the hidden RNA virosphere. |
| topic | RNA Viruses RNA-Dependent RNA Polymerase RNA, Viral Genome, Viral Artificial Intelligence Virome Phylogeny Metagenomics Algorithms Deep Learning Hot Springs Hydrothermal Vents |
| url | https://pubmed.ncbi.nlm.nih.gov/39389057/ |