Comparison of Polymerase Chain Reaction (PCR) assay performance in detecting Decapod penstylhamaparvovirus 1 in penaeid shrimp

Abstract

Decapod Penstylhamaparvovirus 1, commonly known as infectious hypodermal and hematopoietic necrosis virus (IHHNV), remains an economically important viral pathogen for penaeid shrimp aquaculture due to its effects on growth performance. The World Organization for Animal Health (WOAH, Paris, France) recommended methods for the detection of IHHNV include both conventional and real-time PCR. However, published reports and anecdotal evidence suggest the occurrence of non-specific amplifications when testing for IHHNV using the WOAH protocols. Studies were designed to develop a sensitive, robust TaqMan PCR method for detection of IHHNV in the three commercially important penaeid shrimp: Penaeus vannamei, P. monodon and P. stylirostris. We compared the performance of the WOAH-recommended real-time PCR method to several published as well as in-house designed primer/probe sets spanning the entire genome of IHHNV. Our results show that (1) more than one primer/ probe set is needed when testing for the infectious form of IHHNV in all three species of shrimp and (2) primer pairs qIH-Fw/qIH-Rv and 3144F/ 3232R have diagnostic characteristics that would enable IHHNV detection in all three shrimp species. These findings are valuable for a large-scale screening of shrimp using a TaqMan real-time PCR assay.

Keywords: EVE; Endogenous viral element; IHHNV; Infectious hypodermal and hematopoietic necrosis virus; Shrimp.