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Abstract:

Metatranscriptome mining has dramatically expanded the known diversity of riboviruses at all taxonomic levels. We explored in detail the class Stelpaviricetes in the phylum Pisuviricota that so far included two recognized virus families, Astroviridae infecting vertebrates, and Potyviridae, the largest known family of plant viruses. Using a class-specific collection of Hidden Markov Model profiles for the RNA-dependent RNA polymerase (RdRP), the hallmark protein of riboviruses, we identified 331 family-level clades extrapolated to comprise the great majority of families within Stelpaviricetes. All these putative families except for two share a uniform, astrovirus-like genome architecture, encoding three recognizable protein domains, the RdRP, a chymotrypsin-like protease and a single jelly roll capsid protein. The remaining two (putative) families, Potyviridae and their sister group, possess two additional domains, a papain-like protease and a superfamily 2 helicase, whereas the capsid protein is replaced with an unrelated one forming filamentous capsids. The topology of the phylogenetic tree of the RdRP implies that the common ancestor of Stelpaviricetes was an astro-like virus, with major innovations occurring at the base of the potyvirus-like clade. For the vast majority of riboviruses identified in metatranscriptomes, host assignment remains elusive. Nevertheless, analysis of Endogenous Virus Elements combined with information on isolated viruses provides some clues, in particular, suggesting that the common ancestor of the potyvirus-like viruses had a fungal host.