One base pair deletion and high rate of evolution: Keys to viral accommodation of Australian Penaeus stylirostris densovirus

•Penaeus stylirostris densovirus PstDV caused large economic losses to shrimp farming.•Whole genome sequencing identified a 1 base pair deletion in the critical NS1 motif.•A frame shift produced of 2 daughter proteins which we hypothesize lowered virulence.•Two PstDVs in Australia recombined to evolve at 1.55 × 10− 3 substitutions/site/year.•PstDV enhanced fitness during the severe Midcrop Mortality Syndrome years 1996–2003.

Penaeus stylirostris densovirus (PstDV) has caused large economic losses to shrimp farming worldwide. Here, a 1-bp deletion within the nuclear localization signal-encoding sequence of open reading frame 1 (ORF1; NS1) of Australian PstDV was identified as a cause of 199-amino acid shortened NS1 protein and production of a second protein, C-terminal NS1. This mutation is believed to reduce virulence as it strongly modifies the characteristics of NS1, which is responsible for the majority of enzymatic activities in PstDV. This finding supports a hypothesis regarding accommodation of PstDV in Australian prawns in relation to viral genetics. However, a high degree of evolution (1.55 × 10− 3 substitutions/site/year) and genetic variation for the virus was attributable to the viral recombination observed with 10 potential genomic breakpoints identified. With this finding, we suggest that awareness of the emergence of new virulent strains should be increased as a preventative measure against future outbreaks of PstDV in the Australian Indo-Pacific.