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

被引:53
作者
Sittidilokratna, N
Hodgson, RAJ
Cowley, JA
Jitrapakdee, S
Boonsaeng, V
Panyim, S
Walker, PJ
机构
[1] CSIRO, Livestock Ind, Indooroopilly, Qld 4068, Australia
[2] Mahidol Univ, Fac Sci, Dept Biochem & CENTEX Shrimp, Bangkok 10400, Thailand
关键词
yellow head; virus; nidovirus; polymerase;
D O I
10.3354/dao050087
中图分类号
S9 [水产、渔业];
学科分类号
0908 ;
摘要
We report the sequence of an 8503 nucleotide (nt) region of the genome of yellow head virus (YHV) encompassing the open reading frame (ORF) 1b gene. Comparison with the sequence of Australian gill-associated virus (GAV) indicated that the region, comprising similar to30% of the YHV genome, commences 268 nt upstream of the putative ORF1a termination codon and continues through ORF1b to a site 30 nt downstream of the ORF2 initiation codon. YHV ORF1a and ORF1b overlap by 37 nt. MFOLD analysis of the overlap and downstream region predicted a 131 nt folding structure (DeltaG = -47.3 kcal mol(-1)) 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.
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收藏
页码:87 / 93
页数:7
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