A large replicase of nidovirus-like complexity in a putative RNA virus order “Quisvirales” expands the known diversity of helicase superfamilies

Abstract Helicases are essential ATPases that unwind nucleic acids and are classified into six recognized superfamilies (SF1–SF6). All positive-stranded RNA viruses (ssRNA+) with genomes larger than ∼7 kb encode SF1-SF3 helicases, linking them to RNA genome expansion. In the phylum Pisuviricota that includes many pathogens, helicases of SF1-SF3 are integrated into multi-enzyme replicases including 3C(-like) proteases (3CLpro) and RNA-dependent RNA polymerases (RdRp). Here, large-scale mining of invertebrate metastranscriptomes uncovered six related spider-associated ssRNA+ viruses that, based on their conserved 3CLpro–RdRp module, genome size (20–22 kb), and phylogeny, form a putative new order, “Quisvirales” . Quisviruses have similar genome and replicase architectures to enveloped coronaviruses and other nidoviruses. However, the nidovirus SF1 helicase is replaced in quisviruses by a novel superfamily helicase that, like the Picornavirales SF3 helicase, comprises an AAA+ (ATPase-like) domain. Thus, viruses with large replicases of nidovirus-like complexity may have evolved repeatedly from an 3CLpro–RdRp-encoding ancestor.