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

Fusianto, Cahya K.; Hick, Paul; Murwantoko, Murwantoko; Herlambang, Afri; Whittington, Richard J.; Becker, Joy A.

doi:10.1016/j.aqrep.2021.100723

Cited by 11 publications

(9 citation statements)

References 55 publications

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“…Even with advanced methods for identifying intra-host SNVs (iSNVs), the false discovery rate of iSNVs using Oxford Nanopore data alone was ~55% in a rapidly evolving RNA virus, and is expected to be higher in viruses that evolve more slowly, such as ISKNV. In studies where quantification of iSNVs is required, replicated Illumina sequencing libraries per sample, combined with Nanopore data, is recommended for accurate quantification of iSNVs [43][44][45][46][47]. The increased costs and loss of field-based sequencing of this approach would need to be weighed against the likelihood and importance of detecting intra-host variability.…”

Section: Discussionmentioning

confidence: 99%

A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia

Alathari

Chaput

Bolaños

et al. 2023

Viruses

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Tilapia farming is one of the most important sectors in aquaculture worldwide and of major importance to global food security. Infectious spleen and kidney necrosis virus (ISKNV) has been identified as an agent of high morbidity and mortality, threatening tilapia aquaculture. ISKNV was detected in Lake Volta, Ghana, in September 2018 and spread rapidly, with mortality rates between 60 and 90% and losses of more than 10 tonnes of fish per day. Understanding the spread and evolution of viral pathogens is important for control strategies. Here, we developed a tiled-PCR sequencing approach for the whole-genome sequencing of ISKNV, using long read sequencing to enable field-based, real-time genomic surveillance. This work represents the first use of tiled-PCR for whole genome recovery of viruses in aquaculture, with the longest genome target (>110 kb dsDNA) to date. Our protocol was applied to field samples collected from the ISKNV outbreaks from four intensive tilapia cage culture systems across Lake Volta, between October 2018 and May 2022. Despite the low mutation rate of dsDNA viruses, 20 single nucleotide polymorphisms accumulated during the sampling period. Droplet digital PCR identified a minimum requirement of template in a sample to recover 50% of an ISKNV genome at 275 femtograms (2410 viral templates per 5 µL sequencing reaction). Overall, tiled-PCR sequencing of ISKNV provides an informative tool to assist in disease control in aquaculture.

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Section: Discussionmentioning

confidence: 99%

A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia

Alathari

Chaput

Bolaños

et al. 2023

Viruses

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“…This parasite is reported to attack humpback groupers in Indonesia (Sudewa et al 2020;Subekti et al 2021). This parasite even attacks other grouper species, such as Epinephelus spp., Epinephelus coioides Hamilton, 1822, and even hybrid grouper (Epinephelus fuscoguttatus x Epinephelus lanceolatus) (Lestari et al 2020;Fusianto et al 2021;Rumondang 2022). Benedenia is quite dangerous because it is often reported with secondary diseases such as viruses and bacteria that cause mortality (Turgay et al 2019;Fusianto 2021).…”

Section: Morphometric Identificationmentioning

confidence: 99%

“…A previous study stated that Benedenia epinepheli infections were found in groupers up to 57.1% in aquaculture and 51.4% in wild fish (Rückert et al 2010). The parasite cases from Benedenia on grouper need more awareness since it will reduce grouper quality and production (Fusianto et al 2021;Harjuni et al 2023).…”

Section: Introductionmentioning

confidence: 97%

First microphological and molecular parasitological survey of Benedenia in humpback grouper (Cromileptes altivelis) of Lampung and Situbondo, Indonesia

AMIIN,

SUBEKTI,

MASITHAH

et al. 2024

Biodiversitas

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Abstract. Amiin MK, Subekti S, Masithah ED, Nirmala D, Yunus M, Santanumurti MB, Rivaie AR. 2023. First microphological and molecular parasitological survey of Benedenia in humpback grouper (Cromileptes altivelis) of Lampung and Situbondo, Indonesia. Biodiversitas 24: 6858-6867. Capsalid monogenean infections, such as Benedenia, affect grouper aquaculture production. Benedenia will cause lesions and skin damage which will cause fish prices to drop. Secondary infection from bacteria, viruses, and fungi by Benedenia triggers a slow growth rate and even mortality. Benedenia infection on grouper has been conducted in Indonesia, specifically in this study in Lampung and Situbondo. However, molecular identification of this parasite is still lacking. This study aims to determine the microscopic and molecular characteristics of Benedenia from the Hurun Bay waters of Lampung and the North Coast of the Java Sea, Situbondo. The main parameters observed in this study were DNA base sequence, morphology, and phylogenetic tree. Benedenia from Lampung (637 bp) and Situbondo (741 bp) in this study was confirmed by the morphological and molecular close as Benedenia sargocentron with nucleotides. Interestingly, the similarity was less than 98% with B. sargocentron with accession ID JN797597.1 (similarity of 97.15% from Lampung and 86.33% from Situbondo). It could be indicated as a new species of Benedenia. The prevalence of Benedenia in Lampung was 90%, while Situbondo showed 80% with 3 parasite/fish intensity for each location. The outcome of this study is the characteristics of Benedenia from Lampung and Situbondo were similar to B. sargocentron according to morphological and molecular identification. This is the first report of B. sargocentron from Lampung and Situbondo since no molecular identification has been done in those places to confirm their species. Further research by another molecular target apart from 28S rRNA should be needed to identify this parasite more accurately.

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“…Direct Sequencing of Clinical Specimens. Te hybridization capture enrichment method was compared with a direct Illumina MiSeq approach to sequencing nucleic acids purifed from the clinical specimens according to the method described by Fusianto et al [47]. Two samples with the highest load of ISKNV were suitable for determining the whole genome by direct sequencing and were used for the comparison (Samples 12 and 15).…”

Section: Comparison Of Hybridization Capture Enrichment Withmentioning

confidence: 99%

Genotypic Characterization of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Southeast Asian Aquaculture

Fusianto

Becker

Subramaniam

et al. 2023

Transboundary and Emerging Diseases

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Infectious spleen and kidney necrosis virus (ISKNV) is a species within the genus Megalocytivirus (family Iridoviridae), which causes high mortality disease in many freshwater and marine fish species. ISKNV was first reported in Asia and is an emerging threat to aquaculture with increasing global distribution, in part due to its presence in ornamental fish with clinical and subclinical infections. The species ISKNV includes three genotypes: red seabream iridovirus (RSIV), turbot reddish body iridovirus (TRBIV), and ISKNV. There is an increasing overlap in the recognized range of susceptible fish hosts and the geographic distribution of these distinct genotypes. To better understand the disease caused by ISKNV, a nucleic acid hybridization capture enrichment was used prior to sequencing to characterize whole genomes from archived clinical specimens of aquaculture and ornamental fish from Southeast Asia (n = 16). The method was suitable for tissue samples containing 2.50 × 104–4.58 × 109 ISKNV genome copies mg−1. Genome sequences determined using the hybridization capture method were identical to those obtained directly from tissues when there was sufficient viral DNA to sequence without enrichment (n = 2). ISKNV genomes from diverse locations, environments, and hosts had very high similarity and matched established genotype classifications (14 ISKNV genotype Clade 1 genomes with >98.81% nucleotide similarity). Conversely, two different genotypes were obtained at the same time and location (RSIV and ISKNV from grouper, Indonesia with 92.44% nucleotide similarity). Gene-by-gene analysis with representative ISKNV genomes identified 59 core genes within the species (>95% amino acid identity). The 14 Clade 1 ISKNV genomes in this study had 100% aa identity for 92–105 of 122 predicted genes. Despite high overall sequence similarity, phylogenetic analyses using single nucleotide polymorphisms differentiated isolates from different host species, country of origin, and time of collection. Whole genome studies of ISKNV and other megalocytiviruses enable genomic epidemiology and will provide information to enhance disease control in aquaculture.

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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

Cited by 11 publications

References 55 publications

A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia

A Multiplexed, Tiled PCR Method for Rapid Whole-Genome Sequencing of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Tilapia

First microphological and molecular parasitological survey of Benedenia in humpback grouper (Cromileptes altivelis) of Lampung and Situbondo, Indonesia

Genotypic Characterization of Infectious Spleen and Kidney Necrosis Virus (ISKNV) in Southeast Asian Aquaculture

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