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White Spot Syndrome Virus, the type species of the virus family Nimaviridae, is a large dsDNA virus infecting shrimp and other crustaceans. Genomic analysis of three completely sequenced WSSV isolates identified two major polymorphic loci, "variable region ORF14/15" and "variable region ORF23/24". Here, we characterize a WSSV isolate originating from shrimp collected in Thailand in 1996 (TH-96-II). This isolate contains the largest WSSV genome ( approximately 312 kb) identified so far, mainly because of its sequences in both major polymorphic loci. Analysis of "variable region ORF14/15" suggests that TH-96-II may be ancestral to the WSSV isolates described to date. A comparison for virulence was made between TH-96-II and WSSV-TH, a well characterized isolate containing the smallest genome ( approximately 293 kb) identified at present. After injection of the isolates into Penaeus monodon the mortality rates showed that the median lethal time (LT50) of TH-96-II was approximately 14 days, compared to 3.5 days for WSSV-TH. When both isolates were mixed in equal amounts and serially passaged in shrimp, WSSV-TH outcompeted TH-96-II within four passages. These data suggest a higher virulence of WSSV-TH compared to TH-96-II. The molecular basis for the difference in virulence remains unclear, but a replication advantage of the 19 kb smaller WSSV-TH genome could play a role.

White spot syndrome virus (WSSV), member of a new virus family called Nimaviridae, is a major scourge in worldwide shrimp cultivation. Geographical isolates of WSSV identified so far are very similar in morphology and proteome, and show little difference in restriction fragment length polymorphism (RFLP) pattern. We have mapped the genomic differences between three completely sequenced WSSV isolates, originating from Thailand (WSSV-TH), China (WSSV-CN) and Taiwan (WSSV-TW). Alignment of the genomic sequences of these geographical isolates revealed an overall nucleotide identity of 99.32%. The major difference among the three isolates is a deletion of approximately 13 kb (WSSV-TH) and 1 kb (WSSV-CN), present in the same genomic region, relative to WSSV-TW. A second difference involves a genetically variable region of about 750 bp. All other variations >2 bp between the three isolates are located in repeat regions along the genome. Except for the homologous regions ( hr1, hr3, hr8 and hr9), these variable repeat regions are almost exclusively located in ORFs, of which the genomic repeat regions in ORF75, ORF94 and ORF125 can be used for PCR based classification of WSSV isolates in epidemiological studies. Furthermore, the comparison identified highly invariable genomic loci, which may be used for reliable monitoring of WSSV infections and for shrimp health certification.