WSSV Genotypes in Shrimp Aquaculture in Kerala, India Employing Variable Number Tandem Repeat in DNA Segments

Abstract

Disease caused by White spot syndrome virus (WSSV) is a major problem for the shrimp farming industry in India. Monitoring for the distribution and makeup of WSSV genotypes is thus important for identifying virus entry routes and developing strategies to avoid economic losses. Here variable number tandem repeat (VNTR) loci were analyzed to identify the variability and potential origins of WSSV genotypes occurring in shrimp farmed in Kerala. In total, 434 shrimp were screened by PCR. The study revealed that genetic characteristics of Taiwan, Indian and Chinese WSSV were prevalent in Kerala based on VNTR. Samples that are positive for WSSV in both first and second PCR itself were unable to produce amplifications for ORF94, 125 and75. This may be due to the sequence variation at the primer binding site. The potential use of VNTR loci analysis for the source tracking of WSSV in the various shrimp production system and recommends for bigger surveillance on genotyping to identify the unknown source of origin for better visualization of the distribution of shrimp.