Rapid and sensitive detection of salmonid alphavirus using TaqMan real-time PCR

- A sensitive and rapid TaqMan real-time PCR assay for SAV was developed.
- One primer set and specific TaqMan probe were designed.
- This assay has a higher sensitivity than the reported Q_nsP1 assay and conventional RT-PCR method.
- This TaqMan real-time PCR could be a useful tool for the detection of SAV.

Salmonid alphavirus (SAV) infection has led to the spread of salmon pancreas disease (PD) and sleeping disease (SD) to salmonids in several countries in Europe, resulting in tremendous economic losses to the fish farming industry. Recently, with increases in the fish import trade, many countries in which SAV has been unreported, such as China, may be seriously threatened by these diseases. It is therefore necessary to develop efficient detection methods for the prevention and diagnosis of SAV infection. In this study, a rapid and sensitive TaqMan real-time PCR method was established and assessed for this purpose. A specificity assay showed no cross-reactions with other common RNA viruses. Regression analysis and standard curves calculated from the Ct values of 10-fold serial dilutions of the standard plasmid showed that the assay was highly reproducible over a wide range of RNA input concentrations. The real-time PCR assay was able to detect SAV at a concentration as low as 1.5 × 101 copies, indicating that it is 107 times more sensitive than the approved conventional RT-PCR method (detection limit, 1.5 × 107 copies) after use on the same samples. Assessment of infected fish samples showed that this assay has a higher sensitivity than the previously reported Q_nsP1 assay. Thus, this TaqMan real-time PCR assay provides a rapid, sensitive, and specific detection method for SAV, offering improved technical support for the clinical diagnosis and epidemiology of SAV.