GENOTYPING OF WHITE SPOT SYNDROME VIRUS (WSSV) AND INFECTIOUS HYPODERMAL AND HEMATOPOIETIC NECROSIS VIRUS (IHHNV) IN ECUADORIAN CULTURED SHRIMP  

White spot syndrome virus (WSSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV), recently called decapod penstyldensovirus 1 (PstDV1), are two major viral pathogens of cultured shrimp. In Ecuador, despite the improvement of the shrimp production, WSSV still represent the main infectious pathogen. IHHNV also generates economic losses as consequence of growth retardation and runt deformities, even though it does not produce mortalities. To assess the levels of genetic variation and the geographic genetic structure of both viruses, we monitored shrimp farms across the Ecuadorian coast, during 2015-2016. For IHHNV genotyping, a phylogenetic analysis based on the sequence of the viral capsid protein (ORF3) was performed. For the WSSV genotyping, a variable number of tandem repeat (VNTR) analysis with the genotype marker ORF94 and evaluation of differences of insertions/deletions for the open reading frame 14/15 were carried out. Phylogenetic analysis suggested the presence of different genotypes for both circulating viruses.

The phylogenetic analysis of the Ecuadorian IHHNV samples and viral isolates from other shrimp producer countries showed that the Ecuadorian isolates were classified in the infectious IHHNV group and suggesting the presence of different genotypes circulating within the country. On the other hand, variable number of tandem repeat (VNTR) analysis of ORF94 for the WSSV genome also showed high levels of genetic variation with distinct numbers of repeat units (RUs) of VNTRs (Table 1). The comparison of the variable region ORF14/15 showed variable length for the presence of indels in the Ecuadorian samples. We found novel strains of WSSV with a unique insertion in comparison with WSSV isolates from other shrimp producer countries.

The results obtained with both viruses reflect an important variation in the geographic genetic structure for these pathogens in Ecuador.  This may indicate that the viruses originally came from different geographical sources and mutated in this location.