Complete nucleotide sequence analysis of a white spot syndrome virus (WSSV) isolate from Pacific white shrimp

Abstract

White spot syndrome virus (WSSV) is the cause of white spot syndrome disease in cultured shrimps worldwide. This study has determined the fourth complete genome sequence of WSSV from Pacific white shrimp (Litopenaeus vannamei). WSSV Korean strain (WSSV-KR) has a double-stranded circular DNA genome of 295,884 bp encompasses 515 open reading frames (ORFs). 271 ORFs are forwardly transcribed (53%) and 244 ORFs are reversely transcribed (47%). WSSV Korean strain has a total G + C content of 41%. Homology searches were performed with BLAST program and 90 of the ORFs showed no homology to any known proteins. The rest of the ORFs, 425 ORFs are likely to encode functional proteins. The WSSV ORFs may encode enzymes for nucleic acid metabolism, DNA replication and transcription and several major structural virion proteins. The unique features of WSSV are the presence of an intact collagen gene and a very long ORF of 18,222 nucleotides, with unknown function. Linear and dotplot comparison of WSSV Korean strain to other WSSV isolates showed little variation. WSSV Korean strain contains most of the major WSSV structural virion proteins but lack of a nucleocapsid protein, vp35. Determination of the whole genome of WSSV will facilitate better understanding of the molecular mechanism of WSSV pathology and also provide useful information concerning variation of WSSV isolate from this study with other WSSV isolates.