Summary: Hepatitis delta virus delta antigen
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Hepatitis D Edit Wikipedia article
|Group:||Group V ((-)ssRNA)|
|Species:||Hepatitis delta virus|
|Classification and external resources|
Hepatitis D, also referred to as hepatitis D virus (HDV) and classified as Hepatitis delta virus, is a disease caused by a small circular enveloped RNA virus. It is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a subviral satellite because it can propagate only in the presence of the hepatitis B virus (HBV). Transmission of HDV can occur either via simultaneous infection with HBV (coinfection) or superimposed on chronic hepatitis B or hepatitis B carrier state (superinfection).
Both superinfection and coinfection with HDV results in more severe complications compared to infection with HBV alone. These complications include a greater likelihood of experiencing liver failure in acute infections and a rapid progression to liver cirrhosis, with an increased chance of developing liver cancer in chronic infections. In combination with hepatitis B virus, hepatitis D has the highest mortality rate of all the hepatitis infections, at 20%.
Hepatitis D virus was first reported in the mid-1977, by an Italian researcher, Mario Rizzetto, as a nuclear antigen in patients infected with HBV who had severe liver disease  This nuclear antigen was then thought to be a hepatitis B antigen and was called the delta antigen. Subsequent experiments in chimpanzees showed that the hepatitis delta antigen (HDAg) was a structural part of a pathogen that required HBV infection to replicate The entire virus was cloned and sequenced in 1986, and obtained its own genus: Deltavirus. 
 Structure and Genome
|Hepatitis delta virus delta antigen|
oligomerization domain of hepatitis delta antigen
The HDV is a small, spherical virus with a 36 nm diameter. It has an outer coat containing three HBV envelope proteins (called large, medium, and small hepatitis B surface antigens), and host lipids surrounding an inner nucleocapsid. The nucleocapsid contains single-stranded, circular RNA of 1679 nucleotides and about 200 molecules of hepatitis D antigen (HDAg) for each genome. The central region of HDAg has been shown to bind RNA. Several interactions are also mediated by a coiled-coil region at the N terminus of HDAg. The hepatitis D circular genome is unique to animal viruses because of its high GC nucleotide content. The HDV genome exists as an enveloped, negative sense, single-stranded, closed circular RNA. Its nucleotide sequence is 70% self-complementary, allowing the genome to form a partially double-stranded, rod-like RNA structure. With a genome of approximately 1700 nucleotides, HDV is the smallest "virus" known to infect animals. It has been proposed that HDV may have originated from a class of plant viruses called viroids.
 Life Cycle
The receptor that HDV recognizes on human hepatocytes has not been identified; however it is thought to be the same as the HBV receptor because both viruses have the same outer coat. HDV recognizes its receptor via the N-terminal domain of the large hepatitis B surface antigen, HBsAg. Mapping by mutagenesis of this domain has shown that amino acid residues 9-15 make up the receptor binding site. After entering the hepatocyte, the virus is uncoated and the nucleocapsid translocated to the nucleus due to a signal in HDAg Since the nucleocapsid does not contain an RNA polymerase to replicate the virus’ genome, the virus makes use of the cellular RNA polymerases. Initially just RNA pol II, now RNA polymerases I and III have also been shown to be involved in HDV replication Normally RNA polymerase II utilizes DNA as a template and produces mRNA. Consequently, if HDV indeed utilizes RNA polymerase II during replication, it would be the only known animal pathogen capable of using a DNA-dependent polymerase as an RNA-dependent polymerase.
The RNA polymerases treat the RNA genome as double stranded DNA due to the folded rod-like structure it is in. Three forms of RNA are made; circular genomic RNA, circular complementary antigenomic RNA, and a linear polyadenylated antigenomic RNA, which is the mRNA containing the open reading frame for the HDAg. Synthesis of antigenomic RNA occurs in the nucleolus, mediated by RNA Pol I, whereas synthesis of genomic RNA takes place in the nucleoplasm, mediated by RNA Pol II. HDV RNA is synthesized first as linear RNA that contains many copies of the genome. The genomic and antigenomic RNA contain a sequence of 85 nucleotides that acts as a ribozyme, which self-cleaves the linear RNA into monomers. This monomers are then ligated to form circular RNA 
There are eight reported genotypes of HDV with unexplained variations in their geographical distribution and pathogenicity.
 Delta antigens
A significant difference between viroids and HDV is that, while viroids produce no proteins, HDV is known to produce one protein, namely HDAg. It comes in two forms; a 27kDa large-HDAg, and a small-HDAg of 24kDa. The N-terminals of the two forms are identical, they differ by 19 more amino acids in the C-terminal of the large HDAg. Both isoforms are produced from the same reading frame which contains an UAG stop codon at codon 196, which normally produces only the small-HDAg. However, editing by cellular enzyme adenosine deaminase-1 changes the stop codon to UCG, allowing the large-HDAg to be produced  Despite having 90% identical sequences, these two proteins play diverging roles during the course of an infection. HDAg-S is produced in the early stages of an infection and enters the nucleus and supports viral replication. HDAg-L, in contrast, is produced during the later stages of an infection, acts as an inhibitor of viral replication, and is required for assembly of viral particles. Thus RNA editing by the cellular enzymes is critical to the virus’ life cycle because it regulates the balance between viral replication and virion assembly.
The routes of transmission of hepatitis D are similar to those for hepatitis B. Infection is largely restricted to persons at high risk of hepatitis B infection, particularly injecting drug users and persons receiving clotting factor concentrates. Worldwide more than 15 million people are co-infected. HDV is rare in most developed countries, and is mostly associated with intravenous drug use. However, HDV is much more common in the immediate Mediterranean region, sub-Saharan Africa, the Middle East, and the northern part of South America. In all, about 20 million people may be infected with HDV.
 Treatment and prevention
Three genotypes (I-III) were originally described. Genotype I has been isolated in Europe, North America, Africa and some Asia. Genotype II has been found in Japan, Taiwan, and Yakutia (Russia). Genotype III has been found exclusively in South America (Peru, Colombia, and Venezuela). Some genomes from Taiwan and the Okinawa islands have been difficult to type but have been placed in genotype 2. However it is now known that there are at least 8 genotypes of this virus (HDV-1 to HDV-8). Phylogenetic studies suggest an African origin for this pathogen.
An analysis of 36 strains of genotype 3 estimated that the most recent common ancestor of these strains originated ~1930. This genotype spread exponentially from early 1950s to the 1970s in South America. The substitution rate was estimated to be 1.07 × 10-3 substitutions per site per year.
Genotype 8 has also been isolated from South America. This strain is usually only found in Africa and may have been imported into South America with the slave trade.
Genotypes with the exception of type 1 have been found only in certain geographical areas: HDV-2 (previously HDV-IIa) is found in Japan, Taiwan and Yakoutia, Russia; HDV-4 (previously HDV-IIb) in Japan and Taiwan; HDV-3 in the Amazonian region; HDV-5, HDV-6, HDV-7 and HDV-8 in Africa.
 See also
- Makino S, Chang MF, Shieh CK et al. (1987). "Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA". Nature 329 (6137): 343–6. doi:10.1038/329343a0. PMID 3627276.
- Fattovich G, Giustina G, Christensen E et al. (March 2000). "Influence of hepatitis delta virus infection on morbidity and mortality in compensated cirrhosis type B". Gut 46 (3): 420–6. doi:10.1136/gut.46.3.420. PMC 1727859. PMID 10673308.
- Manuale di Gastroenterologia Unigastro pag. 260
- Rizzetto, M; Canese MG, Arico S, Criello O, Trepo C, Bonino F, Verme G (1997). "Immunofluorescence detection of new antigen-antibody system (delta/anti-delta) associated to hepatitis B virus in liver and in serum of HBsAg carriers". Gut 18 (12): 997–1003. doi:10.1136/gut.18.12.997. PMC 1411847. PMID 75123.
- Rizzetto, M; Canese, MG, Purcell, RH, London, WT, Sly, LD, Gerin, JL (1981 Nov-Dec). "Experimental HBV and delta infections of chimpanzees: occurrence and significance of intrahepatic immune complexes of HBcAg and delta antigen". Hepatology (Baltimore, Md.) 1 (6): 567–74. doi:10.1002/hep.1840010602. PMID 7030907.
- Wang, KS; Choo, QL, Weiner, AJ, Ou, JH, Najarian, RC, Thayer, RM, Mullenbach, GT, Denniston, KJ, Gerin, JL, Houghton, M (1986 Oct 9-15). "Structure, sequence and expression of the hepatitis delta (delta) viral genome". Nature 323 (6088): 508–14. doi:10.1038/323508a0. PMID 3762705.
- Fauquet, CM; Mayo MA, Maniloff J, Desselberger U, Ball LA (2005). "Deltavirus". Eight Report of the International Committee on Taxonomy of Viruses. London: 735–8.
- Poisson F, Roingeard P, Baillou A, Dubois F, Bonelli F, Calogero RA, Goudeau A (November 1993). "Characterization of RNA-binding domains of hepatitis delta antigen". J. Gen. Virol. 74 (Pt 11): 2473–8. PMID 8245865.
- Zuccola HJ, Rozzelle JE, Lemon SM, Erickson BW, Hogle JM (July 1998). "Structural basis of the oligomerization of hepatitis delta antigen". Structure 6 (7): 821–30. doi:10.1016/S0969-2126(98)00084-7. PMID 9687364.
- Saldanha JA, Thomas HC, Monjardino JP (July 1990). "Cloning and sequencing of RNA of hepatitis delta virus isolated from human serum". J. Gen. Virol. 71 (7): 1603–6. doi:10.1099/0022-1317-71-7-1603. PMID 2374010.
- Elena SF, Dopazo J, Flores R, Diener TO, Moya A (July 1991). "Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA". Proc. Natl. Acad. Sci. U.S.A. 88 (13): 5631–4. doi:10.1073/pnas.88.13.5631. PMC 51931. PMID 1712103.
- Sureau, C (2006). "The role of the HBV envelope proteins in the HDV replication cycle". Current topics in microbiology and immunology. Current Topics in Microbiology and Immunology 307: 113–31. doi:10.1007/3-540-29802-9_6. ISBN 978-3-540-29801-4. PMID 16903223.
- Barrera, A; Guerra, B, Notvall, L, Lanford, RE (2005 Aug). "Mapping of the Hepatitis B Virus Pre-S1 Domain Involved in Receptor Recognition". Journal of Virology 79 (15): 9786–98. doi:10.1128/JVI.79.15.9786-9798.2005. PMC 1181564. PMID 16014940.
- Engelke, M; Mills, K, Seitz, S, Simon, P, Gripon, P, Schnölzer, M, Urban, S (2006 Apr). "Characterization of a hepatitis B and hepatitis delta virus receptor binding site". Hepatology (Baltimore, Md.) 43 (4): 750–60. doi:10.1002/hep.21112. PMID 16557545.
- Schulze, A; Schieck, A, Ni, Y, Mier, W, Urban, S (2010 Feb). "Fine Mapping of Pre-S Sequence Requirements for Hepatitis B Virus Large Envelope Protein-Mediated Receptor Interaction". Journal of Virology 84 (4): 1989–2000. doi:10.1128/JVI.01902-09. PMC 2812397. PMID 20007265.
- Xia, YP; Yeh, CT, Ou, JH, Lai, MM (1992 Feb). "Characterization of nuclear targeting signal of hepatitis delta antigen: nuclear transport as a protein complex". Journal of Virology 66 (2): 914–21. PMC 240792. PMID 1731113.
- Lehmann E, Brueckner F, Cramer P (November 2007). "Molecular basis of RNA-dependent RNA polymerase II activity". Nature 450 (7168): 445–9. doi:10.1038/nature06290. PMID 18004386.
- Filipovska J, Konarska MM (January 2000). "Specific HDV RNA-templated transcription by pol II in vitro". RNA 6 (1): 41–54. doi:10.1017/S1355838200991167. PMC 1369892. PMID 10668797.
- Greco-Stewart, VS; Schissel, E, Pelchat, M (2009-03-30). "The hepatitis delta virus RNA genome interacts with the human RNA polymerases I and III". Virology 386 (1): 12–5. doi:10.1016/j.virol.2009.02.007. PMID 19246067.
- Li, YJ; Macnaughton, T, Gao, L, Lai, MM (2006 Jul). "RNA-Templated Replication of Hepatitis Delta Virus: Genomic and Antigenomic RNAs Associate with Different Nuclear Bodies". Journal of Virology 80 (13): 6478–86. doi:10.1128/JVI.02650-05. PMC 1488965. PMID 16775335.
- Branch, AD; Benenfeld, BJ, Baroudy, BM, Wells, FV, Gerin, JL, Robertson, HD (1989-02-03). "An ultraviolet-sensitive RNA structural element in a viroid-like domain of the hepatitis delta virus". Science 243 (4891): 649–52. doi:10.1126/science.2492676. PMID 2492676.
- Wu, HN; Lin, YJ, Lin, FP, Makino, S, Chang, MF, Lai, MM (1989 Mar). "Human hepatitis delta virus RNA subfragments contain an autocleavage activity". Proceedings of the National Academy of Sciences of the United States of America 86 (6): 1831–5. doi:10.1073/pnas.86.6.1831. PMC 286798. PMID 2648383.
- Weiner, AJ; Choo, QL, Wang, KS, Govindarajan, S, Redeker, AG, Gerin, JL, Houghton, M (1988 Feb). "A single antigenomic open reading frame of the hepatitis delta virus encodes the epitope(s) of both hepatitis delta antigen polypeptides p24 delta and p27 delta". Journal of Virology 62 (2): 594–9. PMC 250573. PMID 2447291.
- Jayan, GC; Casey, JL (2002 Dec). "Inhibition of Hepatitis Delta Virus RNA Editing by Short Inhibitory RNA-Mediated Knockdown of ADAR1 but Not ADAR2 Expression". Journal of Virology 76 (23): 12399–404. doi:10.1128/JVI.76.23.12399-12404.2002. PMC 136899. PMID 12414985.
- Sato S, Cornillez-Ty C, Lazinski DW (August 2004). "By Inhibiting Replication, the Large Hepatitis Delta Antigen Can Indirectly Regulate Amber/W Editing and Its Own Expression". J. Virol. 78 (15): 8120–34. doi:10.1128/JVI.78.15.8120-8134.2004. PMC 446097. PMID 15254184.
- Taylor, JM (2006). "Structure and replication of hepatitis delta virus RNA". Current topics in microbiology and immunology. Current Topics in Microbiology and Immunology 307: 1–23. doi:10.1007/3-540-29802-9_1. ISBN 978-3-540-29801-4. PMID 16903218.
- Chang, MF; Chen, CJ, Chang, SC (1994 Feb). "Mutational analysis of delta antigen: effect on assembly and replication of hepatitis delta virus". Journal of Virology 68 (2): 646–53. PMC 236498. PMID 8289368.
- Radjef N, Gordien E, Ivaniushina V et al. (March 2004). "Molecular Phylogenetic Analyses Indicate a Wide and Ancient Radiation of African Hepatitis Delta Virus, Suggesting a Deltavirus Genus of at Least Seven Major Clades". J. Virol. 78 (5): 2537–44. doi:10.1128/JVI.78.5.2537-2544.2004. PMC 369207. PMID 14963156.
- Taylor JM (January 2006). "Hepatitis delta virus". Virology 344 (1): 71–6. doi:10.1016/j.virol.2005.09.033. PMID 16364738.
- U.S. National Library of Medicine "Delta Agent (hepatitis D)"
- Tayor, JM (2009). Desk Encyclopedia of Human and Medical Virology. Boston: Academic Press. p. 121. ISBN 0-12-375147-0.
- Celik I, Karataylı E, Cevik E, et al. (December 2011). "Complete genome sequences and phylogenetic analysis of hepatitis delta viruses isolated from nine Turkish patients". Arch. Virol. 156 (12): 2215–20. doi:10.1007/s00705-011-1120-y. PMID 21984217.
- Radjef N, Gordien E, Ivaniushina V, Gault E, Anaïs P, Drugan T, Trinchet JC, Roulot D, Tamby M et al. (2004). "Molecular phylogenetic analyses indicate a wide and ancient radiation of African hepatitis delta virus, suggesting a deltavirus genus of at least seven major clades". J Virol 78 (5): 2537–2544.
- Alvarado-Mora MV, Romano CM, Gomes-Gouvêa MS, Gutierrez MF, Carrilho FJ, Pinho JR (2011) Dynamics of hepatitis D (delta) virus genotype 3 in the Amazon region of South America. Infect Genet Evol 11(6):1462-8. doi: 10.1016/j.meegid.2011.05.020
- Barros LM, Gomes-Gouvêa MS, Pinho JR, Alvarado-Mora MV, Dos Santos A, Mendes-Corrêa MC, Caldas AJ, Sousa MT, Santos MD, Ferreira AS (2011) Hepatitis Delta virus genotype 8 infection in Northeast Brazil: inheritance from African slaves? Virus Res 160(1-2):333-339 doi: 10.1016/j.virusres.2011.07.006
- Le Gal F, Gault E, Ripault MP, Serpaggi J, Trinchet JC, Gordien E, Dény P (2006) Eighth major clade for hepatitis delta virus. Emerg Infect Dis 12(9):1447-1450
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Hepatitis delta virus delta antigen Provide feedback
The hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA . Several interactions are also mediated by a coiled-coil region at the N terminus of the protein .
Poisson F, Roingeard P, Baillou A, Dubois F, Bonelli F, Calogero RA, Goudeau A; , J Gen Virol 1993;74:2473-2478.: Characterization of RNA-binding domains of hepatitis delta antigen. PUBMED:8245865 EPMC:8245865
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002506The Hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA [PUBMED:8245865]. Several interactions are also mediated by a coiled-coil region at the N terminus of the protein [PUBMED:9687364].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||host cell nucleus (GO:0042025)|
|Molecular function||RNA binding (GO:0003723)|
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_808 (release 4.0)|
|Number in seed:||4|
|Number in full:||1108|
|Average length of the domain:||117.60 aa|
|Average identity of full alignment:||80 %|
|Average coverage of the sequence by the domain:||89.58 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
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The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the HDV_ag domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...