Variability in the tandem repetitive DNA sequences of white spot syndrome virus (WSSV) genome and suitability of VP28 gene to detect different isolates of WSSV from India

Abstract

White spot syndrome virus (WSSV), member of a new virus family called Nimaviridae, is an important viral pathogen responsible for severe economic loss to shrimp farmers. The WSSV DNA extracts from 84 samples of WSSV-infected shrimp from 65 ponds of 8 provinces of India gave a variety of amplicons using the primers designed to amplify ORF94 gene (GenBank AF369029), suggesting difference in the number of DNA repeat sequences in isolates from region to region along the coastal line of India. Altogether, 8 different repeat groups having 54 bp DNA repeats from 6 to 13 in ORF94 were found. Among them, WSSV isolate with 8 repeats was found to be the most frequent (about 23%) followed by 9 (18%). Some WSSV-infected samples collected from Andhra Pradesh and Kerala gave 2 PCR amplicons, a strong one for ORF94-8 and a lighter one for ORF94-7 in Andhra Pradesh samples, and 2 amplicons of ORF94-11 and ORF94-8 in Kerala and these findings indicate the possibility of infections in these populations with two strains of WSSV. We have found high variable numbers of repeats in Indian WSSV isolates, but sequence variation within the repeat region was confined to either T or G at position 48. The results of infectivity studies showed that no difference in virulence among the eight repeat groups of Indian WSSV isolates was found. The primer set designed based on VP28 gene (GenBank AF369029) in the present study gave a PCR product of 250 bp with WSSV isolates of different repeat groups from various locations. Antiserum raised against recombinant VP28 protein successfully detected all the repeat groups of Indian WSSV isolates. The results of the present study recommend the use of primers designed from VP28 gene and antibody raised against VP28 protein to detect WSSV to avoid any diagnostic error.