Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings

Zhang, Qingshui; Cao, Yanxin; Wang, Jun; Fu, Guanghua; Sun, Mengxu; Zhang, Lijiao; Meng, Li; Cui, Guolin; Huang, Yu; Hu, Xueying; Su, Jingliang

The complete genome of the SD01 was identified by sequencing of the RT-PCR products and was submitted to the GenBank database under accession number MF772821. The genome was 7175 nucleotides (nt) in length with similar gene organization to other known avastroviruses, consisting of a 5′-UTR of 10 nt, three sequential ORFs (ORF1a, ORF1b and ORF2), a 3′-UTR of 236 nt and a poly (A) tail stretching 30 nt (Fig. 4a) . ORF1a of the isolate was 3255 nt long, encoding a polypeptide of 1084 amino acids (aa) with 27.9-59.5% identity to corresponding regions of other known avian AstVs as determined by BLAST analysis ( Table 1 ). The predicted nonstructural protein contained a trypsin-like peptidase domain as revealed by Pfam analysis with a serine protease motif at position 672 (GNSG), a nuclear localization signal motif at position 773 (KKKGKTK), and four predicted transmembrane domains. As is the case with other known avian AstVs, there was an overlapping region between ORF1a and ORF1b (3247-3265 nt), which contains the highly conserved ribosome frameshift sequence (5′-AAAAAAC-3′) and a downstream hairpin structure (3270-3295 nt) as predicted by RNA folding analysis. ORF1b was 1560 nt long and was predicted to encode a RNA-dependent RNA polymerase. There was an 18 nt spacer between the stop codon of ORF1b and the start codon of ORF2. ORF2 was 2133 nt long encoding a capsid protein of 704 aa. A stem-loop-II-like (s2m) motif consisting of 43 nt was revealed adjacent to 10 nt of ORF2 in the 3′-UTR by Rfam analysis.