Draft genome sequence of <i>scale drop disease virus</i> (SDDV) retrieved from metagenomic investigation of infected barramundi, <i>Lates calcarifer</i> (Bloch, 1790)

Kayansamruaj, Pattanapon; Soontara, Chayanit; Dong, Ha Thanh; Phiwsaiya, Kornsunee; Senapin, Saengchan

doi:10.1111/jfd.13240

Cited by 7 publications

(6 citation statements)

References 43 publications

(60 reference statements)

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“…Te growing number of aquatic pathogens recognized in the genus Megalocytivirus across diverse locations and hosts requires genome sequences and associated metadata to be reported according to standard nomenclature. In addition to the distinct genotypes within the species ISKNV, genomic diversity has been reported in SDDV, causing disease in barramundi [65]. Additional megalocytiviruses have been described from freshwater European chub, Squalius cephalus [67] and euryhaline three-spine stickleback, Gasterosteus aculeatus [68].…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…The virus was designated as scale drop syndrome virus (SDDV) and defined as a novel member in the genus Megalocytivirus [ 13 ]. Nowadays, SDDV was widely prevalent in cultured L. calcarifer in extensive SE countries, including Singapore, Malaysia, Indonesia, and Thailand [ 13 , 15 , 16 , 17 ]. In addition, an SDDV-close ECIV was recently reported in European chub in England [ 18 ].…”

Section: Discussionmentioning

confidence: 99%

“…The virus was classified into the Megalocytivirus genus of the Iridoviridae family [ 13 ]. At present, the outbreaks of SDDV diseases have been widely prevalent in several Southeast Asian countries, including Singapore, Malaysia, Indonesia, and Thailand [ 13 , 15 , 16 , 17 ]. Moreover, the partial genome sequence of Singaporean SDDV isolate (accession no.…”

Section: Introductionmentioning

confidence: 99%

“…NC027778) and the whole genome sequence (accession no. MN562489) of Thailand isolate were determined as 124,244 bp and 131,129 bp, comprised of 129 ORFs and 135 ORFs, respectively [ 13 , 15 ]. A blastn search showed that the Singaporean SDDV identity was low with previous ISKNV/RSIV/TRBIV-like megalocytiviruses, at most 60% depending on the core viral gene.…”

Section: Introductionmentioning

confidence: 99%

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Scale Drop Disease Virus Associated Yellowfin Seabream (Acanthopagrus latus) Ascites Diseases, Zhuhai, Guangdong, Southern China: The First Description

Li²,

et al. 2021

Viruses

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Scale drop disease virus (SDDV), an emerging piscine iridovirus prevalent in farmed Asian seabass Lates calcarifer in Southeast Asia, was firstly scientifically descripted in Singapore in 2015. Here, an SDDV isolate ZH-06/20 was isolated by inoculating filtered ascites from diseased juvenile yellowfin seabream into MFF-1 cell. Advanced cytopathic effects were observed 6 days post-inoculation. A transmission electron microscopy examination confirmed that numerous virion particles, about 140 nm in diameter, were observed in infected MFF-1 cell. ZH-06/20 was further purified and both whole genome and virion proteome were determined. The results showed that ZH-06/20 was composed of 131,122 bp with 135 putative viral proteins and 113 of them were further detected by virion proteome. Western blot analysis showed that no (or weak) cross-reaction was observed among several major viral proteins between ZH-06/20 and ISKNV-like megalocytivirus. An artificial challenge showed that ZH-06/20 could cause 100% death to juvenile yellowfin seabream. A typical sign was characterized by severe ascites, but not scale drop, which was considerably different from SDD syndrome in Asian seabass. Collectively, SDDV was confirmed, for the first time, as the causative agent of ascites diseases in farmed yellowfin seabream. Our study offers useful information to better understanding SDDV-associated diseases in farmed fish.

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“…A major viral disease of Asian sea bass is scale drop disease (SDD), caused by scale drop disease virus (SDDV), which belongs to the genus Megalocytivirus in the family Iridoviridae , according to the phylogenetic analysis based on the major capsid protein (de Groof et al., 2015). Detailed structural and genetic characterization revealed that SDDV virions possess an approximately 140‐nm icosahedral capsid and 131‐kb double‐stranded DNA (dsDNA) genome harbouring 135 ORFs (de Groof et al., 2015; Kayansamruaj et al., 2020). Upon infection with SDDV, fish exhibit a broad range of signs including scale loss, darkening of bodies, fin and tail erosion, gill pallor and occasional exophthalmia (Gibson‐Kueh et al., 2012).…”

Section: Introductionmentioning

confidence: 99%

CRISPR‐based platform for rapid, sensitive and field‐deployable detection of scale drop disease virus in Asian sea bass (Lates calcarifer)

Sukonta

Senapin

Meemetta

et al. 2021

Journal of Fish Diseases

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Asian sea bass or barramundi (Lates calcarifer) is one of the most important farmed fish species in South-East Asia and Australia, with the global production steadily rising in the past decade and reaching 203,064 tonnes in 2019 (FAO, 2021;Nurliyana et al., 2020).However, the high demand for sea bass has spurred rapid expansion and intensification of cultivation that in turn exacerbate the risk of disease outbreaks (Hutson, 2013). A major viral disease of Asian sea bass is scale drop disease (SDD), caused by scale drop disease

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Draft genome sequence of scale drop disease virus (SDDV) retrieved from metagenomic investigation of infected barramundi, Lates calcarifer (Bloch, 1790)

Abstract: Scale drop disease virus (SDDV) is an emerging viral pathogen that has caused outbreaks in farmed barramundi (Lates calcarifer Bloch, 1,790) in several SouthEast Asian countries including Singapore,

Cited by 7 publications

References 43 publications

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

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

Scale Drop Disease Virus Associated Yellowfin Seabream (Acanthopagrus latus) Ascites Diseases, Zhuhai, Guangdong, Southern China: The First Description

CRISPR‐based platform for rapid, sensitive and field‐deployable detection of scale drop disease virus in Asian sea bass (Lates calcarifer)

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