Genome cloning and sequence analysis of hepatopancreatic parvovirus (HPV) isolated from Fenneropenaeus chinensis in China

Abstract

Hepatopancreatic parvovirus(HPV) is a single-stranded DNA virus.A HPV strain named as HPV-Pc was isolated from infected Fenneropenaeus chinensisin from Tangshan of Hebei Province,China.In this study,full-length genomic sequence of HPV-Pc(GenBank Accession no.GU371276) was determined.It consists of 6 085 nucleotides and contains three open reading frames which encode for non-structural protein(NS1 and NS 2) and nucleocapsid protein(CP).The ORF1,ORF2 and ORF3 encode for proteins of 427,578 and 821 amino acids,whose molecular weight are 50.4 kD,68.2 kD and 92 kD,respectively.No inverted terminal repeat(ITR) was de-tected in 5′ terminal end of the genome.The "R" motif rich in "G" in the region of CP was detected,which may result in cleaving of CP protein.The "GAA" direct repeats were found in the region of CP,which was specific to HPV.Genomes of HPV in different shrimp and from different region were different.All of the acquired fragments were spliced by biological software.Full-length HPV genome shows similarity of 78%-91% with other known HPV genome,and the differences existed throughout its sequence.Comparison analysis between HPV-Pc and other HPV strains submitted to GenBank showed that the HPV-Pc had a larger cp gene and longer genome size.The nucleotide homology of HPV-Pc with AY008257(Korea strain) was the highest.Comparison analysis in NS2,NS1 and CP protein sequence also showed the highest homology existing between HPV-Pc and AY008257.These results suggest that HPV-Pc is a new isolate in Parvoviridae.This is the first nucleotide sequence of F.chinensis.