Hepatitis B virus (HBV) is a partially double-stranded DNA virus, a species of the genus Orthohepadnavirus and a member of the Hepadnaviridae family of viruses. This virus causes the disease hepatitis B.
Classification Hepatitis B virus is classified in the genus Orthohepadnavirus, which contains 11 other species. The genus is classified as part of the Hepadnaviridae family, which contains four other genera, Avihepadnavirus, Herpetohepadnavirus, Metahepadnavirus and Parahepadnavirus. This family of viruses is the only member of the viral order Blubervirales. Viruses similar to hepatitis B have been found in all apes (orangutans, gibbons, bonobos, gorillas and chimpanzees), in Old World monkeys, and in New World woolly monkeys (the woolly monkey hepatitis B virus), suggesting an ancient origin for this virus in primates. The viruses that infect apes are classified as the same species as the human HBV, Orthohepadnavirus hominoidei, named after the Hominoidea.Rename all currently listed viral species of the family Orthohepadnaviridae to the binominal nomenclature and Introduce 7 new virus species in the genus Orthohepadnavirus and 2 new species in the genus Avihepadnavirus. (2023). ICTV Change Request 2023.014D. Available online from https://ictv.global/ictv/proposals/2023.014D.Hepadnaviridae_19renam_9nsp.zip.
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. The serotypes and genotypes do not necessarily correspond.
The ape-infecting HBVs are placed in between human HBV genotypes. The different genotypes show evidence of recombination.
Morphology Structure
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.
Components It consists of: HBsAg (hepatitis B surface antigen) was the first hepatitis B virus protein to be discovered. It consists of small (S), medium (M) and large (L) protein. HBcAg (hepatitis B core antigen) is the main structural protein of HBV icosahedral nucleocapsid and it has function in replication of the virus. Capsid formation is the main factor for infection of the cell. 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. Hepatitis B virus DNA polymerase is incorporated into the nucleocapsid along with the pre-genomic RNA (pgRNA). Inside the capsid, the pgRNA undergoes reverse transcription, making the (-) DNA strand. At the same time, most of the RNA template is degraded by the RNase activity of the polymerase. This is followed by (+) DNA strand synthesis, and the polymerase ends up covalently bound to the (-) DNA strand. The polymerase is discarded after the virion infects a new cell. HBeAg (hepatitis B envelope antigen) can be found between the icosahedral nucleocapsid core and the lipid envelope, but is considered "nonparticulate" and is secreted and accumulates in serum. HBeAg and HBcAg are made from the same reading frame. HBx is small, 154 amino acids 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 of many of these activities are unknown. This protein is multifunctional and it activates cellular signaling pathways and is essential for viral infection.
Hepatitis D virus requires HBV envelope particles to become virulent.
Evolution The early evolution of HBV, like that of all viruses, is difficult to establish. The identification of hepadnaviruses in a wide range of vertebrates suggests a long coevolution. The identification of endogenous hepadnaviridae elements shared by various bird species shows the presence of these virus in birds for at least 70M years. Although similar evidence is missing for mammals, the phylogenetic position of orthohepadnaviruses as a sister clade to avihepadnaviruses suggests a presence of the virus in the amniote ancestor and a subsequent coevolution with both birds and mammals after their divergence (>300M years ago). It has also been proposed that a New World bat hepadnavirus may be the origin of the primate hepadnaviruses. Avihepadnaviruses lack the X protein but a vestigial X reading frame is present in the genome of duck hepadnavirus. The X protein may have evolved from a DNA glycosylase.
Recently, the reconstruction of HBV genomes from ancient human remains has allowed investigating the evolution of this virus in humans in more details. In 2021, a study reconstructed 137 ancient HBV genomes and proved the presence of the virus in humans since at least 10,000 years. The most recent common ancestor of all known human HBV lineages was dated to between 20,000 and 12,000 years ago. However, it cannot be said whether the virus was present in humans long before that or acquired shortly before from another animal species. The evolution of HBV in humans was shown to reflect known events of human history such as the first peopling of the Americas during the late Pleistocene and the Neolithic transition in Europe. These studies also showed that some ancient HBV strains still infect humans, while other became extinct. HBV strains found in African and South-East Asian apes (chimpanzees, gorillas, orangutans, bonobos and gibbons) appear related to human HBV strains, which could reflect past cross-species transmission events.
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). Coalescence occurred about 1000 AD. This subgenotype spread from Asia initially to Greenland and then spread westward within the last 400 years.
Genome
Size The genome of HBV is made of circular DNA (cccDNA), 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).
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.
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 (pre-S1 + pre-S2 + S), middle (pre-S2 + S), and small (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. Interestingly, a 40 kDa X-Core fusion protein is encoded by a long viral 3.9-kb transcript, whose function remains unclear. Synthesis of the 3.9 kb RNA initiates at the X gene promoter region and the transcript is polyadenylated only after the second round of transcription. Similar behavior is shared by other long pregenomic/pre-core (pg/pc) RNA species. Thus, the viral transcription machinery must ignore the poly(A) signal at the first transcription round.
Several non-coding RNA elements have been identified in the HBV genome. These include HBV PREalpha, HBV PREbeta and HBV RNA encapsidation signal epsilon.
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.
A possible new "I" genotype has been described, but acceptance of this notation is not universal.
Two further genotypes have since been recognised. The current (2014) listing now runs A through to J. Several subtypes are also recognised.
There are at least 24 subtypes.
Different genotypes may respond to treatment in different ways.
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).