Gill-associated virus of Penaeus monodon prawns: an invertebrate virus with ORF1a and ORF1b genes related to arteri- and coronaviruses

A 20089 nucleotide (nt) sequence was determined for the 5' end of the (+)-s sRNA genome of gill-associated virus (GAV), a yellow head-like virus infect ing Penaeus monodon prawns. Clones were generated from a similar to 22 kb d sRNA purified from lymphoid organ total RNA of GAV-infected prawns. The reg ion contains a single gene comprising two long overlapping open reading fra mes, ORF1a and ORF1b, of 4060 and 2646 amino acids, respectively. The ORFs are structurally related to the ORF1a and ORF1ab polyproteins of coronaviru ses and arteriviruses. The 99 nt overlap between ORF1a and ORF1b contains a putative AAAUUUU 'slippery' sequence associated with -1 ribosomal frameshi fting. A 131 nt stem-loop with the potential to form a complex pseudoknot r esides 3 nt downstream of this sequence. Although different to the G/UUUAAA C frameshift sites and 'H-type' pseudoknots of nidoviruses, in vitro transc ription/translation analysis demonstrated that the GAV element also facilit ates read-through of the ORF1a/1b junction. As in coronaviruses, GAV ORF la encodes a 3C-like cysteine protease domain located between two hydrophobic regions. However, its sequence suggests some structural relationship to th e chymotrypsin-like serine proteases of arteriviruses. ORF1b encodes homolo gues of the 'SDD' polymerase, which among (+)-RNA viruses is unique to nido viruses, as well as metal-ion-binding and helicase domains. The presence of a dsRNA replicative intermediate and ORF1a and ORF1ab polyproteins transla ted by a - 1 frameshift suggests that GAV represents the first invertebrate member of the Order Nidovirales.