Bayesian analysis of diagnostic sensitivity and specificity for detecting infectious salmon anaemia virus (ISAV) using IFAT and real-time RT-PCR testing from laboratories in Atlantic Canada

Infectious Salmon Anaemia virus (ISAV) is the causative agent of Infectious Salmon Anaemia (ISA), an economically important disease in farmed Atlantic salmon (Salmo salar L.). Immunofluorescence antibody test (IFAT) and real-time reverse transcription polymerase chain reaction (qRT-PCR) are commonly used diagnostic tests for ISAV active surveillance in Atlantic Canada; however, their diagnostic accuracy is not well reported. In the absence of a reference test, we used Bayesian latent class analysis methods to estimate diagnostic sensitivity (DSe) and specificity (DSp) of IFAT and qRT-PCR. We compared diagnostic performance of qRT-PCR, performed at two laboratories, and IFAT (performed at another laboratory) using field samples obtained from two separate salmon populations (total n = 130) in province of Newfoundland and Labrador, Canada. Conditional independence models for two tests (IFAT and qRT-PCR) and two populations (low and high prevalence) were run separately on datasets from each laboratory. Informative priors were used for DSe and DSp of qRT-PCR and IFAT based on prior knowledge, while flat priors (beta 1,1) were used for prevalence. qRT-PCRs had similarly high DSe (>91%). IFAT was the least sensitive method (DSe range, 56.9%–60.4%). Both IFAT (DSp > 98.8%) and qRT-PCRs (DSp > 97.9%) showed high DSp. Real-time RT-PCR provided the greatest DSe for routine surveillance of Atlantic salmon farms while not sacrificing DSp. Sample size for the study was not likely adequate to estimate all parameters with very high confidence, which could have influenced the posterior probability interval calculated for DSe, resulting in less diagnostic confidence in the results (posterior probability for Sensitivities for the tests within 10% of the true population value instead of 5%). Although IFAT provided a high DSp, the qRT-PCR performed similarly in this regard. The findings indicate that the qRT-PCR is fit for ISAV surveillance programs.