Isolation and characterisation of an ISKNV-genotype megalocytivirus from imported angelfish Pterophyllum scalare

2020 ◽  
Vol 140 ◽  
pp. 129-141
Author(s):  
Y Kawato ◽  
PG Mohr ◽  
MStJ Crane ◽  
LM Williams ◽  
MJ Neave ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Sea Bream ◽  
Whole Genome ◽  
Red Sea Bream ◽  
Capsid Protein Gene ◽  
Infected Cells ◽  
Clade 1 ◽  
Pterophyllum Scalare

Using cultures of the SKF-9 cell line, megalocytivirus AFIV-16 was isolated from imported angelfish Pterophyllum scalare held in quarantine at the Australian border. The cytopathic effect caused by isolate AFIV-16 presented as cell rounding and enlargement, but complete destruction of the infected cell cultures did not occur. The infected cells demonstrated immunocytochemical reactivity with monoclonal antibody M10, which is used for diagnosis of OIE-listed red sea bream iridoviral disease. Using electron microscopy, the virus particles, consisting of hexagonal nucleocapsids, were observed in the cytoplasm of SKF-9 cells. The replication of AFIV-16 in cultured SKF-9 cells was significantly greater at 28°C incubation than at 22 and 25°C incubation, whereas no difference in growth characteristics was observed for red sea bream iridovirus (RSIV) isolate KagYT-96 across this temperature range. Whole genome sequencing demonstrated that AFIV-16 has a 99.96% similarity to infectious spleen and kidney necrosis virus (ISKNV), the type species in the genus Megalocytivirus. AFIV-16 was classified into ISKNV genotype Clade 1 by phylogenetic analysis of the major capsid protein gene nucleotide sequence. This is the first report of whole genome sequencing of an ISKNV genotype megalocytivirus isolated from ornamental fish.

scholarly journals Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bo-Hye Nam ◽  
DongAhn Yoo ◽  
Young-Ok Kim ◽  
Jung Youn Park ◽  
Younhee Shin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Artificial Selection ◽  
Sea Bream ◽  
Whole Genome ◽  
Red Sea Bream ◽  
Fish Farms ◽  
The Impact

scholarly journals Author Correction: Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bo-Hye Nam ◽  
DongAhn Yoo ◽  
Young-Ok Kim ◽  
Jung Youn Park ◽  
Younhee Shin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Artificial Selection ◽  
Sea Bream ◽  
Whole Genome ◽  
Red Sea Bream ◽  
Fish Farms ◽  
The Impact

scholarly journals ELECTRON MICROSCOPIC STUDY ON ENLARGED CELLS OF RED SEA BREAM, Pagrus major INFECTED BY THE RED SEA BREAM IRIDOVIRUS (RSIV, GENUS Megalocytivirus, FAMILY Iridoviridae)

2009 ◽  
Vol 4 (1) ◽  
pp. 53
Author(s):  
Ketut Mahardika
Keyword(s):  
Electron Microscope ◽  
Inclusion Body ◽  
Red Sea ◽  
Virus Assembly ◽  
Infected Fish ◽  
Sea Bream ◽  
Red Sea Bream ◽  
Electron Microscopic ◽  
Target Organs ◽  
Infected Cells

Most histopathologycal studies of the red sea bream iridovirus (RSIV) disease in red sea bream have been performed by studying enlarged cells as well as necrotized cells in the spleen and other organs. These enlarged cells have been named as inclusion body bearing cells (IBCs). However, few information is available about detail of ultrastructural features of IBCs produced in the target organs of RSIV-infected fish. In the present study, details of ultrastructural features of IBCs that were produced in the spleen tissue of naturally RSIV-infected red sea bream were investigated under electron microscope. Under electron microscope, RSIV-infected red sea bream had the presence of two types of IBCs: typical IBCs allowing virus assembly within viral assembly site (VAS), and atypical IBCs which degenerate organelles without virus assembly. Other infected-cells were observed as necrotized cells forming intracytoplasmic VAS with large numbers of virions, but without the formation of the distinct inclusion body. Morphogenesis steps on RSIV-infected red sea bream were observed as filamentous-filed virions, partially-filled virions and complete virions with 145-150 nm in size. These findings confirmed that RSIV-infected red sea bream were characterized by formation of typical and atypical IBCs as well as necrotized cells.

scholarly journals Comprehensive analysis of RNA-seq and whole genome sequencing data reveals no evidence for SARS-CoV-2 integrating into host genome

2021 ◽  
Author(s):  
Yu-Sheng Chen ◽  
Shuaiyao Lu ◽  
Bing Zhang ◽  
Tingfu Du ◽  
Wen-Jie Li ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Comprehensive Analysis ◽  
Host Genome ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Rna Seq ◽  
Sequencing Data ◽  
Infected Cells

SARS-CoV-2, as the causation of severe epidemic of COVID-19, is one kind of positive single-stranded RNA virus with high transmissibility. However, whether or not SARS-CoV-2 can integrate into host genome needs thorough investigation. Here, we performed both RNA sequencing (RNA-seq) and whole genome sequencing on SARS-CoV-2 infected human and monkey cells, and investigated the presence of host-virus chimeric events. Through RNA-seq, we did detect the chimeric host-virus reads in the infected cells. But further analysis using mixed libraries of infected cells and uninfected zebrafish embryos demonstrated that these reads are falsely generated during library construction. In support, whole genome sequencing also didn't identify the existence of chimeric reads in their corresponding regions. Therefore, the evidence for SARS-CoV-2's integration into host genome is lacking.

scholarly journals Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Siham Fatani ◽  
Yoshimoto Saito ◽  
Mohammed Alarawi ◽  
Takashi Gojobori ◽  
Katsuhiko Mineta
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Red Sea ◽  
Plant Biomass ◽  
Seawater Temperature ◽  
Cellulase Activity ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Isolation And Characterization ◽  
Bacillus Paralicheniformis

Abstract Background Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. Results Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. Conclusions Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes.

scholarly journals Phenotypic Diversity of Infectious Red Sea Bream Iridovirus Isolates from Cultured Fish in Japan

2009 ◽  
Vol 75 (11) ◽  
pp. 3535-3541 ◽  
Author(s):  
Hajime Shinmoto ◽  
Ken Taniguchi ◽  
Takuya Ikawa ◽  
Kenji Kawai ◽  
Syun-ichirou Oshima
Keyword(s):  
Red Sea ◽  
Phenotypic Diversity ◽  
Sea Bream ◽  
Cell Culture Supernatant ◽  
Red Sea Bream ◽  
Virus Family ◽  
Recent Emergence ◽  
Infected Cells

ABSTRACT Megalocytivirus is causing economically serious mass mortality by infecting fish in and around the Pacific region of Asia. The recent emergence of many new iridoviruses has drawn attention to the marked taxonomic variation within this virus family. Most studies of these viruses have not included extensive study of these emergent species. We explored the emergence of red sea bream iridovirus (RSIV) on a fish farm in Japan, and we specifically endeavored to quantify genetic and phenotypic differences between RSIV isolates using in vitro and in vivo methods. The three isolates had identical major capsid protein sequences, and they were closely related to Korean RSIV isolates. In vitro studies revealed that the isolates differed in replication rate, which was determined by real-time quantitative PCR of viral genomes in infected cells and cell culture supernatant, and in cell viability, estimated by the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay for infected cells. In vivo studies showed that the isolates exhibit different virulence characteristics: infected red sea bream showed either acute death or subacute death according to infection with different isolates. Significant differences were seen in the antigenicity of isolates by a formalin-inactivated vaccine test. These results revealed that variant characteristics exist in the same phylogenetic location in emergent iridoviruses. We suggest that this strain variation would expand the host range in iridoviral epidemics.

scholarly journals Complete genome sequencing of Red Sea Bream Iridovirus (RSIV)

2002 ◽  
Vol 68 (sup2) ◽  
pp. 1113-1115 ◽  
Author(s):  
JUN KURITA ◽  
KAZUHIRO NAKAJIMA ◽  
IKUO HIRONO ◽  
TAKASHI AOKI
Keyword(s):  
Genome Sequencing ◽  
Red Sea ◽  
Complete Genome ◽  
Sea Bream ◽  
Red Sea Bream ◽  
Complete Genome Sequencing

scholarly journals 516. SARS-CoV-2 Exhibits Clade-specific Differences in Nasopharyngeal Viral Loads

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S324-S324
Author(s):  
Hannah Nam ◽  
Ramon Lorenzo-Redondo ◽  
Scott C Roberts ◽  
Lacy Simons ◽  
Chad Achenbach ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Clinical Significance ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Upper Airways ◽  
Viral Loads ◽  
Viral Spread ◽  
Clade 1 ◽  
Over Time

Abstract Background The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of distinct viral clades, although their clinical significance has yet to be fully elucidated. While whole genome sequencing efforts have identified viral diversity over time, less is known about the clinical significance of this diversity. This study assessed the nasopharyngeal viral loads within patients over time to determine if these changes affect clinical parameters. Methods Samples were collected from patients presenting to Northwestern Memorial Hospital in Chicago, IL with a positive SARS-CoV-2 RT-PCR from nasopharyngeal swabs. Cycle threshold (Ct) values less than 35 were considered positive, and whole genome sequencing was performed by reverse transcription, multiplex PCR, and Nanopore sequencing. Phylogenetic analysis was conducted on sequenced isolates and compared with publicly available global sequences. Sequence characteristics and viral loads were correlated with each clade. Results 177 samples were analyzed from March 14, 2020, through May 1, 2020. Most of the sequences (92.6%) clustered in three main clades [Figure 1]. Clade IDs were ordered by relative abundance as Clades 1 (n=122, 68.9%), 2 (n=34, 19.2%), and 3 (n=8, 4.5%). Over this time, Clade 1 viruses have been increasing in incidence across the USA and globally while Clade 2 viruses were uniquely predominant in Illinois with limited global distribution. Ct values were compared across clades [Figure 2]. Significantly lower average Ct values (higher viral loads) were observed in Clade 1 relative to both Clade 2 (p=0.0002) and Clade 3 (p=0.0011). These findings were independent of time from symptom onset to specimen collection. Phylogenetic Analysis of SARS-CoV-2 Isolates with Number of Clades and Clade Distribution Associations Between Viral Clade and Ct Value Conclusion These data suggest that SARS-CoV-2 genotype may impact viral load in the upper airways. It remains to be determined whether this difference in clades may impact transmission potential and overall viral spread. Further longitudinal studies with more specimens and associated clinical data are needed. Disclosures Michael G. Ison, MD MS, AlloVir (Consultant)

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular
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