Complete genome sequence of a white spot syndrome virus associated with a disease incursion in Australia

White spot disease is a serious viral panzootic affecting prawn aquaculture. The causative agent is white spot syndrome virus (WSSV), a large double-stranded circular DNA virus. In November 2016, WSSV was identified following the onset of disease in a prawn farm near Brisbane, Queensland, Australia (previously free of white spot disease). The prawn farming industry in Queensland is valued at approximately AU$87 million annually, and the potential impact of establishment of endemic WSD would be severe. We report the complete genome sequence of the Australian WSSV (WSSV-AU) and the analysis of previously described genomic markers that have been reported to show variation among WSSV strains. WSSV-AU genome length was 285,973 bp, shorter than most but within the previously reported size range of 281 kbp to 312 kbp. There are high levels of homology (91–97%) between the WSSV-AU and other reported genomes sequences. The WSSV-AU genome sequence has a number of substantial deletions, most significantly in regions that were previously reported as genomic markers (regions known to contain variable numbers of tandem repeats and regions with deletions of variable length). Additionally, several deletions of regions reported to encode envelope proteins were deleted. It may be that some of the envelope proteins needed for an ancestral natural host infection are redundant, and therefore expendable, with respect to infection of penaeids. Hence, that deletion of redundant regions may show homoplasy and be an unreliable epidemiological tool. In light of the undetermined epidemiological relevance of deletions, including those associated with long tandem repeats, it is concluded that the comparison of reported complete genome sequences cannot identify the source of the virus in Queensland and an alternative genotyping method is required.