Development and Validation of a SYBR Green Real Time PCR Protocol for Detection and Quantification of Nervous Necrosis Virus (NNV) Using Different Standards

Simple Summary In the present report, we designed a reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) for the detection and quantification of the nervous necrosis virus (NNV), a fish virus of great importance in Mediterranean aquaculture. The advantage of this procedure with respect to others is that it ensures the correct diagnosis of any viral type, at extremely low viral loads, thanks to a limit of detection lower than in previous methods, and demonstrates a better diagnostic sensitivity and specificity than PCR and cell culture isolation. Furthermore, this is the first time that an RT-qPCR procedure has been validated for the quantification of NNV, ensuring the reliability of the quantification, regardless of the calibration standard chosen. Therefore, its use would enable the comparison of data between different laboratories. The nervous necrosis virus (NNV) is a threat to fish aquaculture worldwide, especially in Mediterranean countries. Fast and accurate diagnosis is essential to control it, and viral quantification is required to predict the level of risk of new viral detections in field samples. For both, reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) is used by diagnostic laboratories. In the present study, we developed an RT-qPCR procedure for the diagnosis and simultaneous quantification of NNV isolates from any of the four genotypes. The method proved to be highly sensitive in terms of crude virus titer: 5.56-9.88 TCID50/mL (tissue culture infectious dose per mL), depending on the viral strain, and averaging 8.8 TCID50/mL or 0.08 TCID50/reaction. Other standards also yielded very low detection limits: 16.3 genome copies (cps) of purified virus per mL, 2.36 plasmid cps/mL, 7.86 in vitro synthetized RNA cps/mL, and 3.16 TCID50/mL of virus from infected tissues. The diagnostic parameters evaluated in fish samples were much higher in comparison to cell culture isolation and nested PCR. In addition, the high repeatability and reproducibility of the procedure, as well as the high coefficient of determination (R-2) of all the calibration curves with any type of standard tested, ensure the high reliability of the quantification of NNV using this RT-qPCR procedure, regardless of the viral type detected and from the type of standard chosen.

Automated summary

In this study, a reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) was developed for the detection and quantification of the fish virus NNV with high sensitivity and reliability, allowing for accurate diagnosis and quantification at extremely low viral loads.