Structure-guided taxonomic placement of divergent RNA viruses with ViraClass

Metatranscriptomic sequencing has expanded our knowledge of the RNA virosphere far more rapidly than novel viruses can be taxonomically classified. Taxonomic assignment above the family level is particularly difficult because the RNA-dependent RNA polymerase (RdRp) is often the only gene retained across RNA viruses yet exhibits little sequence similarity among highly divergent viruses. Here we show that RdRp protein structure retains taxonomic signal at evolutionary depths where RdRp primary sequence similarity has largely collapsed, and that the organization of this signal is consistent with the current ICTV hierarchy. Based on this, we developed ViraClass, a hierarchical framework for RNA virus taxonomic placement that uses RdRp structure for rank-by-rank assignment from phylum to genus, stopping at the deepest rank supported by confidence thresholds, and calibrated structural clustering for viruses that remain outside existing reference space. Across random-split, prospective and taxonomic hold-out benchmarks, ViraClass outperforms sequence-based and genome-content baselines. The largest gains emerge at deep evolutionary distances, in benchmarks that withhold entire families, orders or classes from the reference, where sequence-based methods lose most of their signal. In challenging boundary cases such as the Flaviviridae, ViraClass's structure-based placements capture the taxonomic boundary tensions highlighted by recent phylogenetic studies. When applied to a large collection of previously unclassified RdRp sequences, ViraClass places high-confidence queries into existing phyla and organizes the remainder into compact structural groups. ViraClass therefore provides a scalable approach from large-scale virus discovery to hierarchical taxonomic interpretation, particularly at the deep evolutionary ranges that current sequence-based pipelines cannot reach.