The white spot syndrome virus (WSSV) continues to be the major pathogen to shrimp aquaculture. The WSSV has been a difficult pathogen to contain from commercial culture environments even more than two decades after its first report and more than fifteen years after its genome fully deciphered. A unique feature of WSSV genome is that it does not show similarity to any other pathogen and hence was placed in a new Genus Whispovirus under Family Nimaviridae. The WSSV genome has been annotated differently for coding sequences (CDS) without uniformity. Except for few features, many CDS were annotated numerically with a common prefix like WSSV (AF440570), wsv (AF332093), ORF (MF768985) etc. in the order in which they were assembled and submitted as linear sequence at GenBank. As the annotation nomenclature varies across genomes, the results inferred on a WSSV genome could not be easily comparable to other genomes. Therefore, we had adopted a strategy to find the deleted CDS, while comparing all isolates to a reference genome. This strategy helped us in finding two major deleted regions like the region between wsv479 and wsv499 and the region between wsv237 and wsv246. Of 15 WSSV isolates, a region of about 8 Kb containing CDS wsv481 to wsv499 was lost in 7 isolates. Another region of about 3 Kb containing wsv489 to wsv499 CDS was lost in 9 isolates. The WSSV isolates from Australia, China, Ecuador and India share an identical deletion profile for wsv237 to wsv242 region and in contrast the other isolates do not contain even a minor deletion in this region. The deleted CDS in several isolates sequenced over a period of time provided new insights on CDS important for WSSV infection.