Outbreak investigation attributes Infectious spleen and kidney necrosis virus as a necessary cause of a mortality epidemic in farmed grouper (Epinephelus spp.) in Bali, Indonesia

In 2016, famers reported mass mortality events in hybrid grouper within 2–4 weeks following transfer to sea cages on the northern coast of Bali. The objective was to obtain an aetiological diagnosis using a broad range of traditional and emerging diagnostic approaches. A group of 24 and 12 fish with and without clinical signs were sampled from 10 affected populations at 9 farms. Samples for histopathology, ectoparasites evaluation and molecular approaches for microbiology were obtained with a diagnostic post-mortem examination. Fish with clinical signs had a significantly higher likelihood of having pale anterior and posterior kidneys and a liver that was pale and reduced in size compared to fish without clinical signs. There were no differences in the prevalence and quantity of Megalocytivus (MCV) or nervous necrosis virus (NNV) in tissues observed from fish with and without clinical signs. Nearly 55 of fish were infected with NNV irrespective of clinical signs. There were no histopathological lesions consistent with virial nervous necrosis and the NNV infections were considered subclinical. 80 of grouper were infected with MCV, irrespective of clinical signs. A significant proportion of fish with clinical signs (true prevalence 94.4 ; 95 CI 79–100) had observed megalocytes and pathology consistent with disease caused by ISKNV compared to those without clinical signs (true prevalence 47.2 ; 95 CI 27–70). Metagenomic sequences generated using Illumina Miseq and taxonomically labelled using BlastN + revealed that the Megalocytivirus was 99.9 similar to Infectious spleen and kidney necrosis virus (ISKNV). The unbiased sequencing did not detect any novel DNA viruses or bacterial pathogens of clinical significance. The monogenean, Benedenia epinepheli and a leech, Zeylanicobdela arugamensis were detected at 6/9 and 9/9 farms, respectively. Our approach identified several pathogens reported in grouper aquaculture with histopathology showing that ISKNV was a necessary cause for the mass mortality events. © 2021 The Author(s)