Using artificial intelligence to document the hidden RNA virosphere

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…

• N
  Nvidia
• NN
  National Natural Science Foundation of China

  Awards: 82341118, 32270160
• IA
  Innovation and Technology Commission
• NS
  Natural Science Foundation of Guangdong Province

  Award: 2022A1515011854
• IA
  Innovation and Technology Fund

  Award: MRP/071/20X
• MR
  Medical Research Council
• NH
  National Health and Medical Research Council

  Award: GNT2017197
• HA
  Health and Medical Research Fund