Specific genomic DNA fragment analysis of different geographical clinical samples of shrimp white spot syndrome virus

White spot syndrome (WSS) has been found in many species of shrimp and crabs, not just in Asia but globally. The causative agent is known as white spot syndrome virus (WSSV). In order to clarify the relatedness of WSSV from various geographic regions, we compared the viral DNA of a number of clinical samples of WSSV: (1) China96-116A from Penaeus chinensis, (2) India95-314 from Penaeus monodon, (3) grocery store95-204 and grocery store96-115 from P. monodon possibly originating from Thailand, (4) crayfish97-25 from Orconectes punctimanus collected from the U.S. National Zoo, (5) Thailand95-46 from experimentally infected Penaeus vannamei, (6) South Carolina97-64 from P. vannamei, and (7) Texas95-242 and Texas96-7 from P. vannamei. These specimens were first examined by dot hybridization analysis with nucleic acid probes derived from a WSSV Taiwan isolate. Although the intensity of the hybridization signals varied, and although some specimens of India95-314, crayfish97-25, Texas95-242 and Texas96-7 failed to give a delectable hybridization signal with certain probes, the broad consistency of dot hybridization data suggests that these WSSV clinical samples from different geographical locations are closely related. Following this analysis, all the specimens were examined using 10 virus-specific polymerase chain reactions (PCR). The amplification products were subsequently digested with Cfo I, Hae III, Hpa II and Rsa I restriction endonucleases to determine if there were any DNA fragment polymorphisms in the WSSV clinical samples. The results highlighted the genetic relatedness of all the WSSV clinical samples with the possible exception of a series of Texas viral samples which could be distinguished from the other geographic samples in some of the PCR-based tests.