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.