Complete ORF1b-gene sequence indicates yellow head virus is an invertebrate nidovirus

Abstract

) with potential to form an RNA pseudoknot. The structure resides 3 nt downstream of a ribosomal frame-shift 'slippery' sequence (AAAUUUU) and a -1 frame-shift at this site would extend the ORF1 polyprotein by 2616 amino acids (299322 Da). In ORF1b, YHV shares 88.9% amino acid sequence identity with GAV and includes conserved polymerase, metal ion binding, helicase and other domains (Motifs 1 and 3) characteristic of nidoviruses. Compared to GAV, the YHV non-coding region linking the ORF1b and ORF2 genes contains a 263 nt insertion. However, the region contains a conserved core sequence of 46 nucleotides (84.8% identity) that includes a stretch of 20 identical nucleotides surrounding a sub-genomic RNA transcription termination site. The data confirms the taxonomic placement of YHV in the Nidovirales and supports biological and topographical evidence that YHV and GAV may be classified as distinct species. KEY WORDS: Yellow head · Virus · Nidovirus · Polymerase Resale or republication not permitted without written consent of the publisherDis Aquat Org 50: [87][88][89][90][91][92][93] 2002 Morphologically, YHV closely resembles gill-associated virus (GAV) that infects Penaeus monodon in Australia and causes a disease with histological characteristics similar to yellow head disease (Spann et al. 1997). On the basis of genome organization and expression strategy, GAV has recently been characterized as the first invertebrate member of the Nidovirales -a taxonomic order which also includes the coronaviruses, toroviruses and arteriviruses (Cowley et al. 2000a,b, Enjuanes et al. 2000. As for other nidoviruses, the 5'-end of the (+) single-stranded RNA GAV genome expresses a long polyprotein encoded in 2 different reading frames (ORF1a and ORF1b) that are aligned during translation by a -1 ribosomal frameshift (Cowley et al. 2000b). The ORF1b gene encodes sequence motifs for polymerase, metal ion-binding and helicase domains that are also characteristic of nidoviruses. A limited comparison of short regions of the ORF1b gene has indicated that YHV has significant sequence homology with GAV, suggesting the viruses are closely related and should be regarded as geographic topotypes in the yellow head complex (Cowley et al. 1999, Walker et al. 2001.In this paper, we describe the complete nucleotide and deduced amino acid sequences of the YHV ORF1b gene and a long non-coding region immediately downstream of ORF1b that together represent approximately 30% of the genome. Analysis of the sequence indicates that YHV, although clearly distinct from GAV, also has characteristics consistent with classification in the Nidovirales as a member of a new taxon for which the name Okavirus has been proposed (Cowley et al. 2000b, Enjuanes et al. 2000. MATERIALS AND METHODSYHV was obtained from moribund Penaeus monodon showing signs of yellow head disease that were collected from a farm in Chachoengsao province, Thailand, in July 1998. A gill extract from diseased shrimp was passaged once in P. monodon and a stock inoculum was prepared by d...

Detection and differentiation of yellow head complex viruses using monoclonal antibodies

“…A DIG-labeled DNA probe was prepared by PCR using a plasmid containing a cDNA of the open reading frame (ORF) 1b region of the YHV genome as the template (Sittidilokratna et al 2002), with primers GY1 (5'-GAC ATC ACT CCA GA-3') and GY4 (5'-GTG AAG TCC ATG TGT GTG AGA CG-3') to amplify a 794 bp DNA fragment. Labelling was carried out using DIG-II-dUDP (Roche Molecular Biochemicals) according to instructions in the product manual (Anonymous 1996).…”

The Gene Encoding the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeus monodon Prawns Is Located Upstream of the Glycoprotein Gene

“…The tubular helical nucleocapsids and rod-shaped, enveloped virions of GAV are morphologically identical to those of Yellow head virus (YHV), which has caused mass deaths in P. monodon prawns cultured in Asia, and both viruses cause similar cytopathologies (2,3,20,34,35,36). Sequence similarity levels in the ORF1b gene and the ORF3 glycoprotein gene indicate that GAV and YHV are closely related geographic topotypes (6,16,28).The complete sequencing of the 26,235-nucleotide (nt) RNA genome of GAV has identified five genes ordered 5Ј-ORF1a/ORF1b-ORF2-ORF3-ORF4-(A) n -3Ј (5, 7). YHV also has a long (Ͼ22-kb) (plus-strand) single-stranded RNA genome (24, 36, 43), but sequences have been reported only for the region from the ORF1b gene to the 3Ј poly(A) tail (16,28,29).…”

Immunological-based assays for specific detection of shrimp viruses

“…The entire crop is typically lost within a few days after the appearance of the gross signs of this disease [49] . YHV is a bacilliform, enveloped, (+) single-stranded RNA virus classified in the new virus genus Okavirus, the new family Roniviridae and the order Nidovirales [50][51][52] . There are at least six distinct genetic lineages (genotypes) of YHV, but only YHV type-1 has caused major disease-related losses [53] .…”