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Retroviruses are enveloped RNA viruses of the family Retroviridae that replicate through a DNA intermediate. Their genome is single-stranded, positive-sense RNA, and it is copied into DNA by the virus-encoded enzyme reverse transcriptase after the virus enters a host cell. The DNA is then inserted into the host chromosome as a provirus. Retroviruses are classified in the Baltimore classification as Group VI. In the International Committee on Taxonomy of Viruses system, they belong to the realm Riboviria and the kingdom Pararnavirae, in the class Revtraviricetes, together with other reverse-transcribing viruses.

The existence of reverse transcription does not contradict the central dogma of molecular biology, which was stated by Francis Crick as a rule that sequence information, once transferred into protein, cannot flow back to nucleic acid. The transfer from RNA to DNA is permitted by the central dogma. The discovery of reverse transcriptase in 1970 by Howard Temin and David Baltimore (independently) was nevertheless important because it showed that information can flow from RNA to DNA. They shared the 1975 Nobel Prize in Physiology or Medicine with Renato Dulbecco.

Rous Sarcoma Virus, Proto-Oncogenes, and Human Retrovirus Isolation

Peyton Rous showed in 1911 that a filterable agent could transmit a sarcoma in chickens. The agent, the Rous sarcoma virus, was the first known oncovirus, and Rous received the Nobel Prize in 1966. Studies of tumor viruses of birds and mice, and of the transforming gene src of Rous sarcoma virus, led J. Michael Bishop and Harold Varmus to show in 1976 that the gene has a cellular counterpart, the proto-oncogene c-src. Human retroviruses were first described in 1980, when human T-lymphotropic virus 1 (HTLV-1) was isolated by Robert Gallo and colleagues. HIV was identified in 1983 by Françoise Barré-Sinoussi, Luc Montagnier, and colleagues, who shared the 2008 Nobel Prize in Physiology or Medicine with Harald zur Hausen.

Orthoretrovirinae, Spumaretrovirinae, and Simple vs. Complex Genomes

The family Retroviridae has two subfamilies:

• Orthoretrovirinae contains the genera Alpharetrovirus (for example Rous sarcoma virus and avian leukosis virus), Betaretrovirus (mouse mammary tumor virus), Gammaretrovirus (murine leukemia virus and feline leukemia virus), Deltaretrovirus (HTLV-1 and bovine leukemia virus), Epsilonretrovirus (fish retroviruses), and Lentivirus (HIV-1, HIV-2, simian and feline immunodeficiency viruses, and visna virus).
• Spumaretrovirinae contains the foamy viruses (Spumavirus), which infect many mammals and cause no known disease in humans. They differ from the others in several features, including the fact that reverse transcription occurs largely late in the cycle, so that the virion carries mostly DNA.

Retroviruses are also divided into simple retroviruses, which encode only the genes gag, pro, pol, and env, and complex retroviruses (the lentiviruses, deltaretroviruses, and spumaviruses), which encode additional regulatory and accessory proteins.

Virion Architecture and Essential Viral Enzymes

A mature virion is roughly spherical, with a diameter of about 80 to 120 nm.

• Envelope. The outer layer is a lipid bilayer that comes from the host cell membrane during budding. The viral surface (SU) and transmembrane (TM) glycoproteins, encoded by env, are embedded in it. In HIV they are called gp120 and gp41. They form trimers that bind to receptors on the target cell and mediate membrane fusion. The envelope also contains some host proteins.
• Matrix. A layer of matrix (MA) protein lines the inner surface of the envelope.
• Capsid. The capsid (CA) protein forms a shell that encloses the genome. In HIV-1, it is a cone-shaped core made of about 1,000 to 1,500 CA subunits arranged in hexamers, with twelve pentamers that close the structure, and the core is about 100 nm long. It protects the genome and also plays roles during entry, in the transport of the genome to the nucleus, and in the uncoating of the virus.
• Genome. The genome consists of two identical copies of linear, single-stranded, positive-sense RNA of about 7 to 12 kb. The two copies are linked non-covalently near their 5′ ends, and the diploid genome allows recombination during reverse transcription. Each RNA has a 5′ cap and a 3′ polyadenylated tail, like a cellular mRNA. A host transfer RNA is bound to the primer binding site of each RNA to prime reverse transcription (tRNA^Lys3 for HIV-1). The nucleocapsid (NC) protein coats the RNA.
• Enzymes. The virion carries reverse transcriptase (RT, which also has an RNase H domain), integrase (IN), and protease (PR). They are encoded by pol and pro, and they are needed in the early steps of infection.

Genome organization

All retroviral genomes have the genes gag (group-specific antigen, which encodes the MA, CA, and NC structural proteins), pro (protease), pol (reverse transcriptase and integrase), and env (the envelope glycoproteins), usually in this order. Gag and Gag-Pol are made as polyproteins that are cleaved by the viral protease during maturation. In HIV-1, Gag-Pol is made by a programmed −1 ribosomal frameshift, at a frequency of about 5 percent of translation events, which sets the ratio of Gag to Gag-Pol at about 20 to 1. The ends of the proviral DNA are long terminal repeats (LTRs), which are made during reverse transcription by duplication of sequences at both ends of the RNA. They contain the promoter and enhancer sequences and the signals for integration and polyadenylation. Complex retroviruses encode regulatory proteins, such as Tat and Rev in HIV-1, and accessory proteins such as Vif, Vpr, Vpu, and Nef, which counteract host defenses.

The Six Steps of Retroviral Replication

A retrovirus passes through the following steps:

1. Attachment and entry. Envelope glycoproteins bind specific receptors and co-receptors, which determines the tropism of the virus. HIV-1 binds CD4 and a chemokine receptor, CCR5 or CXCR4. Murine leukemia viruses use different transporters as receptors. The envelope fuses with the plasma membrane at neutral pH, or after endocytosis in some retroviruses, and the core is released into the cytoplasm.
2. Reverse transcription. In the cytoplasm, as the core traffics to the nucleus, reverse transcriptase makes DNA from the RNA. Starting from the tRNA primer, it makes a minus-strand DNA, and the RNase H activity degrades the RNA of the RNA-DNA hybrid. Two jumps of the enzyme from one end of the template to the other (strand transfers) are needed, and the polypurine tract is a primer for the second strand. The product is a linear double-stranded DNA with an LTR at each end. Reverse transcriptase has no proofreading activity, and it makes a mistake about once in every 10⁴ to 10⁵ nucleotides copied. The enzyme can also switch between the two RNA copies and cause recombination, which happens several times in each cycle in HIV-1. In HIV-1, reverse transcription is thought to be completed inside the intact or partly disassembled capsid.
3. Nuclear import and integration. The DNA, in a complex with viral and host proteins (the preintegration complex), enters the nucleus. Lentiviruses can infect non-dividing cells, because their complexes pass the nuclear pore, and most other retroviruses, such as murine leukemia virus, need the nuclear envelope to break down during mitosis. Integrase cuts the DNA ends and joins them to the host DNA, offset by a few base pairs, which creates short duplications of the host sequence at the site (4 to 6 base pairs, depending on the virus). Integration is not random. HIV-1 integrates preferentially in the active genes in gene-rich regions, helped by the host protein LEDGF/p75, and murine leukemia virus prefers promoters and enhancers.
4. Transcription. The provirus is transcribed by host RNA polymerase II from a promoter in the 5′ LTR. In HIV-1, the viral protein Tat greatly increases the elongation of transcripts. The full-length RNA is the genome and the mRNA for Gag and Gag-Pol, and splicing produces the mRNAs for Env and other proteins. Complex retroviruses have means to export unspliced and partly spliced RNA from the nucleus, such as Rev and the Rev response element in HIV-1.
5. Translation and assembly. Gag and Gag-Pol are translated in the cytoplasm, and Env is made in the endoplasmic reticulum, where it is glycosylated and cleaved by the protease furin. The Gag polyprotein is targeted to the plasma membrane and assembles with two copies of the RNA, which are selected by a packaging signal, and with the Env glycoproteins.
6. Budding and maturation. The immature virion buds from the cell, using the host ESCRT machinery for membrane scission. During or soon after budding, the viral protease cleaves the Gag and Gag-Pol polyproteins, which causes a structural rearrangement and the formation of the mature core, so that the particle becomes infectious.

Latency

A provirus can be transcriptionally silent. In HIV-1 infection, a small pool of latently infected resting memory CD4⁺ T cells persists during antiretroviral therapy. It has a half-life of years, so that the virus rebounds if treatment is stopped. This reservoir is the main barrier to a cure.

Reverse Transcriptase Fidelity, Recombination, and Drug Resistance Kinetics

The high error rate of reverse transcriptase, the rapid turnover of the virus, and recombination allow retroviruses to evolve quickly. The rate of mutation in HIV-1 is about 3 × 10⁻⁵ per base per replication cycle, and a genome of 9.7 kb therefore has about 0.3 mutations per replication. A person with untreated infection produces about 10⁹ to 10¹⁰ virions each day, so that every single-point mutation arises many times a day. The virus exists as a population of related variants, a quasispecies, which is the basis for the rapid evolution of drug resistance and immune escape. For a single-mutation resistance that confers a benefit s under treatment, the variant rises rapidly, and combination therapy is used so that resistance requires several mutations at once, with a probability roughly equal to the product of the mutation rates.

Retroviruses cause disease in many animals. The main effects are immunodeficiency, tumors, and neurological and other diseases.

HIV and AIDS

HIV is a lentivirus. HIV-1 (group M, which has caused the pandemic) and HIV-2 came from simian immunodeficiency viruses of chimpanzees, gorillas, and sooty mangabeys by cross-species transmission in the early twentieth century. HIV infects CD4⁺ T cells, macrophages, and dendritic cells. Loss of CD4⁺ T cells results from direct killing, from other effects of infection, and from chronic immune activation, and untreated infection leads to acquired immunodeficiency syndrome (AIDS), in which opportunistic infections and cancers occur, typically when the CD4⁺ count falls below 200 cells per microliter. The treatment of HIV-1 with a combination of antiretroviral drugs that target reverse transcriptase, protease, integrase, and entry has turned a fatal disease into a chronic condition for people who have access to treatment, and has reduced transmission when viral loads are suppressed. About 39 million people were living with HIV in 2022 according to UNAIDS, and about 630,000 died of causes related to HIV in 2022. Figures change each year.

HTLV and cancer

Human T-lymphotropic virus 1 (HTLV-1) infects about 5 to 10 million people, and the infection is endemic in parts of Japan, the Caribbean, South America, and sub-Saharan Africa. It is transmitted by breast feeding, sexual contact, and blood. Most infected people remain well. About 2 to 5 percent develop adult T-cell leukemia/lymphoma, and a similar fraction develop the neurological disease HTLV-1-associated myelopathy (tropical spastic paraparesis). The viral protein Tax, and the antisense protein HBZ, contribute to transformation.

Oncogenesis by animal retroviruses

Some retroviruses cause cancer in animals by three main mechanisms. Acutely transforming retroviruses, such as Rous sarcoma virus, carry a viral oncogene, which is a modified version of a cellular proto-oncogene (such as v-src), that was picked up from the host genome. Other retroviruses, such as murine leukemia virus and avian leukosis virus, have no oncogene of their own and cause cancer after a delay by insertional mutagenesis, in which the provirus integrates near a proto-oncogene and activates it through the promoter or enhancer of the LTR. The study of these insertions has identified many cancer genes. Others, including HTLV-1, encode regulatory proteins that transform cells. Insertional mutagenesis is also a risk of gene therapy with retroviral vectors, as seen in cases of leukemia in early trials for X-linked severe combined immunodeficiency.

Veterinary retroviruses

Feline leukemia virus and feline immunodeficiency virus infect cats, bovine leukemia virus infects cattle, and visna-maedi virus infects sheep. Koala retrovirus is a gammaretrovirus that is in the process of becoming endogenous in koalas.

Germline Inheritance and Molecular Clock Dating via LTR Divergence

When a retrovirus integrates in a germline cell, the provirus is inherited by the offspring in a Mendelian way, as an endogenous retrovirus (ERV). Most ERVs are defective because of mutations and deletions, and many have been reduced to solo LTRs by recombination between the two LTRs. ERVs make up about 8 percent of the human genome (about 5 to 8 percent, depending on the method of estimation), and they are a large part of the genomes of many vertebrates. Most human ERVs are millions of years old, and the human endogenous retrovirus K (HERV-K) group contains the youngest, some of which are polymorphic among humans. Because proviruses are inserted in the same place in related species, they provide evidence of common descent. A provirus has an LTR at each end, which are identical at the time of insertion. The divergence of the two LTRs accumulates at the neutral mutation rate and can be used to estimate the age of an insertion:

where d is the divergence between the two LTRs per site, μ is the substitution rate per site per year, and the factor of 2 is there because both LTRs accumulate changes. For example, if two LTRs differ at 2 percent of sites (d = 0.02) and μ = 2.5 × 10⁻⁹ per site per year, the insertion is about 0.02 / (5 × 10⁻⁹) = 4 million years old.

Evolutionary Co-Option of Syncytins and Regulatory Elements

ERVs have been co-opted for host functions. The envelope genes syncytin-1 and syncytin-2 of human endogenous retroviruses have been implicated in the formation of the multinucleated syncytiotrophoblast layer of the placenta. Syncytin genes were captured independently in several mammalian lineages, which is an example of convergent evolution. The Arc gene, which has a role in synaptic plasticity, is derived from a gag gene of a retrotransposon, and ERV sequences contribute regulatory elements and are involved in the innate immune response to infection (for example, ERV-derived restriction factors). Some ERVs can be reactivated in disease, but their role in diseases such as cancer and multiple sclerosis is not established.

Related to ERVs are other retrotransposons with LTRs, such as Ty1 of yeast and gypsy of Drosophila, and the non-LTR retrotransposons LINE-1 and Alu, which also use reverse transcription but are not viruses.

APOBEC3G, TRIM5α, Tetherin, SAMHD1, and SERINC5

Cells have innate defenses against retroviruses, called restriction factors. Examples are:

• APOBEC3G, a cytidine deaminase that is packaged into virions and causes mutations of G to A in the new DNA during reverse transcription. HIV-1 Vif targets APOBEC3G for degradation.
• TRIM5α, which binds the capsid of incoming viruses of some species and causes premature uncoating, and so restricts cross-species infection.
• Tetherin (BST-2), which retains budding virions on the cell surface and is counteracted by Vpu.
• SAMHD1, which depletes the cellular dNTP pool and so limits reverse transcription in myeloid cells and resting T cells, and is counteracted by Vpx in HIV-2.
• SERINC5, which is incorporated in virions and reduces infectivity, and is counteracted by Nef.

The evolutionary arms race between these factors and viral antagonists has left signs of positive selection in the genes of the factors.

Classes of Antiretroviral Therapeutics and Combination Therapy

The enzymes and steps of the cycle are targets of drugs:

• Nucleoside and nucleotide reverse transcriptase inhibitors (such as tenofovir, emtricitabine, and lamivudine) lack a 3′-hydroxyl group and terminate DNA synthesis.
• Non-nucleoside reverse transcriptase inhibitors (such as efavirenz and rilpivirine) bind an allosteric pocket.
• Integrase strand transfer inhibitors (such as dolutegravir) block the joining of viral DNA to the host DNA.
• Protease inhibitors (such as darunavir) prevent the maturation of virions.
• Entry inhibitors include the CCR5 antagonist maraviroc and the fusion inhibitor enfuvirtide, and the capsid inhibitor lenacapavir acts on several steps.

Combination antiretroviral therapy is given as three or two drugs and suppresses the virus to undetectable levels in most patients. Pre-exposure prophylaxis with tenofovir-based regimens, and long-acting injectable drugs, such as cabotegravir and lenacapavir, prevent infection. There is no licensed vaccine against HIV, and cure has been reported in a few patients after stem cell transplantation with cells that lack CCR5, but this is not a practical method for most patients.

Self-Inactivating (SIN) Vectors and Ex Vivo Transduction

Retroviruses are used as vectors for gene therapy and research, because they integrate their DNA into the host genome and so give long-term expression. A vector is made by removing the genes of the virus (the gag, pol, and env genes) and replacing them with a therapeutic or marker gene. The vector is produced in packaging cells that supply the viral proteins in trans, so that the vector can infect cells once but cannot replicate.

• Gammaretroviral vectors (derived from murine leukemia virus) infect only dividing cells. They have been used in clinical trials for severe combined immunodeficiency. Insertional activation of the oncogene LMO2 caused leukemia in some patients in early trials. Safer designs include self-inactivating vectors with a deleted enhancer in the LTR.
• Lentiviral vectors (derived from HIV-1 and other lentiviruses) transduce non-dividing cells, and are usually pseudotyped with the glycoprotein of vesicular stomatitis virus (VSV-G) for a broad host range. They are used to modify hematopoietic stem cells and T cells ex vivo, and they are used in approved therapies such as CAR-T cell products for leukemia and lymphoma, and gene therapies for blood disorders such as beta thalassemia and cerebral adrenoleukodystrophy. They are also used in laboratory research to deliver genes, RNA interference constructs, and CRISPR components.

Adeno-associated virus and other non-retroviral vectors are used where integration is not wanted.

Why are retroviruses pseudodiploid, carrying two copies of their single-stranded RNA genome?

Retroviral virions package two non-covalently dimerized copies of positive-sense single-stranded RNA, making them pseudodiploid (only one provirus is synthesized per infection event). This dual-template architecture rescues replication when single-strand RNA breaks occur and enables frequent copy-choice recombination: reverse transcriptase switches between the two RNA templates during minus-strand DNA synthesis, shuffling beneficial mutations to accelerate immune escape and multi-drug resistance.

How do lentiviruses infect non-dividing cells while gammaretroviruses require mitosis?

Gammaretroviruses (such as murine leukemia virus) possess a preintegration complex (PIC) tethered to capsid proteins that cannot traverse the intact nuclear pore complex (NPC), requiring mitotic nuclear envelope breakdown to access host chromatin. Conversely, lentiviruses (such as HIV-1) traffic their intact conical capsid shell directly through the central channel of the NPC via specific interactions with nucleoporins (Nup358 and Nup153) and host cofactor CPSF6, uncoating inside the nucleus of non-dividing macrophages and resting T cells.

How does the programmed −1 ribosomal frameshift regulate the 20:1 Gag to Gag-Pol stoichiometry?

Retroviruses require roughly 20-fold more structural Gag proteins (MA, CA, NC) than catalytic Pol enzymes (PR, RT, IN) to assemble infectious virions. In HIV-1, the pol open reading frame lacks its own initiation codon and overlaps the 3′ end of gag in the −1 reading frame; a slippery heptanucleotide sequence (UUUUUUA) followed by a stable RNA stem-loop stalls ~5% of translating ribosomes, shifting them backward by one nucleotide to bypass the gag stop codon and synthesize the Gag-Pol polyprotein.

• HIV
• Reverse transcriptase
• Endogenous retrovirus
• Provirus
• Viral vector
• Gene therapy
• Retrotransposon