Prevalence and genomic analysis of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in Litopenaeus vannamei shrimp farmed in Shanghai, China

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is prevalent among farmed shrimp and results in significant reductions in shrimp production. In order to gain a better understanding of the prevalence of IHHNV in the Litopenaeus vannamei shrimp population of Shanghai, China, samples were collected during two cultivation seasons and subjected to diagnostic PCR. The results of this study showed that 167 out of 200 shrimp were positive for IHHNV, indicating a high viral prevalence (83.5 %) in farmed shrimp populations. Our results also indicated that there was a moderate correlation between IHHNV prevalence and water temperature, salinity and pH and only a slight correlation with the concentration of dissolved oxygen (DO). A mathematical model was developed in order to predict the relationship between these four characteristics of water quality and IHHNV prevalence, ultimately resulting in an estimate of the best water quality criteria (IHHNV prevalence = 0) where T = 30 °C pH = 8.0, DO = 18.3 mg/L, and salinity = 1.5 ‰. Additionally, two IHHNV genotypes were identified, the sequencing of which revealed a high similarity to the known IHHNV genotypes based on a comparison of their nucleotide and amino acid sequences. Two types of repetitive sequences were detected at both the 5′ and 3′ ends of the non-coding regions, which are commonly found in other IHHNV genomic sequences. Phylogenetic analysis indicated that the IHHNV Shanghai genotypes were closely related to strains from Ganyu and Sheyang, but not to strains originating from Fujian, China. This finding suggests that IHHNVs have emerged independently several times in China.