Charting Viral Dark Matter: Discovery, Classification, and Ecology of Uncultured Viruses

Metagenomic and long-read sequencing are revealing extensive viral diversity that remains uncultured, poorly classified, or absent from reference databases. This expanding “viral dark matter” includes highly divergent RNA and DNA viruses from animal, human, and environmental systems and is reshaping understanding of viral evolution, host range, and ecosystem function. Recent studies have developed improved assembly, binning, genome-rescue, and taxonomic approaches, while virome surveys have identified novel lineages in gut, oral, and environmental samples. However, sequence discovery alone rarely establishes host association, replication competence, pathogenic potential, or ecological role. The interpretation of highly divergent genomes is further complicated by incomplete databases, contamination, endogenous viral elements, and uncertainty in genome annotation. Research that links discovery with classification, validation, host inference, and ecological interpretation is therefore needed to move beyond cataloguing novelty.This Research Topic aims to advance the discovery, classification, and ecological interpretation of uncultured and poorly characterised viruses in non-plant systems. It will prioritise studies that improve confidence in viral genome identification and provide evidence about host range, evolutionary relationships, biological activity, or ecosystem relevance.To gather further insights in animal, human, and environmental virome discovery, we welcome articles addressing, but not limited to, the following themes:o Metagenomic discovery of novel RNA and DNA viruseso Viral dark matter in animal, human, gut, oral, and environmental sampleso Taxonomic and phylogenetic frameworks for divergent viral lineageso Long-read sequencing, assembly, binning, and genome-rescue methodso Host-range and host-association inferenceo Ecological roles of newly discovered viruseso Methods for detecting, annotating, and validating uncultured viral genomeso Comparative analyses of virome diversity across environments and host communities Topic editors: Matías Castells, María José Benítez-Galeano Source: https://www.frontiersin.org/research-topics/86323/charting-viral-dark-matter-discovery-classification-and-ecology-of-uncultured-viruses