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

Abstract

A segment of Madagascar hepatopancreatic parvovirus (HPV) genomic sequence (5742 nucleotides) was determined through PCR and direct sequencing. This nucleotide sequence was compared to isolates from Australia, Thailand, Korea, and Tanzania, and the mean distance was determined to be 17%. The Madagascar HPV is closest to the Tanzania isolate (12%), followed by isolates from Korea (15%), Australia (17%) and Thailand (20%). Analysis of the genomic structure revealed that this HPV sequence is comprised of one partial Left open reading frame (ORF) (349 amino acids, aa) and complete Mid (578 aa) and Right (820 aa) ORFs. The amino acid sequences of the 3 ORFs were compared among isolates. The Right ORF was found to have the highest variation with a mean distance of 24%. This was followed by the Left and Mid ORF with distances of 13 and 7%, respectively. A phylogenetic analysis based on the amino acid sequence of the Right ORF divides 7 HPV isolates into 3 well-separated groups: Korea, Thailand, and Australia. The Madagascar HPV clustered with the Korea and Tanzania isolates. In Madagascar, HPV has been detected by histological examination since the 1990s. PCR analysis of a recent (2007) sampling showed a 100% prevalence. HPV was also detected in Mozambique with a 100% prevalence. High (95%) prevalence of HPV was found in wild Penaeus merguinesis collected from New Caledonia. These results indicate that HPV displays a high degree of genetic diversity and is distributed worldwide among populations of penaeid shrimp.

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

“…These samples were collected from 1991 to 2009 and stored at -70°C in the Aquaculture Pathology Lab at the University of Arizona, Tucson, USA. They were determined to be positive for MBV and/or HPV by the conventional PCR using specific primers: MBV261F (5'-AAT CCT AGG CGA TCT TAC CA-3'), MBV261R (5'-CGT TCG TTG ATG AAC ATC TC-3'), HPV-2F (5'-GGA AGC CTG TGT TCC TGA CT-3'), HPV-2R (5'-CGT CTC CGG ATT GCT CTG AT-3') (Surachetpong et al 2005, Tang et al 2008. Among these, Penaeus monodon samples collected from Malaysia, Indonesia and Thailand were also used for quantification of viral load with the duplex real-time PCR assay.…”

“…HPV can infect 11 species of penaeid shrimps (OIE Aquatic Animal Disease Cards 2007) over a wide geographic distribution. HPV is highly prevalent in some areas, it has been found in nearly 100% of the populations of wild P. monodon in Africa and also in the wild stock of P. merguiensis in New Caledonia (Tang et al 2008). In India, the prevalence of HPV was found in 46% of the wild populations (Manjanaik et al 2005).…”

Complete nucleotide sequence analysis of a Korean strain of hepatopancreatic parvovirus (HPV) from Fenneropenaeus chinensis

“…2). In the previous report, HPV strains were grouped into three genotypes based on the amino acid sequence of the VP: genotype I from Korea, Tanzania, and Madagascar, genotype II from Thailand and Indonesia, and genotype III from Australia and New Caledonia [21]. This was further confirmed in the phylogenetic tree constructed using the NS1 protein sequence, which showed the same clustering as VP (Fig.…”

“…Additionally, incomplete or partial genomic sequences are available for other strains including HPV isolated from F. chinensis in Korea and China (AY008257, GU371276). Phylogenetic analysis results based on the amino acid sequence of the right open reading frame (ORF) from seven isolates suggest that three HPV genotypes exist: type I (Korea, Madagascar, Tanzania), type II (Thailand, Indonesia), and type III (Australia, New Caledonia) [21].…”

Immunological-based assays for specific detection of shrimp viruses

“…Two Asian types of PmDNV have been characterized at the molecular level. One type has been identified in P. chinensis from South Korea [77] , P. monodon from Madagascar, Mozambique and Tanzania and P. merguiensis from New Caledonia [79] and Australia [80] . The other type has been identified Chaivisuthangkura P et al .…”