Partial validation of a TaqMan quantitative polymerase chain reaction for the detection of the three genotypes of Infectious spleen and kidney necrosis virus

• Published in: PloS one 2023-02, Vol.18 (2), p.e0281292-e0281292
• Main Authors: Koda, Samantha A, Subramaniam, Kuttichantran, Hick, Paul M, Hall, Evelyn, Waltzek, Thomas B, Becker, Joy A
• Format: Article
• Language: English
• Subjects: Analysis; Animal diseases; Animal health; Animals; Aquaculture; Aquaculture industry; Assaying; Biology and Life Sciences; Cloning; Confidence limits; Correlation coefficient; Correlation coefficients; Deoxyribonucleic acid; Dilution; Disease; DNA; DNA Virus Infections - diagnosis; DNA Virus Infections - epidemiology; DNA Virus Infections - veterinary; DNA viruses; Earth Sciences; Epidemics; Evaluation; Fish; Fish diseases; Fish Diseases - epidemiology; Fishes; Food industry; Freshwater fish; Genetic aspects; Genomes; Genotype; Genotype & phenotype; Genotypes; Health aspects; Infections; International economic relations; Iridoviridae - genetics; Kidneys; Laboratories; Management; Marine fish; Mathematical analysis; Medical diagnosis; Medicine and Health Sciences; Mortality; Necrosis; Ornamental fish; Pathogens; Perciformes - genetics; Plasmids; Polymerase Chain Reaction; Real-Time Polymerase Chain Reaction; Research and Analysis Methods; Sea Bream - genetics; Sensitivity analysis; Spleen; Stranding; Surveillance; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0281292

Megalocytiviruses (MCVs) are double-stranded DNA viruses known to infect important freshwater and marine fish species in the aquaculture, food, and ornamental fish industries worldwide. Infectious spleen and kidney necrosis virus (ISKNV) is the type species within the genus Megalocytivirus that causes red seabream iridoviral disease (RSIVD) which is a reportable disease to the World Animal Health Organization (WOAH). To better control the transboundary spread of this virus and support WOAH reporting requirements, we developed and partially validated a TaqMan real-time qPCR assay (ISKNV104R) to detect all three genotypes of ISKNV, including the two genotypes that cause RSIVD. Parameters averaged across 48 experiments used a 10-fold dilution series of linearized plasmid DNA (107-101 copies), carrying a fragment of the three-spot gourami iridovirus (TSGIV) hypothetical protein revealed that the assay was linear over 7 orders of magnitude (107-101), a mean efficiency of 99.97 ± 2.92%, a mean correlation coefficient of 1.000 ± 0.001, and a limit of detection (analytical sensitivity) of ≤10 copies of TSGIV DNA. The diagnostic sensitivity and specificity for the ISKNV104R qPCR assay was evaluated and compared to other published assays using a panel of 397 samples from 21 source populations with different prevalence of ISKNV infection (0-100%). The diagnostic sensitivity and specificity for the ISKNV104R qPCR assay was 91.99% (87.28-95.6; 95% CI) and 89.8% (83.53-94.84). The latent class analysis showed that the ISKNV104R qPCR assay had similar diagnostic sensitivities and specificities with overlapping confidence limits compared to a second TaqMan qPCR assay and a SYBR green assay. This newly developed TaqMan assay represents a partially validated qPCR assay for the detection of the three genotypes of the species ISKNV. The ISKNV104R qPCR assay once fully validated, will serve as an improved diagnostic tool that can be used for ISKNV surveillance efforts and diagnosis in subclinical fish to prevent further spread of MCVs throughout the aquaculture and ornamental fish industries.