Nucleotide sequence analysis of the VP2-NS-VP3 genes of infectious pancreatic necrosis virus DRT strain

Abstract

The cDNA of the infectious pancreatic necrosis virus (IPNV) DRT strain was synthesized using the reverse transcriptase (RT)-polymerase chain reaction (PCR) and its cDNA nucleotide sequence was determined. The cDNA nucleotide sequence of the segment A was 3,155 base pairs (bp) in length and con tained two overlapping open reading frames (ORFs). The large ORF was 2,916 bp and predicted a polyprotein of a molecular weight of 106,641 daltons, whereas the small ORF was a 444 bp and predicted a protein of a molecular weight of 17,369 in lPNV-DRT. The large ORF contains three genes, VP2-NS-VP3, which make a polyprotein. lPNV-ORT and lPNV-Jasper polyproteins are closely related (99% amino acid homology). Most of the amino acid mismatches are in VP2 sequences, mainly within the area of the serotype-specific epitope. The small ORF overlapped with the N-terminal part of polyprotein. The 3' terminal sequence of the ORT strain is longer by 58 bp and 51 bp, respectively, than those of the Jasper and N 1 strains. The ORT strain segment A sequence may not contain a tetranucleotide sequence (CCCC) at the 3' end. The nucleotide sequence data of the segment A in this paper has been deposited with the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases and has been assigned accession number 026526.