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J. Virol. doi:10.1128/JVI.01758-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Characterization of White bream virus reveals a novel genetic cluster of nidoviruses

Institutes of Molecular Biology, Infectology, and Diagnostic Virology of the Friedrich-Loeffler-Institut, 17493 Greifswald - Insel Riems, Germany; Centre for Cancer Research and Cell Biology, School of Biomedical Sciences, The Queen's University of Belfast, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom; Institute of Virology and Immunology, University of Würzburg, Versbacher, Strae 7, 97078 Würzburg, Germany

^* To whom correspondence should be addressed. Email: j.ziebuhr{at}qub.ac.uk.

	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, called 1a, 1b, 2, 3, and 4. In WBV-infected cells, three subgenomic RNAs expressing the structural protein 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 (‘3C-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 non-mammalian nidoviruses to better understand the evolution of these largest known RNA viruses.