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 the longest RNA virus genome (nido-like virus) documented to date, at 47,250 nucleotides. 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 varying substantially among ecosystems. The study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.