Development of an overlapping PCR method to clone the full genome of infectious hypodermal and hematopoietic necrosis virus (IHHNV)

Accurate and rapid detection of six viral pathogens in penaeid shrimp by using a novel multiplex PCR

Shrimp viral diseases, primarily caused by Taura syndrome virus (TSV), white spot syndrome virus (WSSV), infectious hypodermal and hematopoietic necrosis virus (IHHNV)/Penaeus stylirostris penstyldensovirus 1 (PstDV1), hepatopancreatic parvovirus (HPV), Penaeus monodon-type baculovirus (MBV)/P. monodon nudivirus (PmNV) and yellow head virus (YHV), posed a significant global challenge and resulted in enormous financial losses in the shrimp cultivation industry. In this research, six pairs of specific primers of the above six viruses were designed according to the highly conserved sequences of the viruses to amplify conserved gene segments of each virus and generate the corresponding PCR products of different sizes. Following system optimization, a multiplex PCR method was established to simultaneously detect and differentiate the six viruses mentioned above in penaeid shrimp. The assay exhibited high specificity with no cross-reactivity towards other non-target shrimp viruses or shrimp nucleic acids. The limit of detection (LOD) of the multiplex PCR assay was 5 × 102 copies/μL for TSV, WSSV, IHHNV, HPV and YHV, and 5 × 103 copies/μL for MBV. Using this assay, 1180 shrimp samples that were divided into 236 pools of five samples each pool were tested for further assessment. The total positive rate for all pools was 30.5 %, with IHHNV at 22.88 %, WSSV at 7.2 %, HPV at 0.42 %, and TSV, MBV, and YHV were undetected. The agreement rates between the multiplex PCR and conventional singleplex PCRs as well as real-time singleplex PCRs were all higher than 98.5 %. Overall, the multiplex PCR developed here is thus a sensitive and cost-effective diagnostic tool for the detection and daily monitoring of TSV, WSSV, IHHNV, HPV, MBV and YHV in shrimps.

Real-time PCR tests to specifically detect IHHNV lineages and an IHHNV EVE integrated in the genome of Penaeus monodon

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) can cause mass mortalities in western blue shrimp Penaeus stylirostris, runt deformity syndrome in Pacific white shrimp P. vannamei and scalloped abdominal shell deformities in black tiger shrimp P. monodon. In P. monodon, however, PCR-based diagnosis of IHHNV can be complicated by the presence of a chromosome-integrated, non-replicating endogenous viral element (EVE). To facilitate high-throughput screening of P. monodon for IHHNV infection and/or EVE sequences, here we report real-time PCR tests designed to specifically detect IHHNV Lineage I, II and III but not EVE Type A sequences and vice versa. Using 108 dsDNA copies of plasmid (p)DNA controls containing either IHHNV or EVE-Type A sequences, both tests displayed absolute specificity. The IHHNV-q309 PCR reliably detected down to ≤10 copies of pDNA, at which levels a 309F/R PCR amplicon was just detectable, and the presence of an IHHNV-EVE sequence did not significantly impact its sensitivity. The IHHNV-qEVE PCR was similarly sensitive. Testing of batches of P. monodon clinical samples from Vietnam/Malaysia and Australia identified good diagnostic concordance between the IHHNV-q309 and 309F/R PCR tests. As expected for a sequence integrated into host chromosomal DNA, IHHNV-qEVE PCR Ct values were highly uniform among samples from shrimp in which an EVE was present. The highly specific and sensitive IHHNV-q309 and IHHNV-qEVE real-time PCR tests described here should prove useful for selecting broodstock free of IHHNV infection and in maintaining breeding populations of P. monodon specific pathogen free for IHHNV, and if desired, also free of IHHNV-EVE sequences.