Microarray Analysis Of Genomic Variations Of White Spot Syndrome Virus In Different Years

White spot syndrome virus (WSSV) is the heaviest pathogen to shrimp culture, causing catastrophic economic losses in cultured penaeid shrimp worldwide. Prevention and inhibition of WSSV can be difficult due to its extremely virulence and a wide host range including most of aquatic crustacean and targets various tissues. The pertinent study for import genes may be the most important for WSSV study. To obtain variety information of gene transcription, we collectd the WSSV isolates in 1996,1998,2000 and 2002 respectively, and studied the transcriptional profile of WSSV with DNA microarray.With the capability and availability of the entire sequence of WSSV genome, 190 primer pairs were synthesized to amplify each potential WSSV ORF. So PCR products by using the complete set of primer pairs were expected to cover the entire WSSV genome. The PCR amplified products were spotted onto the nylon membrane to generate arrays using SpotBot Personal Microarrayer system. WSSV-free crayfishes were infected with the virus inoculum prepared from four WSSV isolates prepared in 1996, 1998, 2000 and 2002, respectively. mRNA and genomic DNA of WSSV were isolated and labeled with Bio-11-dUTP and DIG-11-dUTP respectively. Each labeled probe was hybridized to a microarray. The results indicated the majority of the genes were expressed. Genetic analysis revealed that the 1996 WSSV isolate has full length genomic DNA, the 1998 and 2000 WSSV isolates having the deletion in wsv493 and wsv495, and the 2002 WSSV isolate additionally has the deletion in wsv479, wsv482 and wsv489. Reverse transcription-polymerase chain reaction (RT-PCR) and PCR was performed to validate the microarray results. The results confirm the exact position of the unstable region in WSSV and indicate that WSSV in China is in a phase of time-dependent genetic evolution with a deletion pattern.