Descriptive epidemiology of variants of infectious salmon anaemia virus in four Atlantic salmon farms in Newfoundland and Labrador, Canada.

An incursion of infectious salmon anaemia virus (ISAV) was detected in 2020 in southern Newfoundland, Canada. This resulted in an outbreak affecting four marine farms stocking Atlantic salmon (Salmo salar L.) vaccinated against ISAV. This study provides the first description of epidemiologic characteristics of an ISAV outbreak in 2020 and 2021, and detected ISAV variants at the population level. Fish kidneys were screened for ISAV by real-time RT-PCR and non-negative samples were submitted for genotyping and further diagnostic testing. Nine distinct ISAV variants were identified: five European and three North American (NA) HPRΔ ISAV, and one NA-HPR0 ISAV variant. A notable finding was the concurrent detection of both an HPR0 and an HPRΔ ISAV variant in one individual fish. In two farms, both European and NA variants were simultaneously detected, while in the other two farms either NA or European variants were identified, but not both together. Generally, mortality increases followed rises in ISAV prevalence and cycle threshold values on RT-PCR decreased with time. Epidemiologic descriptions of ISAV outbreaks in Atlantic Canada contributes to the understanding of local disease dynamics and identification of changes thereof. Such insights are essential for the strengthening of disease management plans.

Application of surveillance data in evaluation of diagnostic tests for infectious salmon anemia.

Infectious salmon anemia (ISA) is a viral disease in farmed Atlantic salmon Salmo salar, characterized by lethargy, anorexia, anemia and death. Test methods used for regulatory decisions to remove infected cages include the indirect fluorescent antibody test (IFAT), the reverse transcription-polymerase chain reaction test (RT-PCR), and virus isolation (VI). However, no thorough evaluation of these diagnostic tests has been carried out on field samples. The objective of this study was to evaluate the sensitivity and specificity of ISA diagnostic tests as individual tests and in combinations, using data collected by the provincial government surveillance program. Because a 'gold standard' reference test for ISA was not available, cage status was based on clinical disease records. A pool of fish from negative farms that had never had clinical ISA and a pool of fish from positive cages that were experiencing an outbreak of clinical ISA were obtained and assumed to be uninfected and infected respectively. A total of 1071 fish were used in this study. Depending on the test's cut-off value, the sensitivity and specificity for histopathology ranged from 30 to 73 and 72 to 99% respectively. IFAT had sensitivities and specificities in the range of 64 to 83 and 96 to 100% respectively. For the RT-PCR, sensitivity and specificity were 93 and 98% respectively. Test performances were also evaluated in series and in parallel combinations. Sensitivities are maximized when tests are evaluated in parallel, and ranged from 75 to 98%. Specificities are maximized when the tests are evaluated in series, and ranged from 99 to 100%. Current surveillance testing protocols should be reviewed to capitalize on this newly available information on test characteristics.