Novel, closely related, white spot syndrome virus (WSSV) genotypes from Madagascar, Mozambique and the Kingdom of Saudi Arabia

White spot syndrome virus (WSSV) is highly pathogenic to penaeid shrimp and has caused significant economic losses in the aquaculture industry around the world. During 2010 to 2012, WSSV caused severe mortalities in cultured penaeid shrimp in Saudi Arabia, Mozambique and Madagascar. To investigate the origins of these WSSV, we performed genotyping analyses at 5 loci: the 3 open reading frames (ORFs) 125, 94 and 75, each containing a variable number of tandem repeats (VNTR), and deletions in the 2 variable regions, VR_14/15 and VR_23/24. We categorized the WSSV genotype as {N₁₂₅, N ₉₄, N₇₅, δX_14/15, δX _23/24} where N is the number of repeat units in a specific ORF and δX is the length (base pair) of deletion within the variable region. We detected 4 WSSV genotypes, which were characterized by a full-length deletion in ORF94/95, a relatively small ORF75 and one specific deletion length in each variable region. There are 2 closely related genotypes in these 3 countries: {6₁₂₅, del₉₄, 375, δ5950_14/15, δ1097_123/24} and {7₁₂₅, del₉₄, 375, δ5950_14/15, δ1097123/24}, where del is the full-length ORF deletion. In Saudi Arabia, 2 other related types of WSSV were also found: {6₁₂₅, 794, 375, δ5950_14/15, δ1097 _123/24} and {8₁₂₅, 1394, 375, δ5950_14/15, δ1097_123/24}. The identical patterns of 3 loci in these 4 types indicate that they have a common lineage, and this suggests that the WSSV epidemics in these 3 countries were from a common source, possibly the environment.