[Comparative analysis of variable region of white spot syndrome virus genome in Penaeus vannamei in Guangxi, China].

Comparative analysis of variable region ORF14/15 genes of white spot syndrome virus (WSSV) genome in Guangxi Penaeus vannamei (P. vannamei) could provide useful information for the evaluation of genetic diversity and genetic evolutionary relationship among WSSV isolates from Guangxi, China and other places. Based on geographical and temporal considerations, 40 WSSV-positive P. vannamei samples were collected during the period between May 2010 and July 2013 from Beihai, Qinzhou, and Fangchenggang, which were the main P. vannamei production areas in Guangxi, and the variable region ORF14/15 genes of the WSSV genome from all infected samples were amplified by PCR and then subjected to cloning and sequence analysis. Pairwise and multiple alignment analysis was then conducted to evaluate the degree of genetic divergence between different strains. The variable region ORF14/15 genes from 25 of 40 WSSV positive samples were successfully cloned and sequenced; among the ORF14/15 genes of 25 WSSV-positive strains, 22 was 619 bp in length and 3 was 620 bp. All the 25 Guangxi strains carried a 5949-bp deletion in the ORF14/15 region relative to TH-96-II, which has the longest nucleotide sequence in this region; the deletion of Guangxi strains occurred in the middle region of ORF14/15 gene, with only 190 bp and 429 bp/ 430 bp at 5' and 3' ends, respectively, which were coincident with WSSV-IN-05-I in deletion length and position. Sixteen of 25 Guangxi strains had completely identical nucleotide sequences in the variable re gion, and the homology between other strains also exceeded 97.9%. There were single nucleotide substi tution, deletion, and insertion in the ORF14/15 region of Guangxi strains compared with other strains in GenBank. In the phylogenetic tree based on WSSV variable region ORF14/15, the Guangxi strains were closely related and formed a separate branch with Indian strain IN-05-I, but far from other strains in GenBank. The ORF14/15 gene of WSSV isolates in cultured P. vannamei in Guangxi has a large deletion in the middle of the variable region, and the Guangxi WSSV strains show no significant spatio-temporal differences; the Guangxi strains are closer in genetics to Indian strain IN-05-I than other strains in GenBank.