Hepatitis B virus
Hepatitis B virus, abbreviated HBV, is of the double stranded DNA type, a species of the genus Orthohepadnavirus, which is likewise a part of the Hepadnaviridae family of viruses. This virus causes the disease hepatitis B.
|Hepatitis B virus|
|TEM micrograph showing hepatitis B viruses|
|Group:||Group VII (dsDNA-RT)|
|Species:||Hepatitis B virus|
The hepatitis B virus is classified as the type species of the Orthohepadnavirus, which contains three other species: the Ground squirrel hepatitis virus, Woodchuck hepatitis virus, and the Woolly monkey hepatitis B virus. The genus is classified as part of the Hepadnaviridae family, which contains two other genera, the Avihepadnavirus and a second which has yet to be assigned. This family of viruses have not been assigned to a viral order. Viruses similar to hepatitis B have been found in all apes (orangutan, gibbons, gorillas and chimpanzees), in Old World monkeys, and in a New World woolly monkeys suggesting an ancient origin for this virus in primates.
The virus is divided into four major serotypes (adr, adw, ayr, ayw) based on antigenic epitopes present on its envelope proteins. These serotypes are based on a common determinant (a) and two mutually exclusive determinant pairs (d/y and w/r). The viral strains have also been divided into ten genotypes (A–J) and forty subgenotypes according to overall nucleotide sequence variation of the genome. The genotypes have a distinct geographical distribution and are used in tracing the evolution and transmission of the virus. Differences between genotypes affect the disease severity, course and likelihood of complications, and response to treatment and possibly vaccination. The serotypes and genotypes do not necessarily correspond.
A number of as yet unclassified Hepatitis B like species have been isolated from bats.
Hepatitis B virus is a member of the Hepadnavirus family. The virus particle, called Dane particle (virion), consists of an outer lipid envelope and an icosahedral nucleocapsid core composed of protein. The nucleocapsid encloses the viral DNA and a DNA polymerase that has reverse transcriptase activity similar to retroviruses. The outer envelope contains embedded proteins which are involved in viral binding of, and entry into, susceptible cells. The virus is one of the smallest enveloped animal viruses with a virion diameter of 42 nm, but pleomorphic forms exist, including filamentous and spherical bodies lacking a core. These particles are not infectious and are composed of the lipid and protein that forms part of the surface of the virion, which is called the surface antigen (HBsAg), and is produced in excess during the life cycle of the virus.
It consists of:
- HBcAg (HBeAg is a splice variant)
- Hepatitis B virus DNA polymerase
- HBx. The function of this protein is not yet well known, but evidence suggests it plays a part in the activation of the viral transcription process.
The early evolution of the Hepatitis B, like that of all viruses, is difficult to establish.
The divergence of orthohepadnavirus and avihepadnavirus occurred ~125,000 years ago (95% interval 78,297–313,500). Both the Avihepadnavirus and Orthohepadna viruses began to diversify about 25,000 years ago. The branching at this time lead to the emergence of the Orthohepadna genotypes A–H. Human strains have a most recent common ancestor dating back to 7,000 (95% interval: 5,287–9,270) to 10,000 (95% interval: 6,305–16,681) years ago.
The rate of nonsynonymous mutations in this virus has been estimated to be about 2×10−5 amino acid replacements per site per year. The mean number of nucleotide substitutions/site/year is ~7.9×10−5.
A second estimate of the origin of this virus suggests a most recent common ancestor of the human strains evolved ~1500 years ago. The most recent common ancestor of the avian strains was placed at 6000 years ago. The mutation rate was estimated to be ~10−6 substitutions/site/year.
Another analysis with a larger data set suggests that Hepatitis B infected humans 33,600 years ago (95% higher posterior density 22,000-47,100 years ago. The estimated substitution rate was 2.2 × 10−6 substitutions/site/year. A significant increase in the population was noted within the last 5,000 years. Cross species infection to orangutans and gibbons occurred within the last 6,100 years.
Examination of sequences in the zebra finch have pushed the origin of this genus back at least to  Chimpanzee, gorilla, orangutan, and gibbons species cluster with human isolates. Non primate species included the woodchuck hepatitis virus, the ground squirrel hepatitis virus and arctic squirrel hepatitis virus. A number of bat infecting species have also been described. It has been proposed that a New World bat species may be the origin of the primate species.and possibly to .
The genome of HBV is made of circular DNA, but it is unusual because the DNA is not fully double-stranded. One end of the full length strand is linked to the viral DNA polymerase. The genome is 3020–3320 nucleotides long (for the full length strand) and 1700–2800 nucleotides long (for the short length strand).
The negative-sense, (non-coding) strand is complementary to the viral mRNA. The viral DNA is found in the nucleus soon after infection of the cell. The partially double-stranded DNA is rendered fully double-stranded by completion of the (+) sense strand by cellular DNA polymerases (viral DNA polymerase is used for a later stage) and removal of a protein molecule from the (-) sense strand and a short sequence of RNA from the (+) sense strand. Non-coding bases are removed from the ends of the (-)sense strand and the ends are rejoined.
The viral genes are transcribed by the cellular RNA polymerase II in the cell nucleus from a covalently closed circular DNA (cccDNA) template. Two enhancers designated enhancer I (EnhI) and enhancer II (EnhII) have been identified in the HBV genome. Both enhancers exhibit greater activity in cells of hepatic origin, and together they drive and regulate the expression of the complete viral transcripts. There are four known genes encoded by the genome called C, P, S, and X. The core protein is coded for by gene C (HBcAg), and its start codon is preceded by an upstream in-frame AUG start codon from which the pre-core protein is produced. HBeAg is produced by proteolytic processing of the pre-core protein. The DNA polymerase is encoded by gene P. Gene S is the gene that codes for the surface antigen (HBsAg). The HBsAg gene is one long open reading frame but contains three in frame "start" (ATG) codons that divide the gene into three sections, pre-S1, pre-S2, and S. Because of the multiple start codons, polypeptides of three different sizes called large, middle, and small (pre-S1 + pre-S2 + S, pre-S2 + S, or S) are produced. The function of the protein coded for by gene X is not fully understood, but some evidence suggests that it may function as a transcriptional transactivator.
Genotypes differ by at least 8% of the sequence and have distinct geographical distributions and this has been associated with anthropological history. Within genotypes subtypes have been described: these differ by 4–8% of the genome.
There are eight known genotypes labeled A through H.
Two further genotypes have since been recognised. The current (2014) listing now runs A though to J. Several subtypes are also recognised.
There are at least 24 subtypes.
- Individual genotypes
Type F which diverges from the other genomes by 14% is the most divergent type known. Type A is prevalent in Europe, Africa and South-east Asia, including the Philippines. Type B and C are predominant in Asia; type D is common in the Mediterranean area, the Middle East and India; type E is localized in sub-Saharan Africa; type F (or H) is restricted to Central and South America. Type G has been found in France and Germany. Genotypes A, D and F are predominant in Brazil and all genotypes occur in the United States with frequencies dependent on ethnicity.
The E and F strains appear to have originated in aboriginal populations of Africa and the New World, respectively.
Type A has two subtypes: Aa (A1) in Africa/Asia and the Philippines and Ae (A2) in Europe/United States.
Type B has two distinct geographical distributions: Bj/B1 ('j'—Japan) and Ba/B2 ('a'—Asia). Type Ba has been further subdivided into four clades (B2–B4).
Type C has two geographically subtypes: Cs (C1) in South-east Asia and Ce (C2) in East Asia. The C subtypes have been divided into five clades (C1–C5). A sixth clade (C6) has been described in the Philippines but only in one isolate to date. Type C1 is associated with Vietnam, Myanmar and Thailand; type C2 with Japan, Korea and China; type C3 with New Caledonia and Polynesia; C4 with Australia; and C5 with the Philippines. A further subtype has been described in Papua, Indonesia.
Type D has been divided into 7 subtypes (D1–D7).
Type F has been subdivided into 4 subtypes (F1–F4). F1 has been further divided into 1a and 1b. In Venezuela subtypes F1, F2, and F3 are found in East and West Amerindians. Among South Amerindians only F3 was found. Subtypes Ia, III, and IV exhibit a restricted geographic distribution (Central America, the North and the South of South America respectively) while clades Ib and II are found in all the Americas except in the Northern South America and North America respectively.
- The virus gains entry into the cell by binding to a receptor on the surface of the cell and enters it by clathrin-dependent endocytosis. The cell surface receptor has been identified as the Sodium/Bile acid cotransporting peptide SLC10A1 (also named NTCP).
- The virus membrane then fuses with the host cell's membrane releasing the DNA and core proteins into the cytoplasm.
- Because the virus multiplies via RNA made by a host enzyme, the viral genomic DNA has to be transferred to the cell nucleus. It is thought the capsid is transported on the microtubules to the nuclear pore. The core proteins dissociate from the partially double stranded viral DNA which is then made fully double stranded (by host DNA polymerases) and transformed into covalently closed circular DNA (cccDNA) that serves as a template for transcription of four viral mRNAs.
- The largest mRNA, (which is longer than the viral genome), is used to make the new copies of the genome and to make the capsid core protein and the viral RNA-dependant-DNA-polymerase.
- These four viral transcripts undergo additional processing and go on to form progeny virions which are released from the cell or returned to the nucleus and re-cycled to produce even more copies.
- The long mRNA is then transported back to the cytoplasm where the virion P protein synthesizes DNA via its reverse transcriptase activity.
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