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What is JoVE Visualize?

Using artificial intelligence to document the hidden RNA virosphere

Affiliations
  • 1National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
  • 2Apsara Lab, Alibaba Cloud Intelligence, Alibaba Group, Hangzhou, China.
  • 3Wuhan Centers for Disease Control and Prevention, Wuhan, China.
  • 4Polar Research Institute of China, Shanghai, China.
  • 5Department of Nursing, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
  • 6School of Geospatial Engineering and Science, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai, China; Key Laboratory of Comprehensive Observation of Polar Environment, Ministry of Education, Sun Yat-sen University, Zhuhai, China.
  • 7Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University Shanghai, Shanghai, China.
  • 8Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW, Australia; School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
  • 9College of Life Sciences, Zhejiang University, Hangzhou, China.
  • 10School of Life Science, Guangzhou University, Guangzhou, China.
  • 11Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
  • 12Guangzhou National Laboratory, Guangzhou International Bio-Island, Guangzhou, China.
  • 13Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China.
  • 14School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China. Electronic address: edward.holmes@sydney.edu.au.
  • 15Apsara Lab, Alibaba Cloud Intelligence, Alibaba Group, Hangzhou, China. Electronic address: zhaorong.lzr@alibaba-inc.com.

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October 10, 2024

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 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.

Keywords:

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