Phylogenomic characterization of red seabream iridovirus from Florida pompano Trachinotus carolinus maricultured in the Caribbean Sea

Koda, Samantha A.; Subramaniam, Kuttichantran; Pouder, Deborah B.; Yanong, Roy P.; Waltzek, Thomas B.

doi:10.1007/s00705-019-04155-7

Cited by 9 publications

(11 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…represented by red seabream iridovirus (RSIV), infectious spleen and kidney necrosis virus (ISKNV) and turbot reddish body iridovirus (TRBIV) (Go et al, 2016;Kim et al, 2019;Koda et al, 2019;Kurita & Nakajima, 2012). The RSIV-type infects widely host range marine cultured fish species; ISKNV type has been isolated from freshwater and brackish water fish, marine fish and ornamental fish (Baoprasertkul & Kaenchan, 2019;Fu et al, 2011;Go et al, 2016;He et al, 2001); and TRBIV type particularly infects flatfish species (Shi et al, 2004).…”

mentioning

confidence: 99%

Development of single nucleotide polymorphism (SNP) application for detection and genotyping of RSIV‐type megalocytiviruses

Sakseepipad

Nozaki

Yoshii

et al. 2021

Journal of Fish Diseases

View full text Add to dashboard Cite

Red sea bream iridovirus (RSIV) belonging to the genus Megalocytivirus of the family Iridoviridae is the cause of serious mass mortality of cultured marine fishes. RSIV‐type megalocytiviruses show extremely high nucleotide sequence identities. Thus, epidemiological studies on this virus are limited. This study developed two primer sets amplifying the regions possessing single nucleotide polymorphism (SNP) to determine the relationships and divergence of RSIV‐type megalocytiviruses isolated from cultured marine fishes in Japan. The two regions were designed according to the genome sequences of the representative RSIV genotype II of megalocytivirus members in GenBank. The SNP 1 and 2 regions have sequences homologous to hypothetical protein ORF 24 and ORF 31, respectively, of RSIV (accession no. AP017456.1). By sequencing the regions, 53 polymorphic sites were identified. The phylogenetic analysis of 25 RSIV‐type megalocytivirus isolates, classified into RSIV cluster, was clustered into eight haplotypes (seven haplotypes from Oita, two haplotypes from Ehime, and one haplotype shared between Oita and Ehime). These findings suggested that SNP in the RSIV genome is a powerful application for the detection and identification of RSIV‐type megalocytiviruses.

show abstract

mentioning

confidence: 99%

Development of single nucleotide polymorphism (SNP) application for detection and genotyping of RSIV‐type megalocytiviruses

Sakseepipad

Nozaki

Yoshii

et al. 2021

Journal of Fish Diseases

View full text Add to dashboard Cite

show abstract

“…Te RSIV genotype associated with marine fshes in Japan [7] was also detected in Korea [19] and China [20]. Subsequently, the range has expanded with RSIV-related diseases in marine fsh in the Dominican Republic [18], barramundi (Lates calcarifer) in estuary-based cages in India [21], and the freshwater mandarin fsh in China in locations previously impacted by the ISKNV genotype [22]. Te ISKNV genotype identifed initially in freshwater aquaculture [6] is globally widespread, impacting freshwater and marine fsh in Asian countries including China [23], India [24], Indonesia [15,[25][26][27], Malaysia [28,31], Vietnam [11], and Tailand [30].…”

Section: Introductionmentioning

confidence: 87%

“…Phylogenetic characterization of ISKNV based on the major capsid protein (MCP) gene and the ATPase gene has identifed a consistent diferentiation between three genotypes named ISKNV, RSIV, and turbot reddish body iridovirus (TRBIV) [10]. Tese genotypes and two clades within each have been supported by analysis of increasing numbers of complete ISKNV genomes, providing a sound nomenclature for the classifcation of isolates within the species [18].…”

Section: Introductionmentioning

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

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…Samples representing five of the six ISKNV clades (except clade 1 of the TRBIV genotype) were used to test the inclusivity of the ISKNV TaqMan qPCR. The ISKNV Clade 1, RSIV Clade 1, and TRBIV Clade 2 samples have been previously described by Koda et al [77], Koda et al [78], and Koda et al [8], respectively. The genotype ISKNV clade 2 infected tissue DNA was extracted from the spleen and kidney from a Banggai cardinalfish Pterapogon kauderni that was confirmed by full genome sequencing (GenBank acc.…”

Section: Estimation Of Qpcr Assay Analytical Sensitivity and Specificitymentioning

confidence: 99%

Partial validation of a TaqMan quantitative polymerase chain reaction for the detection of the three genotypes of Infectious spleen and kidney necrosis virus

et al. 2023

Self Cite

View full text Add to dashboard Cite

Megalocytiviruses (MCVs) are double-stranded DNA viruses known to infect important freshwater and marine fish species in the aquaculture, food, and ornamental fish industries worldwide. Infectious spleen and kidney necrosis virus (ISKNV) is the type species within the genus Megalocytivirus that causes red seabream iridoviral disease (RSIVD) which is a reportable disease to the World Animal Health Organization (WOAH). To better control the transboundary spread of this virus and support WOAH reporting requirements, we developed and partially validated a TaqMan real-time qPCR assay (ISKNV104R) to detect all three genotypes of ISKNV, including the two genotypes that cause RSIVD. Parameters averaged across 48 experiments used a 10-fold dilution series of linearized plasmid DNA (107–101 copies), carrying a fragment of the three-spot gourami iridovirus (TSGIV) hypothetical protein revealed that the assay was linear over 7 orders of magnitude (107–101), a mean efficiency of 99.97 ± 2.92%, a mean correlation coefficient of 1.000 ± 0.001, and a limit of detection (analytical sensitivity) of ≤10 copies of TSGIV DNA. The diagnostic sensitivity and specificity for the ISKNV104R qPCR assay was evaluated and compared to other published assays using a panel of 397 samples from 21 source populations with different prevalence of ISKNV infection (0–100%). The diagnostic sensitivity and specificity for the ISKNV104R qPCR assay was 91.99% (87.28–95.6; 95% CI) and 89.8% (83.53–94.84). The latent class analysis showed that the ISKNV104R qPCR assay had similar diagnostic sensitivities and specificities with overlapping confidence limits compared to a second TaqMan qPCR assay and a SYBR green assay. This newly developed TaqMan assay represents a partially validated qPCR assay for the detection of the three genotypes of the species ISKNV. The ISKNV104R qPCR assay once fully validated, will serve as an improved diagnostic tool that can be used for ISKNV surveillance efforts and diagnosis in subclinical fish to prevent further spread of MCVs throughout the aquaculture and ornamental fish industries.

show abstract

Phylogenomic characterization of red seabream iridovirus from Florida pompano Trachinotus carolinus maricultured in the Caribbean Sea

Cited by 9 publications

References 17 publications

Development of single nucleotide polymorphism (SNP) application for detection and genotyping of RSIV‐type megalocytiviruses

Development of single nucleotide polymorphism (SNP) application for detection and genotyping of RSIV‐type megalocytiviruses

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

Partial validation of a TaqMan quantitative polymerase chain reaction for the detection of the three genotypes of Infectious spleen and kidney necrosis virus

Contact Info

Product

Resources

About