title: Characterization of White bream virus reveals a novel genetic cluster of nidoviruses.
abstract: The order Nidovirales comprises viruses from the families Coronaviridae (genera Coronavirus and Torovirus), Roniviridae (genus Okavirus), and Arteriviridae (genus Arterivirus). In this study, we characterized White bream virus (WBV), a bacilliform plus-strand RNA virus isolated from fish. Analysis of the nucleotide sequence, organization, and expression of the 26.6-kb genome provided conclusive evidence for a phylogenetic relationship between WBV and nidoviruses. The polycistronic genome of WBV contains five open reading frames (ORFs), called ORF1a, -1b, -2, -3, and -4. In WBV-infected cells, three subgenomic RNAs expressing the structural proteins S, M, and N were identified. The subgenomic RNAs were revealed to share a 42-nucleotide, 5' leader sequence that is identical to the 5'-terminal genome sequence. The data suggest that a conserved nonanucleotide sequence, CA(G/A)CACUAC, located downstream of the leader and upstream of the structural protein genes acts as the core transcription-regulating sequence element in WBV. Like other nidoviruses with large genomes (>26 kb), WBV encodes in its ORF1b an extensive set of enzymes, including putative polymerase, helicase, ribose methyltransferase, exoribonuclease, and endoribonuclease activities. ORF1a encodes several membrane domains, a putative ADP-ribose 1"-phosphatase, and a chymotrypsin-like serine protease whose activity was established in this study. Comparative sequence analysis revealed that WBV represents a separate cluster of nidoviruses that significantly diverged from toroviruses and, even more, from coronaviruses, roniviruses, and arteriviruses. The study adds to the amazing diversity of nidoviruses and appeals for a more extensive characterization of nonmammalian nidoviruses to better understand the evolution of these largest known RNA viruses.
authors.affiliation: The Queen's University of Belfast, School of Biomedical Sciences, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom.
authors.forename: Heike
authors.initials: H
authors.lastname: Schütze
authors.forename: Rachel
authors.initials: R
authors.lastname: Ulferts
authors.forename: Barbara
authors.initials: B
authors.lastname: Schelle
authors.forename: Sonja
authors.initials: S
authors.lastname: Bayer
authors.forename: Harald
authors.initials: H
authors.lastname: Granzow
authors.forename: Bernd
authors.initials: B
authors.lastname: Hoffmann
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Mettenleiter
authors.forename: John
authors.initials: J
authors.lastname: Ziebuhr
mesh_terms: D003332:Coronaviridae / Q000145:classification / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000502:physiology*; D028381:Nidovirales / Q000145:classification / Q000235:genetics* / Q000648:ultrastructure; D016366:Open Reading Frames; D012328:RNA Viruses / Q000235:genetics; D012367:RNA, Viral / Q000032:analysis; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase