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

Abstract

Hepatopancreatic parvovirus (HPV) of shrimp is distributed worldwide and the entire genome of Thailand and Indian strains (PmDNV) and one Australian strain (PmergDNV) have now been reported. The complete nucleotide sequence of a HPV strain isolated from the fleshy prawn Fenneropenaeus chinensis in Korea (FcDNV) was determined and compared to previously reported sequences. The entire genome of FcDNV contains 6,336 nucleotides, with 40% G+C content, which is the biggest of the known HPV strains. The HPV genome has three open reading frames (ORFs) with a slight overlap between the first and second ORFs. The three ORFs encode the NS2 and NS1 proteins and VP that consist of 425, 578, and 820 amino acids, respectively. Among the three proteins, the NS1 protein shows the highest sequence similarity to the NS1 protein of other known HPV strains, followed by the NS2 protein and the VP protein. Phylogenetic analyses showed that HPV can be grouped into three genotypes, as previously reported, and FcDNV can be grouped as genotype I, with HPV strains isolated in Madagascar and Tanzania. The nucleotide sequences of the noncoding regions at the 5'- and 3'-ends of the plus-strand genome showed a Y-shaped hairpin structure and simple hairpin structure, respectively.

Biology, Genome Organization, and Evolution of Parvoviruses in Marine Shrimp

“…A closer look of the HPV clade shows the different isolates arranged in four subclusters as opposed to the three previously suggested ( Jeeva et al, 2012;Tang et al, 2008). Previously described Genotypes II and III can be clearly identified; however, Genotype I is formed by the Tanzania and Madagascar HPV isolates excluding the Korean isolate (Fig.…”

“…PmDNV-India showed 33, 32, and 91 amino acid substitutions compared to the PmDNV-Thailand in the NS2, NS1, and VP, respectively (Safeena et al, 2010). The NS1 protein showed highest homology to other reported HPV strains followed by the NS2 protein and the VP protein ( Jeeva et al, 2012). For example, the NS2 of PmergDNV is 255 bases and 261 bases shorter than the homologous genes of the Indian and Thai isolates of PmDNV, respectively (La Fauce, Elliman, et al, 2007;La Fauce, Layton, & Owens, 2007;Safeena et al, 2010).…”

“…Phylogenetic clustering suggests the existence of three distinct HPV genotypes ( Jeeva et al, 2012;Tang et al, 2008). Phylogenetic clustering suggests the existence of three distinct HPV genotypes ( Jeeva et al, 2012;Tang et al, 2008).…”

“…Recently, the genomic sequences from isolates of an Australian (PmergDNV; La Fauce, Elliman, & Owens, 2007), an Indian (PmDNV-India; Safeena et al, 2010), and a Korean (PmDNV-Korea; Jeeva et al, 2012) strain of HPV have been reported. The PmDNV-India has ORFs coding 426, 577, and 819 amino acids, respectively and shows closest homology at the nucleotide level (88%) with PmDNV-Thailand.…”

“…The sequence analysis of HPV isolates from different geographic areas have shown consistently and relatively high levels of sequence similarities at the amino acid and nucleotide levels of the HPV genome ( Jeeva et al, 2012;La Fauce, Elliman, et al, 2007;Safeena et al, 2010). The highest level of sequence similarity has been found in the amino acid sequence of ORF2 that codes for the NS1 (97.1-99.8%) ( Jeeva et al, 2012).…”