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PreprintCited by 162Bacteriophages and microbial interactionsGenomics and Phylogenetic StudiesPlant and Fungal Interactions Research

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Using artificial intelligence to document the hidden RNA virosphere

Open access
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·2023·Cell
DOI 10.1101/2023.04.18.537342

Preprint — published as 10.1016/j.cell.2024.09.027 · Paper page

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Abstract

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 were confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs and hydrothermal vents, and both virus diversity and abundance varied 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.

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Metadata

Authors
Hou, X., He, Y., Fang, P., Mei, S.-Q., Xu, Z., Wu, W.-C., Tian, J.-H., Zhang, S., Zeng, Z.-Y., Gou, Q.-Y., Xin, G.-Y., Le, S.-J., Xia, Y.-Y., Zhou, Y.-L., Hui, F.-M., Pan, Y.-F., Eden, J.-S., Yang, Z.-H., Han, C., Shu, Y.-L., Guo, D., Li, J., Holmes, E. C., Li, Z.-R., & Shi, M.
Affiliations
  • Sun Yat-sen University (CN)
  • Alibaba Group (China) (CN)
  • Wuhan Center for Disease Control and Prevention (CN)
  • The University of Sydney (AU)
  • Guangzhou University (CN)
  • Guangzhou Laboratory (CN)
  • City University of Hong Kong (HK)
Corresponding author
  • Holmes, Edward C
  • Li, Zhao-Rong
ORCID
Venue
Cell
Publisher
openRxiv
Published
2023-04-18
Volume
187
Issue
24
Pages
6929-6942.e16
ISSN
0092-8674 (ISSN-L)
DOI
10.1101/2023.04.18.537342
OpenAlex
W4403245162
Cited by
162
References
1
Citations by year
2026: 55 · 2025: 79 · 2024: 27 · 2023: 1
FWCI
44.07
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • CityU Scholars (submittedVersion, cc-by)
Funders
  • Nvidia
  • National Natural Science Foundation of China (82341118, 32270160)
  • Innovation and Technology Commission
  • Natural Science Foundation of Guangdong Province (2022A1515011854)
  • Innovation and Technology Fund (MRP/071/20X)
  • Medical Research Council
  • National Health and Medical Research Council (2017197)
  • Health and Medical Research Fund (COVID190206)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Immunology and Microbiology › Virology › Plant and Fungal Interactions Research
Keywords
RNA viruses, RNA-dependent RNA polymerase, deep learning, metatranscriptomics, virus discovery, RNA virome, viral diversity, hot springs, hydrothermal vents, airborne viruses
MeSH terms
Deep Learning, Virome, Algorithms, Artificial Intelligence, Phylogeny, RNA-Dependent RNA Polymerase, RNA Viruses, RNA, Viral, Genome, Viral, Hot Springs, Metagenomics, Hydrothermal Vents

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