scholarly journals Variable In Vivo Hepatitis D Virus (HDV) RNA Editing Rates According to the HDV Genotype

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1572
Author(s):  
Samira Dziri ◽  
Christophe Rodriguez ◽  
Athenaïs Gerber ◽  
Ségolène Brichler ◽  
Chakib Alloui ◽  
...  
Keyword(s):  
Rna Editing ◽  
Stop Codon ◽  
Genome Replication ◽  
Hepatitis D ◽  
Reading Frame ◽  
Delta Antigen ◽  
B Virus ◽  
Virion Morphogenesis ◽  
Kinetics Of

Human hepatitis delta virus (HDV) is a small defective RNA satellite virus that requires hepatitis B virus (HBV) envelope proteins to form its own virions. The HDV genome possesses a single coding open reading frame (ORF), located on a replicative intermediate, the antigenome, encoding the small (s) and the large (L) isoforms of the delta antigen (s-HDAg and L-HDAg). The latter is produced following an editing process, changing the amber/stop codon on the s-HDAg-ORF into a tryptophan codon, allowing L-HDAg synthesis by the addition of 19 (or 20) C-terminal amino acids. The two delta proteins play different roles in the viral cell cycle: s-HDAg activates genome replication, while L-HDAg blocks replication and favors virion morphogenesis and propagation. L-HDAg has also been involved in HDV pathogenicity. Understanding the kinetics of viral editing rates in vivo is key to unravel the biology of the virus and understand its spread and natural history. We developed and validated a new assay based on next-generation sequencing and aimed at quantifying HDV RNA editing in plasma. We analyzed plasma samples from 219 patients infected with different HDV genotypes and showed that HDV editing capacity strongly depends on the genotype of the strain.

scholarly journals Hepatitis D virus RNA editing is inhibited by a GFP fusion protein containing a C-terminally deleted delta antigen

2004 ◽  
Vol 85 (4) ◽  
pp. 947-957 ◽  
Author(s):  
Ko-Nien Shih ◽  
Ya-Ting Chuang ◽  
Hsuan Liu ◽  
Szecheng J. Lo
Keyword(s):  
Rna Editing ◽  
Fusion Proteins ◽  
Cellular Localization ◽  
Stop Codon ◽  
Pcr Analysis ◽  
Restriction Enzyme Digestion ◽  
Nuclear Speckles ◽  
Hepatitis D ◽  
Hepatitis D Virus ◽  
Delta Antigen

During its life cycle, hepatitis D virus (HDV) produces two forms of delta antigen (HDAg), small delta antigen (SDAg) and large delta antigen (LDAg), which differ in their C-terminal 19 amino acids. Host enzymes termed ADARs (adenosine deaminases that act on double-stranded RNA) are required for LDAg production. These enzymes change the stop codon (UAG) of SDAg to a tryptophan codon (UGG). However, the temporal and spatial regulation of HDV RNA editing is largely unknown. In this study, we constructed three GFP fusion proteins containing different lengths of SDAg and characterized their cellular localization and effects on HDV replication. One of these fusion proteins, designated D(1–88)-GFP, inhibited LDAg but not SDAg production, suggesting that D(1–88)-GFP inhibits HDV RNA editing. Two experiments further supported this supposition: (i) RT-PCR analysis combined with NcoI restriction enzyme digestion revealed that HDV RNA editing was reduced by 42 % in HeLa-D(1–88)-GFP when compared with HeLa cells; and (ii) the ratio of SDAg/LDAg production from the reporter RNAs was reduced in cells co-transfected with ADAR-expressing and reporter plasmids in the presence of D(1–88)-GFP. Double fluorescence microscopy found that D(1–88)-GFP was either associated with SC-35 or was adjacent to PML (premyelocytic leukaemia antigen) at nuclear speckles, but D(1–88)-GFP was not co-localized with ADAR, which was mainly located in the nucleolus. In situ hybridization showing co-localization of HDV RNA with D(1–88)-GFP at nuclear speckles suggested that HDV RNA editing might occur in the nuclear speckles and require other nuclear factor(s), in addition to ADAR.

scholarly journals A Divergent Hepatitis D-Like Agent in Birds

Viruses ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 720 ◽  
Author(s):  
Michelle Wille ◽  
Hans Netter ◽  
Margaret Littlejohn ◽  
Lilly Yuen ◽  
Mang Shi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hepatitis B Virus ◽  
Sequence Analysis ◽  
Hepatitis B ◽  
Hepatitis Delta Virus ◽  
Amino Acid Similarity ◽  
Hepatitis D ◽  
Delta Antigen ◽  
B Virus ◽  
Delta Virus

Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.

scholarly journals Murine cytomegalovirus open reading frame m29.1 augments virus replication both in vitro and in vivo

2007 ◽  
Vol 88 (11) ◽  
pp. 2941-2951 ◽  
Author(s):  
Mohammad M. Ahasan ◽  
Clive Sweet
Keyword(s):  
Virus Replication ◽  
Post Infection ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Open Reading Frame ◽  
Murine Cytomegalovirus ◽  
Reading Frame ◽  
Codon Mutation

Murine cytomegalovirus mutant Rc29, with a premature stop codon mutation in the m29 open reading frame (ORF), produced no apparent phenotype in cell culture or following infection of BALB/c mice. In contrast, a similar mutant virus, Rc29.1, with a premature stop codon mutation in its m29.1 ORF, showed reduced virus yields (2–3 log10 p.f.u. ml−1) in tissue culture. Mutant virus yields in BALB/c mice were delayed, reduced (∼1 log10 p.f.u. per tissue) and persisted less well in salivary glands compared with wild-type (wt) and revertant (Rv29.1) virus. In severe combined immunodeficiency mice, Rc29.1 virus showed delayed and reduced replication initially in all tissues (liver, spleen, kidneys, heart, lung and salivary glands). This delayed death until 31 days post-infection (p.i.) compared with wt (23 days p.i.) but at death virus yields were similar to wt. m29 gene transcription was initiated at early times post-infection, while production of a transcript from ORF m29.1 in the presence of cycloheximide indicated that it was an immediate-early gene. ORFs m29.1 and M28 are expressed from a bicistronic message, which is spliced infrequently. However, it is likely that each ORF expresses its own protein, as antiserum derived in rabbits to the m29.1 protein expressed in bacteria from the m29.1 ORF detected only one protein in Western blot analysis of the size predicted for the m29.1 protein. Our results suggest that neither ORF is essential for virus replication but m29.1 is important for optimal viral growth in vitro and in vivo.

scholarly journals Interaction and Replication Activation of Genotype I and II Hepatitis Delta Antigens

2004 ◽  
Vol 78 (6) ◽  
pp. 2693-2700 ◽  
Author(s):  
Sheng-Chieh Hsu ◽  
Jaw-Ching Wu ◽  
I-Jane Sheen ◽  
Wan-Jr Syu
Keyword(s):  
Genotype I ◽  
Hepatitis Delta ◽  
Hepatitis D ◽  
Virus Surface ◽  
Delta Antigen ◽  
B Virus ◽  
Hepatitis Delta Antigen ◽  
Different Origins ◽  
Genotype Ii ◽  
Hdv Genotype

ABSTRACT The nucleotide sequences of hepatitis D viruses (HDV) vary 5 to 14% among isolates of the same genotype and 23 to 34% among different genotypes. The only viral-genome-encoded antigen, hepatitis delta antigen (HDAg), has two forms that differ in size. The small HDAg (HDAg-S) trans-activates viral replication, while the large form (HDAg-L) is essential for viral assembly. Previously, it has been shown that the packaging efficiency of HDAg-L is higher for genotype I than for genotype II. In this study, the question of whether other functional properties of the HDAgs are affected by genotype differences is addressed. By coexpression of the two antigens in HuH-7 cells followed by specific antibody precipitation, it was found that HDAgs of different origins interacted without genotypic discrimination. Moreover, in the presence of hepatitis B virus surface antigen, HDAg-S was incorporated into virion-like particles through interaction with HDAg-L without genotype restriction. As to the differences in replication activation of genotype I HDV RNA, all HDAg-S clones tested had some trans-activation activity, and this activity varied greatly among isolates. As to the support of HDV genotype II replication, only clones of HDAg-S from genotype II showed trans-activation activity, and this activity also varied among isolates. In conclusion, genotype has no effect on HDAg interaction and genotype per se only partly predicts how much the HDAg-S of an HDV isolate affects the replication of a second HDV isolate.

scholarly journals A divergent hepatitis D-like agent in birds

2018 ◽  
Author(s):  
Michelle Wille ◽  
Hans J. Netter ◽  
Margaret Littlejohn ◽  
Lilly Yuen ◽  
Mang Shi ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Hepatitis Delta Virus ◽  
Amino Acid Similarity ◽  
Hepatitis Delta ◽  
Hepatitis D ◽  
Delta Antigen ◽  
B Virus ◽  
Severe Liver Disease ◽  
Delta Virus

AbstractHepatitis delta virus (HDV) is currently only found in humans, and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and subviral agents.ImportanceHepatitis delta virus (HDV) is currently only found in humans, and coinfections of HDV and Hepatitis B virus (HBV) in humans result in severe liver disease. There are a number of hypotheses for the origin of HDV, although a key component of all is that HDV only exists in humans. Here, we describe a novel deltavirus-like agent identified in wild birds. Although this agent is genetically divergent, it exhibits important similarities to HDV, such as the presence of ribosymes and self-complementarity. The discovery of an avian HDV-like agent challenges our understanding of both the origin and the co-evolutionary relationships of subviral agents with helper viruses.

scholarly journals The guanine nucleoside analog penciclovir is active against chronic duck hepatitis B virus infection in vivo.

1996 ◽  
Vol 40 (2) ◽  
pp. 413-418 ◽  
Author(s):  
E Lin ◽  
C Luscombe ◽  
Y Y Wang ◽  
T Shaw ◽  
S Locarnini
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Nucleoside Analog ◽  
Genome Replication ◽  
Viral Dna ◽  
Duck Hepatitis B Virus ◽  
Protein Levels ◽  
Duck Hepatitis ◽  
B Virus

Ducks congenitally infected with duck hepatitis B virus (HBV) were treated with the antiviral guanine nucleoside analog penciclovir for 4 weeks at a dose of 10 mg/kg of body weight per day. The effects of treatment on viremia and intrahepatic viral genome replication, transcription, and translation were examined. In seven of eight penciclovir-treated ducks, viremia was barely detectable after a week of treatment. After 4 weeks of treatment, molecular hybridization studies showed that intrahepatic viral DNA, RNA, and protein levels were significantly reduced compared with those in placebo-treated controls. Synthesis of all viral replicative intermediates, including the normally persistent viral supercoiled DNA species, was inhibited by penciclovir treatment. Examination of liver tissue sections after in situ DNA hybridization or immunohistochemical staining confirmed that viral DNA and protein synthesis had been profoundly inhibited in most hepatic parenchymal cells. However, small subpopulations of cells, in particular the small bile duct epithelial cells, remained strongly positive for duck HBV antigens and DNA despite treatment. There was no evidence of toxicity associated with penciclovir therapy. This study confirms the safety and potent antihepadnaviral activity of penciclovir in vivo but indicates that further improvements in antiviral therapy will be required to completely eliminate HBV infection.

scholarly journals Regulation of the ORF61 Promoter and ORF61 Functions in Varicella-Zoster Virus Replication and Pathogenesis

2009 ◽  
Vol 83 (15) ◽  
pp. 7560-7572 ◽  
Author(s):  
Li Wang ◽  
Marvin Sommer ◽  
Jaya Rajamani ◽  
Ann M. Arvin
Keyword(s):  
Varicella Zoster Virus ◽  
Binding Sites ◽  
Transient Transfection ◽  
Cellular Proteins ◽  
Histone Deacetylase Inhibition ◽  
Reading Frame ◽  
Varicella Zoster ◽  
Virion Morphogenesis ◽  
Simplex Virus

ABSTRACT Varicella-zoster virus (VZV) open reading frame 61 (ORF61) encodes a protein that transactivates viral and cellular promoters in transient-transfection assays and is the ortholog of herpes simplex virus ICP0. In this report, we mapped the ORF61 promoter and investigated its regulation by viral and cellular proteins in transient-expression experiments and by mutagenesis of the VZV genome (parent Oka strain). The 5′ boundary of the minimal ORF61 promoter required for IE62 transactivation was mapped to position −95 relative to the mRNA start site, and three noncanonical GT-rich Sp1-binding sites were documented to occur within the region comprising positions −95 to −45. Contributions of the three Sp1-binding-site motifs, designated Sp1a, Sp1b, and Sp1c, to ORF61 expression and viral replication were varied despite their similar sequences. Two sites, Sp1a and Sp1c, functioned synergistically. When both sites were mutated in the pOka genome to produce pOka-61proΔSp1ac, the mutant virus expressed significantly less ORF61 protein. Using this mutant to investigate ORF61 functions resulted in reductions in the expression levels of IE proteins, viral kinases ORF47 and ORF66, and the major glycoprotein gE, with the most impact on gE. Virion morphogenesis appeared to be intact despite minimal ORF61 expression. Pretreating melanoma cells with sodium butyrate enhanced titers of pOka-61proΔSp1ac but not pOka, suggesting that ORF61 has a role in histone deacetylase inhibition. Growth of pOka-61proΔSp1ac was impaired in SCIDhu skin xenografts, indicating that the regulation of the ORF61 promoter by Sp1 family proteins is important for ORF61 expression in vivo and that ORF61 contributes to VZV virulence at skin sites of replication.

scholarly journals Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades

2004 ◽  
Vol 78 (5) ◽  
pp. 2537-2544 ◽  
Author(s):  
Nadjia Radjef ◽  
Emmanuel Gordien ◽  
Valeria Ivaniushina ◽  
Elyanne Gault ◽  
Patricia Anaïs ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Hepatitis D ◽  
Delta Antigen ◽  
Phylogenetic Reconstructions ◽  
B Virus ◽  
Molecular Phylogenetic ◽  
Full Length Genome ◽  
Delta Virus

ABSTRACT Hepatitis D virus (HDV) is a satellite of hepatitis B virus (HBV) for transmission and propagation and infects nearly 20 million people worldwide. The HDV genome is a compact circular single-stranded RNA genome with extensive intramolecular complementarity. Despite its different epidemiological and pathological patterns, the variability and geographical distribution of HDV are limited to three genotypes and two subtypes that have been characterized to date. Phylogenetic reconstructions based on the delta antigen gene and full-length genome sequence data show an extensive and probably ancient radiation of African lineages, suggesting that the genetic variability of HDV is much more complex than was previously thought, with evidence of additional clades. These results relate the geographic distribution of HDV more closely to the genetic variability of its helper HBV.

scholarly journals d-Ala:d-Ala Ligase Gene Flanking the vanC Cluster: Evidence for Presence of Three Ligase Genes in Vancomycin-Resistant Enterococcus gallinarum BM4174

2002 ◽  
Vol 46 (1) ◽  
pp. 95-100 ◽  
Author(s):  
Ole-Herman Ambúr ◽  
Peter E. Reynolds ◽  
Cesar A. Arias
Keyword(s):  
Biochemical Characterization ◽  
Stop Codon ◽  
Structural Similarity ◽  
Amino Acid Identity ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
Plasmid Construct ◽  
Vancomycin Resistant ◽  
Enterococcus Gallinarum

ABSTRACT An open reading frame located 230 nucleotides downstream from the stop codon of vanS c and in the opposite direction relative to the other genes of the vanC cluster was identified in Enterococcus gallinarum BM4174. This gene (designated ddl2) encoded a protein of 343 amino acids that had significant predicted structural similarity to d-Ala:d-Ala ligases and displayed 33 and 35% amino acid identity to VanC-1 and the previously reported partial sequence of Ddl from E. gallinarum, respectively. Biochemical characterization by thin-layer chromatography confirmed that Ddl2 is a d-Ala:d-Ala ligase with no detectable d-Ala:d-Ser ligase activity. The vancomycin dependence of Enterococcus faecalis BM4320 (ddl mutant) was lost on electroporation of a plasmid construct expressing ddl2 constitutively. The latter strain was able to grow in the absence of vancomycin, and peptidoglycan precursor analysis under the same conditions indicated the synthesis of pentapeptide[d-Ala] as the main precursor, confirming the activity of Ddl2 in vivo. Expression of ddl and ddl2 in BM4174 was tested by reverse transcription-PCR: results suggested that both d-Ala:d-Ala ligases were expressed concomitantly. Our findings indicate that vancomycin-resistant E. gallinarum BM4174 is likely to express one d-Ala:d-Ser and two d-Ala:d-Ala ligase genes.

scholarly journals Attenuation of Marek's Disease Virus by Deletion of Open Reading Frame RLORF4 but Not RLORF5a

2005 ◽  
Vol 79 (18) ◽  
pp. 11647-11659 ◽  
Author(s):  
Keith W. Jarosinski ◽  
Nikolaus Osterrieder ◽  
Venugopal K. Nair ◽  
Karel A. Schat
Keyword(s):  
Virus Isolation ◽  
Cultured Cells ◽  
Artificial Chromosome ◽  
Marek's Disease ◽  
Marek’S Disease ◽  
Reading Frame ◽  
Multiple Organs ◽  
Kinetics Of

ABSTRACT Marek's disease (MD) in chickens is caused by the alphaherpesvirus MD virus (MDV) and is characterized by the development of lymphoblastoid tumors in multiple organs. The recent identification and cloning of RLORF4 and the finding that four of six attenuated strains of MDV contained deletions within RLORF4 suggested that it is involved in the attenuation process of MDV. To assess the role of RLORF4 in MD pathogenesis, its coding sequence was deleted in the pRB-1B bacterial artificial chromosome clone. Additionally, RLORF5a was deleted separately to examine its importance for oncogenesis. The sizes of plaques produced by MDV reconstituted from pRB-1BΔRLORF5a (rRB-1BΔRLORF5a) were similar to those produced by the parental pRB-1B virus (rRB-1B). In contrast, virus reconstituted from pRB-1BΔRLORF4 (rRB-1BΔRLORF4) produced significantly larger plaques. Replication of the latter virus in cultured cells was higher than that of rRB-1B or rRB-1BΔRLORF5a using quantitative PCR (qPCR) assays. In vivo, both deletion mutants and rRB-1B replicated at comparable levels at 4, 7, and 10 days postinoculation (p.i.), as determined by virus isolation and qPCR assays. At 14 days p.i., the number of PFU of virus isolated from chickens infected with rRB-1BΔRLORF4 was comparable to that from chickens infected with highly attenuated RB-1B and significantly lower than that from rRB-1B-infected birds. The number of tumors and kinetics of tumor production in chickens infected with rRB-1BΔRLORF5a were similar to those of P2a chickens infected with rRB-1B. In stark contrast, none of the chickens inoculated with rRB-1BΔRLORF4 died up to 13 weeks p.i.; however, two chickens had tumors at the termination of the experiment. The data indicate that RLORF4 is involved in attenuation of MDV, although the function of RLORF4 is still unknown.

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