Complete nucleotide sequence and genomic organization of hepatopancreatic parvovirus (HPV) of Penaeus monodon

Abstract

We have determined the genome of hepatopancreatic parvovirus (HPV), a minus, single-stranded DNA virus isolated from infected Penaeus monodon in Thailand. Its genome consisted of 6321 nucleotides, representing three large open reading frames (ORFs) and two non-coding termini. The left (ORF1), mid (ORF2), and right (ORF3) ORFs on the complementary (plus) strand may code for 428, 579, and 818 amino acids, equivalent to 50, 68, and 92 kDa, respectively. The 5' and 3' ends of viral genome contained hairpin-like structure length of approximately 222 and 215 bp, respectively. No inverted terminal repeat (ITR) was detected. The ORF2 contained conserved replication initiator motif, NTP-binding and helicase domain similar to NS-1 of other parvoviruses. Therefore, it most likely encoded the major nonstructural protein (NS-1). The ORF1 encoded putative nonstructural protein-2 (NS-2) with unknown function. The ORF3 of the HPV genome encoded a capsid protein (VP) of approximately 92 kDa. This may be later cleaved after arginine residue to produce a 57-kDa structural protein. A phylogenetic tree based on conserved amino acid sequences (119 aa) revealed that it is closely related to Brevidensoviruses, which are shrimp parvovirus (IHHNV) and mosquito densoviruses (AaeDNV and AalDNV). However, the overall genomic organization and genome size of HPV were different from these parvoviruses, for instance, the non-overlapping of NS1 and NS2, the larger VP gene, and the bigger genome size. This suggested that this HPV virus is a new type in Parvoviridae family. We therefore propose to rename this virus P. monodon densovirus (PmDNV).

Duplex real-time PCR for detection and quantification of monodon baculovirus (MBV) and hepatopancreatic parvovirus (HPV) in Penaeus monodon

“…The results showed that they were 95% identical to the published Thai sequence (Sukhumsirichart et al 2006). When comparing with the sequence of HPVth primers/probe binding sites, there are 3 mismatched nucleotides (all adenine to guanine nucleotide changes) locating at nucleotide position 12 of the forward primer and nucleotide positions 11 and 29 in the probe-binding region.…”

“…MBV is a large (270 × 72 nm), rod-shaped, enveloped baculovirus with a genome size estimated to be between 80 and 160 kb (Mari et al 1993). However, HPV is a small (22 nm), icosahedral parvovirus that contains a single-stranded DNA genome of ~6 kb (Bonami et al 1995, Sukhumsirichart et al 2006, La Fauce et al 2007a). …”

Nucleotide sequence of a Madagascar hepatopancreatic parvovirus (HPV) and comparison of genetic variation among geographic isolates

“…6 kb with a hairpin structure at both 5' and 3' ends , Sukhumsirichart et al 2006, La Fauce et al 2007). Based on morphological and biochemical characteristics, HPV is taxonomically placed within the family Parvoviridae .…”

“…The Mid ORF could encode a non-structural protein 1 (NS1) with a length of 579 aa (or 578 aa by La Fauce et al 2007). The Right ORF starts 424 nucleotides (nt) downstream from the Mid ORF and may encode a 820 aa polypeptide that consists of a viral capsid protein (Sukhumsirichart et al 2006). One major (57 kDa) and 2 minor (92 and 54 kDa) structural proteins were detected in the viral preparation, indicating a post-translational modification for genesis of the viral capsid protein.…”

Immunological-based assays for specific detection of shrimp viruses

“…The complete genome of PmDNV isolated from infected P. monodon in Thailand consists of 6321 nucleotides, representing three ORFs and two non-coding termini. ORF3 encodes a capsid protein of approximately 92 kDa, which may later be cleaved after the first or second arginine residue to produce a 57 kDa or 54 kDa structural protein, respectively [82] . MAbs raised against purified PmDNV isolated from Thailand have been produced, four of which react with a 54 kDa protein by Western blotting and to intranuclear inclusion bodies in tubule epithelial cells in PmDNVinfected tissue by immunohistochemistry [83] .…”