Viral Replication

General Features of Virus Replication

Virologists describe the formation of viruses during the infection process in target host cells as viral replication.

Learning Objectives

Outline the features of viral replication

Key Takeaways

Key Points

  • Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
  • The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses: attachment, penetration (viral entry), uncoating, replication, and lysis.
  • Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host’s chromosome.

Key Terms

  • lysis: The disintegration or destruction of cells
  • leukocyte: A white blood cell.
  • uncoating: A process in which the viral capsid of a virus is removed, leading to the release of the viral genomic nucleic acid.
  • attachment: specific binding between viral capsid proteins and specific receptors on the host cellular surface

Multiplication Within the Host Cell

Viral replication is the term used indicate the formation of biological viruses during the infection process in the target host cells. Viruses must first penetrate and enter the cell before viral replication can occur. From the perspective of the virus, the purpose of viral replication is to allow reproduction and survival of its kind. By generating abundant copies of its genome and packaging these copies into viruses, the virus is able to continue infecting new hosts.

Replication between viruses is varied and depends on the type of genes involved. Most DNA viruses assemble in the nucleus; most RNA viruses develop solely in cytoplasm. Viral populations do not grow through cell division, because they are acellular. Instead, they hijack the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble inside the cell.

The life cycle of viruses differs greatly between species but there are six common basic stages:

Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range of a virus. For example, HIV can infect only a limited range of human leukocytes. Its surface protein, gp120, specifically interacts only with the CD4 molecule – a chemokine receptor – which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favor those viruses that infect only cells within which they are capable of replication. Attachment to the receptor can fore the viral envelope protein to undergo either changes that result in the fusion of viral and cellular membranes, or changes of non-enveloped virus surface proteins that allow the virus to enter.

Penetration follows attachment. Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. This is often called viral entry. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall. However, nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata. Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. However, since bacterial cell walls are much less thick than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside.

Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral or host enzymes or by simple dissociation. In either case the end-result is the release of the viral genomic nucleic acid.

Replication of viruses depends on the multiplication of the genome. This is accomplished through synthesis of viral messenger RNA (mRNA) from “early” genes (with exceptions for positive sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mRNA synthesis: “late” gene expression is, in general, of structural or virion proteins.

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Hepatitis C virus: A simplified diagram of the Hepatitis C virus replication cycle.

Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell.

Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present. This is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host’s chromosome. The viral genome is then known as a provirus or, in the case of bacteriophages a prophage. Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host; however, at some point the provirus or prophage may give rise to active virus, which may lyse the host cells. Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process the virus acquires its envelope, which is a modified piece of the host’s plasma or other internal membrane. The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses.

Steps of Virus Infections

Viral infection involves the incorporation of viral DNA into a host cell, replication of that material, and the release of the new viruses.

Learning Objectives

List the steps of viral replication and explain what occurs at each step

Key Takeaways

Key Points

  • Viral replication involves six steps: attachment, penetration, uncoating, replication, assembly, and release.
  • During attachment and penetration, the virus attaches itself to a host cell and injects its genetic material into it.
  • During uncoating, replication, and assembly, the viral DNA or RNA incorporates itself into the host cell’s genetic material and induces it to replicate the viral genome.
  • During release, the newly-created viruses are released from the host cell, either by causing the cell to break apart, waiting for the cell to die, or by budding off through the cell membrane.

Key Terms

  • virion: a single individual particle of a virus (the viral equivalent of a cell)
  • glycoprotein: a protein with covalently-bonded carbohydrates
  • retrovirus: a virus that has a genome consisting of RNA

Steps of Virus Infections

A virus must use cell processes to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in the host cell, which may cause cell damage. These changes, called cytopathic (causing cell damage) effects, can change cell functions or even destroy the cell. Some infected cells, such as those infected by the common cold virus known as rhinovirus, die through lysis (bursting) or apoptosis (programmed cell death or “cell suicide”), releasing all progeny virions at once. The symptoms of viral diseases result from the immune response to the virus, which attempts to control and eliminate the virus from the body and from cell damage caused by the virus. Many animal viruses, such as HIV (Human Immunodeficiency Virus), leave the infected cells of the immune system by a process known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo lysis and is not immediately killed. However, the damage to the cells that the virus infects may make it impossible for the cells to function normally, even though the cells remain alive for a period of time. Most productive viral infections follow similar steps in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release.

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Pathway to viral infection: In influenza virus infection, glycoproteins attach to a host epithelial cell. As a result, the virus is engulfed. RNA and proteins are made and assembled into new virions.

Attachment

A virus attaches to a specific receptor site on the host cell membrane through attachment proteins in the capsid or via glycoproteins embedded in the viral envelope. The specificity of this interaction determines the host (and the cells within the host) that can be infected by a particular virus. This can be illustrated by thinking of several keys and several locks where each key will fit only one specific lock.

Entry

The nucleic acid of bacteriophages enters the host cell naked, leaving the capsid outside the cell. Plant and animal viruses can enter through endocytosis, in which the cell membrane surrounds and engulfs the entire virus. Some enveloped viruses enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell, the viral capsid is degraded and the viral nucleic acid is released, which then becomes available for replication and transcription.

Replication and Assembly

The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to make additional DNA that is transcribed to messenger RNA (mRNA), which is then used to direct protein synthesis. RNA viruses usually use the RNA core as a template for synthesis of viral genomic RNA and mRNA. The viral mRNA directs the host cell to synthesize viral enzymes and capsid proteins, and to assemble new virions. Of course, there are exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes supply the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must be reverse transcribed into DNA, which then is incorporated into the host cell genome.

To convert RNA into DNA, retroviruses must contain genes that encode the virus-specific enzyme reverse transcriptase, which transcribes an RNA template to DNA. Reverse transcription never occurs in uninfected host cells; the needed enzyme, reverse transcriptase, is only derived from the expression of viral genes within the infected host cells. The fact that HIV produces some of its own enzymes not found in the host has allowed researchers to develop drugs that inhibit these enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the activity of the enzyme without affecting the host’s metabolism. This approach has led to the development of a variety of drugs used to treat HIV and has been effective at reducing the number of infectious virions (copies of viral RNA) in the blood to non-detectable levels in many HIV-infected individuals.

Egress

The last stage of viral replication is the release of the new virions produced in the host organism. They are then able to infect adjacent cells and repeat the replication cycle. As you have learned, some viruses are released when the host cell dies, while other viruses can leave infected cells by budding through the membrane without directly killing the cell.

Tissue Tropism in Animal Viruses

Host tropism refers to the way in which viruses/pathogens determine which cells become infected by a given pathogen.

Learning Objectives

Explain viral tropism

Key Takeaways

Key Points

  • Viruses must bind to specific cell surface receptors in order to enter a cell.
  • If a cell does not express these receptors then the virus cannot normally infect it.
  • In virology, Tissue tropism is the cells and tissues of a host which support growth of a particular virus or bacteria. Some viruses have a broad tissue tropism and can infect many types of cells and tissues. Other viruses may infect primarily a single tissue.

Key Terms

  • dendritic cell: Any cell, having branching processes, that forms part of the mammalian immune system.
  • macrophage: A white blood cell that phagocytizes necrotic cell debris and foreign material, including viruses, bacteria, and tattoo ink. It presents foreign antigens on MHC II to lymphocytes. Part of the innate immune system.

A tropism is a biological phenomenon, indicating growth or turning movement of a biological organism in response to an environmental stimulus. In tropisms, this response is dependent on the direction of the stimulus (as opposed to nastic movements which are non-directional responses). Viruses and other pathogens also affect what is called “host tropism” or “cell tropism. ” Case tropism refers to the way in which different viruses/pathogens have evolved to preferentially target specific host species or specific cell types within those species.

Host tropism is the name given to a process of tropism that determines which cells can become infected by a given pathogen. Host tropism is determined by the biochemical receptor complexes on cell surfaces that are permissive or non-permissive to the docking or attachment of various viruses.

Various factors determine the ability of a pathogen to infect a particular cell. For example, viruses must bind to specific cell surface receptors to enter a cell. If a cell does not express these receptors then the virus cannot normally infect it. Viral tropism is determined by a combination of susceptibility and permissiveness: a host cell must be both permissive (allow viral entry) and susceptible (possess the receptor complement needed for viral entry) for a virus to establish infection. An example of this is the HIV virus, which exhibits tropism for CD4 related immune cells (e.g. T helper cells, macrophages or dendritic cells). These cells express a CD4 receptor, to which the HIV virus can bind, through the gp120 and gp41 proteins on its surface.

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Human papillomavirus vaccine: Gardasil is a human papillomavirus vaccine on the market and it protects against HPV-16 and HPV-18 which cause 70% of cervical cancers, 80% of anal cancers, 60% of vaginal cancers, and 40% of vulvar cancers.

In virology, Tissue tropism is the cells and tissues of a host that support growth of a particular virus or bacteria. Some viruses have a broad tissue tropism and can infect many types of cells and tissues. Other viruses may infect primarily a single tissue.

Factors influencing viral tissue tropism include: 1) the presence of cellular receptors permitting viral entry, 2) availability of transcription factors involved in viral replication, 3) the molecular nature of the viral tropogen, and 4) the cellular receptors are the proteins found on a cell or viral surface.

These receptors are like keys allowing the viral cell to fuse with a cell or attach itself to a cell. The way that these proteins are acquired is through similar process to that of an infection cycle.

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HIV life cycle: HIV has a gp120 which is precisely what the CD4 marker is on the surface of the macrophages and T cells. Therefore, HIV can enter T cells and macrophages.

Animal Viruses

Animal viruses have their genetic material copied by a host cell after which they are released into the environment to cause disease.

Learning Objectives

Describe various animal viruses and the diseases they cause

Key Takeaways

Key Points

  • Animal viruses may enter a host cell by either receptor -mediated endocytosis or by changing shape and entering the cell through the cell membrane.
  • Viruses cause diseases in humans and other animals; they often have to run their course before symptoms disappear.
  • Examples of viral animal diseases include hepatitis C, chicken pox, and shingles.

Key Terms

  • receptor-mediated endocytosis: a process by which cells internalize molecules (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being internalized

Animal Viruses

Animal viruses, unlike the viruses of plants and bacteria, do not have to penetrate a cell wall to gain access to the host cell. Non-enveloped or “naked” animal viruses may enter cells in two different ways. When a protein in the viral capsid binds to its receptor on the host cell, the virus may be taken inside the cell via a vesicle during the normal cell process of receptor-mediated endocytosis. An alternative method of cell penetration used by non-enveloped viruses is for capsid proteins to undergo shape changes after binding to the receptor, creating channels in the host cell membrane. The viral genome is then “injected” into the host cell through these channels in a manner analogous to that used by many bacteriophages. Enveloped viruses also have two ways of entering cells after binding to their receptors: receptor-mediated endocytosis and fusion. Many enveloped viruses enter the cell by receptor-mediated endocytosis in a fashion similar to some non-enveloped viruses. On the other hand, fusion only occurs with enveloped virions. These viruses, which include HIV among others, use special fusion proteins in their envelopes to cause the envelope to fuse with the plasma membrane of the cell, thus releasing the genome and capsid of the virus into the cell cytoplasm.

After making their proteins and copying their genomes, animal viruses complete the assembly of new virions and exit the cell. Using the example of HIV, enveloped animal viruses may bud from the cell membrane as they assemble themselves, taking a piece of the cell’s plasma membrane in the process. On the other hand, non-enveloped viral progeny, such as rhinoviruses, accumulate in infected cells until there is a signal for lysis or apoptosis, and all virions are released together.

Animal viruses are associated with a variety of human diseases. Some of them follow the classic pattern of acute disease, where symptoms worsen for a short period followed by the elimination of the virus from the body by the immune system with eventual recovery from the infection. Examples of acute viral diseases are the common cold and influenza. Other viruses cause long-term chronic infections, such as the virus causing hepatitis C, whereas others, like herpes simplex virus, cause only intermittent symptoms. Still other viruses, such as human herpes viruses 6 and 7, which in some cases can cause the minor childhood disease roseola, often successfully cause productive infections without causing any symptoms at all in the host; these patients have an asymptomatic infection.

In hepatitis C infections, the virus grows and reproduces in liver cells, causing low levels of liver damage. The damage is so low that infected individuals are often unaware that they are infected, with many infections only detected by routine blood work on patients with risk factors such as intravenous drug use. Since many of the symptoms of viral diseases are caused by immune responses, a lack of symptoms is an indication of a weak immune response to the virus. This allows the virus to escape elimination by the immune system and persist in individuals for years, while continuing to produce low levels of progeny virions in what is known as a chronic viral disease. Chronic infection of the liver by this virus leads to a much greater chance of developing liver cancer, sometimes as much as 30 years after the initial infection.

As mentioned, herpes simplex virus can remain in a state of latency in nervous tissue for months, even years. As the virus “hides” in the tissue and makes few if any viral proteins, there is nothing for the immune response to act against; immunity to the virus slowly declines. Under certain conditions, including various types of physical and psychological stress, the latent herpes simplex virus may be reactivated and undergo a lytic replication cycle in the skin, causing the lesions associated with the disease. Once virions are produced in the skin and viral proteins are synthesized, the immune response is again stimulated and resolves the skin lesions in a few days by destroying viruses in the skin. As a result of this type of replicative cycle, appearances of cold sores and genital herpes outbreaks only occur intermittently, even though the viruses remain in the nervous tissue for life. Latent infections are common with other herpes viruses as well, including the varicella-zoster virus that causes chickenpox. After having a chickenpox infection in childhood, the varicella-zoster virus can remain latent for many years and reactivate in adults to cause the painful condition known as “shingles”.

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Chicken pox virus: (a) Varicella-zoster, the virus that causes chickenpox, has an enveloped icosahedral capsid visible in this transmission electron micrograph. Its double-stranded DNA genome incorporates into the host DNA and reactivates after latency in the form of (b) shingles, often exhibiting a rash.

Plant Virus Life Cycles

Plant viruses are often spread from plant to plant by organisms known as vectors.

Learning Objectives

Outline plant virus life cycles

Key Takeaways

Key Points

  • Plant viruses are harmless to humans and other animals because they can only reproduce in living plant cells.
  • For the virus to reproduce and thereby establish infection, it must enter cells of the host organism and use those cells’ materials.
  • A virus must take control of the host cell’s replication mechanisms. At this stage a distinction between susceptibility and permissibility of a host cell is made.
  • After control is established and the environment is set for the virus to begin making copies of itself, replication occurs quickly by the millions.

Key Terms

  • vector: A carrier of a disease-causing agent.

Plant viruses are viruses that affect plants. Like all other viruses, plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without a host. Plant viruses are pathogenic to higher plants.

There are many types of plant virus, but often they only cause a loss of yield, and it is not economically viable to try to control them. Plant viruses are often spread from plant to plant by organisms ( vectors ). These are normally insects, but some fungi, nematode worms and single-celled organisms have been shown to be vectors. When control of plant virus infections is considered economical, (for perennial fruits for example), efforts are concentrated on killing the vectors and removing alternate hosts such as weeds. Plant viruses are harmless to humans and other animals because they can only reproduce in living plant cells.

Viral Life Cycle

For the virus to reproduce and thereby establish infection, it must enter cells of the host organism and use those cells’ materials. To enter the cells, proteins on the surface of the virus interact with proteins of the cell. Attachment, or adsorption, occurs between the viral particle and the host cell membrane. A hole forms in the cell membrane, then the virus particle or its genetic contents are released into the host cell, where viral reproduction may commence. Next, a virus must take control of the host cell’s replication mechanisms. At this stage, a distinction between susceptibility and permissibility of a host cell is made. Permissibility determines the outcome of the infection. After control is established and the environment is set for the virus to begin making copies of itself, replication occurs quickly by the millions. After a virus has made many copies of itself, it usually has exhausted the cell of its resources. The host cell is now no longer useful to the virus, therefore the cell often dies and the newly produced viruses must find a new host. The process by which virus progeny are released to find new hosts, is called shedding. This is the final stage in the viral life cycle. Some viruses can “hide” within a cell, either to evade the host cell defenses or immune system, or simply because it is not in the best interest of the virus to continually replicate. This hiding is deemed latency. During this time, the virus does not produce any progeny, it remains inactive until external stimuli—such as light or stress—prompts it to activate.

Viruses can be spread by direct transfer of sap, and by contact of a wounded plant with a healthy one. Such contact may occur during agricultural practices, when damage is caused by tools or hands, or naturally, when an animal feeds on the plant. Generally Tobacco mosaic virus (TMV), potato viruses, and cucumber mosaic viruses are transmitted via sap.

Tobacco mosaic virus and Cauliflower mosaic virus (CaMV) are frequently used in plant molecular biology. Of special interest is the CaMV 35S promoter, which is a very strong promoter most frequently used in plant transformations.

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Tobacco Mosaic Virus: Tobacco mosaic virus (TMV) is a positive-sense single stranded RNA virus that infects plants, especially tobacco and other members of the family Solanaceae. The infection causes characteristic patterns (mottling and discoloration) on the leaves (hence the name). TMV was the first virus to be discovered. Although it was known from the late 19th century that an infectious disease was damaging tobacco crops, it was not until 1930 that the infectious agent was determined to be a virus.