title: Gill-associated nidovirus of Penaeus monodon prawns transcribes 3'-coterminal subgenomic mRNAs that do not possess 5'-leader sequences.
abstract: Sequence analysis of the approximately 20 kb 5'-terminal portion of the ssRNA genome of gill-associated virus (GAV) of Penaeus monodon prawns has previously established that it contains an ORF1a-1b replicase gene equivalent to those of the coronavirus and arterivirus members of the order Nidovirales. Sequence analysis of the remaining approximately 6.2 kb of the GAV genome downstream of ORF1a-1b to a 3'-poly(A) tail has identified two highly conserved intergenic sequences in which 29/32 nucleotides are conserved. Northern hybridization using probes to the four putative GAV ORFs and either total or poly(A)-selected RNA identified two 3'-coterminal subgenomic (sg) mRNAs of approximately 6 kb and approximately 5.5 kb. Primer extension and 5'-RACE analyses showed that the sgmRNAs initiate at the same 5'-AC positions in the central region of the two conserved intergenic sequences. Neither method provided any evidence that the GAV sgmRNAs are fused to genomic 5'-leader RNA sequences as is the case with vertebrate coronaviruses and arteriviruses. Intracellular double-stranded (ds)RNAs equivalent in size to the 26.2 kb genomic RNA and two sgRNAs were also identified by RNase/DNase digestion of total RNA from GAV-infected prawn tissue. The identification of only two sgmRNAs that initiate at the same position in conserved intergenic sequences and the absence of 5'-genomic leader sequences fused to these sgmRNAs confirms that GAV has few genes and suggests that it utilizes a transcription mechanism possibly similar to the vertebrate toroviruses but distinct from coronaviruses and arteriviruses.
authors.affiliation: Cooperative Research Centre for Aquaculture, CSIRO Livestock Industries, Long Pocket Laboratories, 120 Meiers Road, Indooroopilly 4068, Australia1.
authors.forename: Jeff A
authors.initials: JA
authors.lastname: Cowley
authors.affiliation: Cooperative Research Centre for Aquaculture, CSIRO Livestock Industries, Long Pocket Laboratories, 120 Meiers Road, Indooroopilly 4068, Australia1.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Dimmock
authors.affiliation: Cooperative Research Centre for Aquaculture, CSIRO Livestock Industries, Long Pocket Laboratories, 120 Meiers Road, Indooroopilly 4068, Australia1.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Walker
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D028381:Nidovirales / Q000235:genetics*; D016366:Open Reading Frames; D033561:Penaeidae / Q000821:virology*; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger