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Hepatitis B virus

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For the disease, see Hepatitis B.
Hepatitis B virus
TEM micrograph showing Hepatitis B virus virions
Transmission electron microscopy micrograph showing Hepatitis B virus virions
Virus classification Edit this classification
(unranked): Virus
Realm: Riboviria
Kingdom: Pararnavirae
Phylum: Artverviricota
Class: Revtraviricetes
Order: Blubervirales
Family: Hepadnaviridae
Genus: Orthohepadnavirus
Species:
Hepatitis B virus

Hepatitis B virus (HBV), is a partially double-stranded DNA virus,[1] a species of the genus Orthohepadnavirus and a member of the Hepadnaviridae family of viruses.[2] This virus causes the disease hepatitis B.[3]

Disease

Main article: Hepatitis B

In addition to causing hepatitis, infection with HBV can lead to cirrhosis and hepatocellular carcinoma.[4]

It has also been suggested that it may increase the risk of pancreatic cancer.[3]

Roles in disease

Viral infection by Hepatitis B virus (HBV) causes many hepatocyte changes due to the direct action of a protein encoded by the virus, HBx, and to indirect changes due to a large increase in intracellular reactive oxygen species (ROS) after infection. HBx appears to dysregulate a number of cellular pathways. HBx causes dysregulation in part by binding to genomic DNA, changing expression patterns of miRNAs, affecting histone methyltransferases, binding to SIRT1 protein to activate transcription, and cooperating with histone methylases and demethylases to change cell expression patterns.[5] HBx is partly responsible for the approximate 10,000-fold increase in intracellular ROS upon chronic HBV infection.[6] Increased ROS can be caused, in part, by localization of HBx to the mitochondria where HBx decreases the mitochondrial membrane potential.[7] In addition, another HBV protein, HBsAg, also increases ROS through interactions with the endoplasmic reticulum.[7]

The increase in reactive oxygen species (ROS) after HBV infection causes inflammation, which leads to a further increase in ROS.[6] ROS cause more than 20 types of DNA damage.[8] Oxidative DNA damage is mutagenic.[9] In addition, repair of the DNA damage can cause epigenetic alterations at the site of the damage during repair of the DNA.[10] Epigenetic alterations and mutations may cause defects in the cellular machinery that then contribute to liver disease. By the time accumulating epigenetic and mutational changes eventually cause progression to cancer, epigenetic alterations appear to have a larger role in this carcinogenesis than mutations. Only one or two genes, TP53[11] and perhaps ARID1A,[12] are mutated in more than 20% of liver cancers while 41 genes each have hypermethylated promoters (repressing gene expression) in more than 20% of liver cancers, with seven of these genes being hypermethylated in more than 75% of liver cancers.[11] In addition to alterations at the sites of DNA repair, epigenetic alterations are also caused by HBx recruiting the DNA methyltransferase enzymes, DNMT1 and/or DNMT3A, to specific gene loci to alter their methylation levels and gene expression.[13] HBx also alters histone acetylation that can affect gene expression.[13]

Several thousand protein-coding genes appear to have HBx-binding sites.[5][14] In addition to protein coding genes, about 15 microRNAs and 16 Long non-coding RNAs are also affected by the binding of HBx to their promoters.[14] Each altered microRNA can affect the expression of several hundred messenger RNAs (see microRNA).

Classification

Hepatitis B virus is classified as the type species of the Orthohepadnavirus, which contains eight other species.[15] The genus is classified as part of the Hepadnaviridae family, which contains one other genus, Avihepadnavirus.[15] This family of viruses have not been assigned to a viral order.[16] Viruses similar to hepatitis B have been found in all apes (orangutans, gibbons, gorillas and chimpanzees), in Old World monkeys,[17] and in New World woolly monkeys (the woolly monkey hepatitis B virus), 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.[18] 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.[19][20] The serotypes and genotypes do not necessarily correspond.

Genotype D has 10 subgenotypes.[21][18]

Unclassified species

A number of as yet unclassified Hepatitis B-like species have been isolated from bats.[22]

Morphology

Structure

The structure of Hepatitis B virus

Hepatitis B virus is a member of the Hepadnavirus family.[23] The virus particle, called Dane particle[24] (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.[25] 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.[26]

Components

It consists of:

  • HBsAg - Hepatitis B surface antigen (HBsAg) was the first hepatitis B virus protein to be discovered.[27] It consists of small (S), medium (M) and large (L) protein.[28]
  • HBcAg (HBeAg is a splice variant) - HBcAg is the main structural protein of HBV icosahedral nucleocapsid and it has function in replication of the virus.[29] Capsid formation of HBV antigen (HBcAg) is the main factor for infection of the cell.[30] HBcAg contributes to HBV clearance in vivo, but it is unknown whether HBcAg has to be in the capsid form to contribute to viral clearance.[31]
  • Hepatitis B virus DNA polymerase
  • HBx. Hepatitis B virus protein HBx is small,[32] 154 amino acid long, nonstructural and has an important role in HBV-associated liver disease and in HBV replication in HepG2 cells. Many activities have been linked to expression of HBx. However, the molecular mechanisms many of these activities are unknown.[33] This protein is multifunctional and it activates cellular signaling pathways and is essential for viral infection.[34]

Hepatitis D virus requires HBV envelope particles to become virulent.[35]

Evolution

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).[36] Both the Avihepadnavirus and Orthohepadna viruses began to diversify about 25,000 years ago.[36] 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 Avihepadnavirus lack a X protein but a vestigial X reading frame is present in the genome of duck hepadnavirus.[37] The X protein may have evolved from a DNA glycosylase.

The rate of nonsynonymous mutations in this virus has been estimated to be about 2×10−5 amino acid replacements per site per year.[38] 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.[39] 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.[40] 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 40 million years ago and possibly to 80 million years ago.[41] 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.[42]

A study of isolates from the circumpolar Arctic human population has proposed that the ancestor of the subgenotype B5 (the endemic type found in this population) that the ancestral virus originated in Asia about 2000 years ago (95% HPD 900 BC - 830 AD).[43] Coalescence occurred about 1000 AD. This subgenotype spread from Asia initially to Greenland and then spread westward within the last 400 years.

The oldest evidence of hepatitis B infection dates to Bronze Age.[44][45] The evidence was obtained from 4,500-year-old human remains.[45] According to the 2018 study, the viral genomes obtained by shotgun sequencing became the oldest ever recovered from vertebrate samples.[45] It was also found that some ancient hepatitis viral strains still infect humans, while other became extinct.[45] This disproved the belief that hepatitis B originated in the New World and spread to Europe around 16th century.[45]

Genome

The genome organisation of HBV. The genes overlap.

Size

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).[46]

Encoding

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 the viral polymerase protein (P) 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.[47][48][49] 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.[50] The function of the protein coded for by gene X is not fully understood,[51] but some evidence suggests that it may function as a transcriptional transactivator.

Several non-coding RNA elements have been identified in the HBV genome. These include: HBV PREalpha, HBV PREbeta and HBV RNA encapsidation signal epsilon.[52][53]

Genotypes

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.[19]

A possible new "I" genotype has been described,[54] but acceptance of this notation is not universal.[55]

Two further genotypes have since been recognised.[56] The current (2014) listing now runs A though to J. Several subtypes are also recognised.

There are at least 24 subtypes.

Different genotypes may respond to treatment in different ways.[57][58]

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.[59] 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.[60]

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.

Life cycle

Hepatitis B virus replication

The life cycle of Hepatitis B virus is complex. Hepatitis B is one of a few known non-retroviral viruses which use reverse transcription as a part of its replication process.

Attachment
The virus gains entry into the cell by binding to receptors on the surface of the cell and entering it by endocytosis mediated by either clathrin or caveolin-1.[61] HBV initially binds to heparin sulfate proteoglycan. The pre-S1 segment of the HBV L protein then binds tightly to the cell surface receptor sodium taurocolate cotransporting polypeptide (NTCP), encoded by the SLC10A1gene.[62] NTCP is mostly found in the sinusoidal membrane of liver cells. The presence of NTCP in liver cells correlates with the tissue specificity of HBV infection.[61]
Penetration
Following endocytosis, the virus membrane fuses with the host cell's membrane, releasing the nucleocapsid into the cytoplasm.[63]
Uncoating
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.
Replication
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-dependent-DNA-polymerase.
Assembly
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.[50][64]
Release
The long mRNA is then transported back to the cytoplasm where the virion P protein synthesizes DNA via its reverse transcriptase activity.

Transactivated genes

HBV has the ability to transactivate FAM46A.[65]

See also

References

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