Genotypic variation in the white spot syndrome virus detected from giant tiger shrimp (Penaeus monodon) in North Western and Eastern provinces of Sri Lanka

Shrimp farming in Sri Lanka accounting for 70 % of the exports in the field of aquaculture in Sri Lanka. However, it encounters substantial obstacles as a result of the white spot syndrome virus (WSSV) affecting the giant tiger shrimp (Penaeus monodon). This study focused on comprehending the current state of the disease and the genetic diversity present in the North Western and Eastern provinces in Sri Lanka. By extracting genomic DNA from the gills and pleopods of suspected infected shrimps and post-larvae, the study identified a high infection rate of at least 83 % (88/106), with varying incidence in sampled farms across regions. The analysis of the genome indicated distinct sizes of PCR products, suggesting the presence of variation in the tandem repeat units within the ORF94 region of the WSSV. Notably, the study discovered single nucleotide polymorphisms (SNPs) in Sri Lankan WSSV strains, which showed the change between T (Thymine) and G (Guanine) at the 48th site of the RU sequence, which is designated as K (keto) as indicated in the IUPAC code, indicating genetic diversity. Phylogenetic analysis suggested two distinct origins for Sri Lankan WSSVs, with possible links to North America and Mexico strains, highlighting a potential common source of outbreaks. This study emphasizes the intricate nature of WSSV infections in Sri Lanka and emphasizes the necessity for customized approaches to address this significant risk to the shrimp aquaculture industry. •High prevalence of white spot syndrome virus (WSSV) in Sri Lanka as high as 83.01 %•Three genotypes with 5 different SNP patterns in the Sri Lankan Penaeus monodon shrimp culture•Identified three genotypes (6-RUs, 9-RUs, 12-RUs) and 4 distinct SNP patterns at position 48 were different from global strains.•Two Sri Lankan WSSVs were closely related to North American and Mexican strains.