Amazing stuff! Apparently, we are surrounded by a lot more viruses than we previously realized.
"Researchers have used artificial intelligence (AI) to uncover 70,500 viruses previously unknown to science, many of them weird and nothing like known species. The RNA viruses were identified using metagenomics, in which scientists sample all the genomes present in the environment without having to culture individual viruses. The method shows the potential of AI to explore the ‘dark matter’ of the RNA virus universe. ...
But RNA viruses evolve quickly, so existing methods for identifying RNA viruses in genomic sequence data probably miss many. A common method is to look for a section of the genome that encodes a key protein used in RNA replication, called RNA-dependent RNA polymerase (RdRp). But if the sequence that encodes this protein in a virus is vastly different from any known sequence, researchers won’t recognize it. ..."
From the highlights and abstract:
"Highlights
• AI-based metagenomic mining greatly expands the diversity of the global RNA virosphere
• Developed a deep learning model that integrates sequence and structural information
• 161,979 putative RNA virus species and 180 RNA virus supergroups were identified
• RNA viruses are ubiquitous and are even found in the most extreme global environments
Summary
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."
Graphical abstract
Figure 1 The global RNA virosphere
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