Taxonomic Structure of the Family
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Virions are spherical, enveloped and 80-100 nm in diameter. Glycoprotein surface projections are about 8 nm in length. The internal core encapsidates the viral nucleocapsid. The apparently spherical nucleocapsid (nucleoid) is eccentric for members of the genus Betaretrovirus, concentric for members of the genera Alpharetrovirus, Gammaretrovirus, Deltaretrovirus, and Spumavirus, and rod or truncated cone-shape for members of the genus Lentivirus (Fig. 1).
Two distinct morphogenic pathways exist. Historically, a nomenclature based on electron microscopy classified members of the Alphavirus and Gammaretrovirus genera, which assemble their immature capsids at the plasma membrane, as C-type viruses. Members of the Betaretrovirus genus in contrast were said to assemble A-type particles (immature capsids) in the cytoplasm which then budded with either a B-type (MMTV) or D-type (Mason-Pfizer monkey virus, M-PMV) morphology.
Physicochemical and Physical Properties
Virion buoyant density is 1.16-1.18 g/cm3 in sucrose. Virion S20W is approximately 600 S in sucrose. Virions are sensitive to heat, detergents and formaldehyde. The surface glycoproteins may be partially removed by proteolytic enzymes. Virions are relatively resistant to UV light.
The viral genome consists of a dimer of linear, positive sense, ssRNA, each monomer 7 to 11 kb in size. The RNA constitutes about 2% of the virion dry weight. The monomers are held together by hydrogen bonds. Each monomer of RNA is polyadenylated at the 3
-end and has a cap structure (type 1) at the 5-end. The purified virion RNA is not infectious. Each monomer is associated with a specific molecule of tRNA that is base-paired to a region (termed the primer binding site) near the 5-end of the RNA and involves about 18 bases at the 3-end of the tRNA. Other host derived RNAs (and small DNA fragments) found in virions are believed to be incidental inclusions.
Proteins constitute about 60% of the virion dry weight. There are 2 envelope proteins: SU (surface) and TM (transmembrane) encoded by the viral env gene. There are 3-6 internal, non-glycosylated structural proteins (encoded by the gag gene). These are, in order from the amino terminus, (1) MA (matrix), (2) in some viruses a protein of undetermined function, (3) CA (capsid protein), and (4) NC (nucleocapsid). The MA protein is often acylated with a myristyl moiety covalently linked to the amino terminal glycine. Other proteins are a protease (PR, encoded by the pro gene), a reverse transcriptase (RT, encoded by the pol gene) and an integrase (IN, encoded by the pol gene). In some viruses a dUTPase (DU, role unknown) is also present.
Lipids constitute about 35% of the virion dry weight. They are derived from the plasma membrane of the host cell.
Virions are composed of about 3% carbohydrate by weight. This value varies, depending on the virus. At least one (SU), but usually both envelope surface proteins are glycosylated. Cellular glycolipids are also found in the viral envelope.
Genome Organization and Replication
Virions carry two copies of the genome. Infectious viruses have 4 main genes coding for the virion proteins in the order: 5-gag-pro-pol-env-3. Some retroviruses contain genes encoding non-structural proteins important for the regulation of gene expression and virus replication. Others carry cell-derived sequences that are important in pathogenesis. These cellular sequences are either inserted in a complete retrovirus genome (e.g., some strains of Rous sarcoma virus, RSV), or in the form of substitutions for deleted viral sequences (e.g., Murine sarcoma virus). Such deletions render the virus replication-defective and dependent on non-transforming, helper viruses for production of infectious progeny. In many cases the cell-derived sequences form a fused gene with a viral structural gene that is then translated into one chimeric protein (e.g., gag-onc protein).
Entry into the host cell is mediated by interaction between a virion glycoprotein and specific receptors at the host cell surface, resulting in fusion of the viral envelope with the plasma membrane, either directly or following endocytosis. Receptors are cell surface proteins. Several have been identified. For Human immunodeficiency virus (HIV), both the CD4 protein, which is an immunoglobulin-like molecule with a single transmembrane region and a chemokine receptor (CCR5 or CXCR4) which span the membrane seven times are required for membrane fusion. The receptors for ecotropic Murine leukemia virus (MLV), amphotropic MLV and Gibbon ape leukemia virus (GALV), are involved in the transport of small molecules and have a complex structure with multiple transmembrane domains. For the avian leukosis viruses (ALVs) two receptors have been identified: that for subgroup A viruses is a small molecule with a single transmembrane domain, distantly related to a cell receptor for low-density lipoprotein while that for subgroup B viruses is related to the TNF-receptor family of proteins.
The process of intracellular uncoating of viral particles is not understood. Subsequent early events are carried out in the context of a nucleoprotein complex derived from the capsid.
Replication starts with reverse transcription (by RT) of virion RNA into cDNA using the 3-end of the tRNA as primer for synthesis of a negative-sense cDNA transcript. The initial short product (to the 5-end of the genome) transfers and primes further cDNA synthesis from the 3-end of the genome by virtue of duplicated end sequences at the ends of the viral RNA species. cDNA synthesis involves the concomitant digestion of the viral RNA (RNAse H activity of the RT protein). The products of this hydrolysis serve to prime virus-sense cDNA synthesis on the negative sense DNA transcripts. In its final form, the linear dsDNA transcripts derived from the viral genome contain long terminal repeats (LTRs) composed of sequences from the 3 (U3) and 5 (U5)-ends of the viral RNA flanking a sequence (R) found near both ends of the RNA. The process of reverse transcription is characterized by a high frequency of recombination due to the transfer of the RT from one template RNA to the other.
Retroviral DNA becomes integrated into the chromosomal DNA of the host to form a provirus by a mechanism involving the viral IN protein. The ends of the virus DNA are joined to cell DNA, involving the removal of two bases from the ends of the linear viral DNA and generating a short duplication of cell sequences at the integration site. Virus DNA can integrate at many sites in the cellular genome. However, once integrated, a sequence is apparently incapable of further transposition within the same cell. The map of the integrated provirus is co-linear with that of unintegrated viral DNA. Integration appears to be a prerequisite for virus replication.
The integrated provirus is transcribed by cellular RNA polymerase II into virion RNA and mRNA species in response to transcriptional signals in the viral LTRs. In some genera, transcription is also regulated by viral encoded transactivators. There are several classes of mRNA depending on the virus and the genetic map of the retrovirus. An mRNA comprising the whole genome serves for the translation of the gag, pro, and pol genes (positioned in the 5 half of the RNA). This results in the formation of polyprotein precursors which are cleaved to yield the structural proteins, protease, RT and IN, respectively. A smaller mRNA consisting of the 5-end of the genome spliced to sequences from the 3-end of the genome and including the env gene and the U3 and R regions, is translated into the precursor of the envelope proteins. In viruses that contain additional genes, other forms of spliced mRNA are also made; however, all these spliced mRNAs share a common sequence at their 5-ends. Spumaviruses are unique in that they make use of an internal promoter (IP) located in the env gene upstream of the accessory reading frames. Most primary translational products in retrovirus infections are polyproteins which require proteolytic cleavage before becoming functional. The gag, pro and pol products are generally produced from a nested set of primary translation products. For pro and pol, translation involves bypassing translational termination signals by ribosomal frameshifting or by read-through at the gag-pro and/or the pro-pol boundaries.
Capsids assemble either at the plasma membrane (a majority of the genera), or as intracytoplasmic particles (Betaretrovirus and Spumavirus) and are released from the cell by a process of budding. Polyprotein processing of the internal proteins occurs concomitant with or just subsequent to the maturation of virions.
Virion proteins contain type-specific and group-specific determinants. Some type-specific determinants of the envelope glycoproteins are involved in antibody-mediated virus neutralization. Group-specific determinants are shared by members of a serogroup and may be shared between members of different serogroups within a particular genus. There is evidence for weak cross-reactivities between members of different genera. Epitopes that elicit T-cell responses are found on many of the structural proteins. Antigenic properties are infrequently used in classification of members of the family Retroviridae.
Retroviruses are widely distributed as exogenous infectious agents of vertebrates. Endogenous proviruses that have resulted at some time from infection of germ line cells are inherited as Mendelian genes. They occur widely among vertebrates.
Retroviruses are associated with a variety of diseases. These include: malignancies including certain leukemias, lymphomas, sarcomas and other tumors of mesodermal origin; mammary carcinomas and carcinomas of liver and kidney; immunodeficiencies (such as AIDS); autoimmune diseases; lower motor neuron diseases; and several acute diseases involving tissue damage. Some retroviruses are non-pathogenic. Transmission of retroviruses is horizontal via a number of routes, including blood, saliva, sexual contact, etc., and vertical via direct infection of the developing embryo, or via milk or perinatal routes. Endogenous retroviruses are transmitted by inheritance of proviruses.
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