DNA Viruses in Eukaryotes

Plant DNA Viruses

DNA viruses are relatively rare in plants, but are responsible for a significant amount of crop damage worldwide.

Learning Objectives

Differentiate between ssDNA and dsDNA plant viruses

Key Takeaways

Key Points

  • DNA viruses are relatively rare in plants, compared to their RNA counterparts.
  • Like most viruses, the genomes of most single stranded DNA viruses are small, encoding only a few proteins, and are therefore dependent on host cell factors for replication.
  • Double stranded DNA viruses only infect lower species of plants, such as algae. These viruses are huge dsDNA viruses with genomes ranging from 160 to 560 kb with up to 600 protein-encoding genes, making them distinctly different from viruses infecting higher plants.
  • Plant viruses are generally spread through vectors, such as insects, but can also be passed from generation to generation.

Key Terms

  • Baltimore Classification System: The Baltimore classification, developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc.) and their method of replication.
  • plasmodesmata: Plasmodesmata (singular: plasmodesma) are microscopic channels which traverse the cell walls of plant cells and some algal cells, enabling transport and communication between them.
  • capsid: The outer protein shell of a virus.

A DNA virus is a virus with DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. DNA viruses belong to either Group I (double-stranded DNA; dsDNA) or Group II (single-stranded DNA; ssDNA) of the Baltimore classification system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells.

DNA viruses are relatively rare in plants. Seventeen percent of plant viruses are ssDNA, while dsDNA viruses infect only lower plants, such as eukaryotic algae. The rarity of dsDNA plant viruses is notable when compared to other taxonomic kingdoms; a quarter of animal viruses and three quarters of bacterial viruses are dsDNA.

Plant viruses are transmitted through a variety of different methods, and generally require breach of protective barriers. Viruses can be spread by direct transfer of sap by contact of a wounded plant with a healthy one, most commonly resulting from agricultural practices, as by damage caused by tools or hands. More often, viruses are spread through vector intermediaries such as insects, nematodes, or protozoa which pick up viruses by feeding on infected plants, and then spread the virus to healthy plants.

Viral transmission from generation to generation occurs in about 20% of plant viruses. When viruses are transmitted by seeds, the seed is infected in the generative cells and the virus is maintained in the germ cells, or occasionally in the seed coat. Little is known about the mechanisms involved in the transmission of plant viruses via seeds, though environment is known to play a key role.

Single-Stranded DNA Viruses

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Geminiviruses: Drawing of geminiviruses, characterized by elongated, geminate capsids with two incomplete T=1 icosahedra joined at the missing vertex.

The Geminiviridae and Nanoviridae are the two families of ssDNA viruses known to infect plants. Geminiviridae is the largest known family of single-stranded DNA viruses. It contains a wide range of plant viruses including bean golden mosaic virus, beet curly top virus, maize streak virus, and tomato pseudo-curly top virus, which together are responsible for a significant amount of crop damage worldwide. The genome can either be a single component between 2500-3100 nucleotides, or, in the case of some begomoviruses, two similar-sized components each between 2600 and 2800 nucleotides. They have elongated, geminate capsids with two incomplete T=1 icosahedra joined at the missing vertex. The capsids range in size from 18-20 nm in diameter with a length of about 30 nm. Begomoviruses possess two component genomes separated into two different particles, both of which must usually be transmitted together to initiate a new infection within a suitable host cell. Like many viruses, geminivirus genomes encode only a few proteins, and are therefore dependent on host cell factors for replication. Geminiviruses replication occurs within the nucleus of an infected plant cell via a rolling circle mechanism, similar to that seen in bacteriophages, such as M13, and many plasmids. The resulting ssDNA is packaged into germinate particles in the nucleus. It is not clear if these particles can then leave the nucleus and be transmitted to surrounding cells as virions, or whether ssDNA is trafficked from cell to cell via the plasmodesmata. These viruses tend to be introduced into and initially infect differentiated plant cells, via the piercing mouthparts of the vector insect: however, these cells generally lack the host enzymes necessary for DNA replication, making it difficult for the virus to replicate. To overcome this block geminiviruses can induce plant cells to reenter the cell cycle from a quiescent state so that viral replication can occur.

The Nanoviridae are a family of single-stranded DNA viruses that infect plants. Their name is derived from the Greek word ‘nano’ (dwarf) because of their small genome and their stunting effect on infected plants.

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Maize Streak Virus: The black-faced leafhopper (Graminella nigrifrons) transmits both maize fine streak virus and maize chlorotic dwarf virus.

Virions of this family have a capsid and are non-enveloped. The capsid is icosahedral with diameter of 18-20 nm. The genome is composed of 6 to 11 segments of single-stranded circular DNA each ~1 kb in length, with the exact number of segments varying depending on the genus. The segments each encode a single protein. There is a putative stem loop structure in the non-coding region of each segment which has a conserved 9-nucleotide sequence at its apex. Each member has up to 4 segments encoding replication proteins of ~33 kDa. The other segments encode products of 10-20 kDa in size and include a coat protein of ~19 kDa and a protein with a retinoblastoma binding motif.

Double-Stranded DNA Viruses

Double-stranded DNA viruses of plants are rare, and only infect lower plants, such as algae. These viruses (family Phycodnaviridae) are huge dsDNA viruses with genomes ranging from 160 to 560 kb with up to 600 protein-encoding genes, making them distinctly different from viruses infecting higher plants. They are found in aqueous environments throughout the world and play dynamic, albeit largely undocumented, roles in regulating algal communities such as the termination of massive algal blooms commonly referred to as red and brown tides.

Replication of Double-Stranded DNA Viruses of Animals

Most double-stranded DNA viruses replicate within the host cell nucleus.

Learning Objectives

Differentiate the ways which different classes of dsDNA viruses replicate

Key Takeaways

Key Points

  • From the perspective of the virus, the purpose of viral replication is to allow production and survival of its kind.
  • Most double-stranded DNA viruses replicate within the host cell nucleus, including polyomaviruses, adenoviruses, and herpesviruses—poxviruses, however, replicate in the cytoplasm.
  • Adenoviruses and herpes viruses encode their own replication factors.

Key Terms

  • Okazaki fragments: Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.
  • polymerase: Any of various enzymes that catalyze the formation of polymers of DNA or RNA using an existing strand of DNA or RNA as a template.

Viral replication is the formation of biological viruses during the infection process in the target host cells. Viruses must first get into the cell before viral replication can occur. From the perspective of the virus, the purpose of viral replication is to allow production 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 greatly varied and depends on the type of genes involved in them. Most DNA viruses assemble in the nucleus while most RNA viruses develop solely in cytoplasm.

Double-stranded DNA viruses usually must enter the host nucleus before they are able to replicate. Some of these viruses require host cell polymerases to replicate their genome, while others, such as adenoviruses or herpes viruses, encode their own replication factors. However, in either cases, replication of the viral genome is highly dependent on a cellular state permissive to DNA replication and, thus, on the cell cycle. The virus may induce the cell to forcefully undergo cell division, which may lead to transformation of the cell and, ultimately, cancer. An example of a family within this classification is the Adenoviridae.

Polyomaviruses, adenoviruses, and herpesviruses are all nuclear-replicating DNA viruses, each with their own specific approaches to replication. There is only one well-studied example in which a double-stranded DNA virus does not replicate within the nucleus. This is the Poxvirus family, which comprises highly pathogenic viruses that infect vertebrates.

Polyomaviruses

Polyomaviridae is a family of viruses whose natural hosts are primarily mammals and birds. Most of these viruses, such as BK virus and JC virus, are very common and typically asymptomatic in most human populations studied. However, some polyomaviruses are associated with human disease, particularly in immunocompromised individuals. Some members of the family are oncoviruses, meaning they can cause tumors; they often persist as latent infections in a host without causing disease, but may produce tumors in a host of a different species, or in individuals with ineffective immune systems. The name polyoma refers to the viruses’ ability to produce multiple (poly-) tumors (-oma).

Replication

Prior to genome replication, the processes of viral attachment, entry and uncoating occur. Polyomavirus virions are subsequently endocytosed and transported first to the endoplasmic reticulum where a conformational change occurs; then by an unknown mechanism the virus is exported to the nucleus. Polyomaviruses replicate in the nucleus of the host.

Adenoviruses

Adenoviruses (members of the family Adenoviridae) are medium-sized (90–100 nm), nonenveloped (without an outer lipid bilayer) viruses with an icosahedral nucleocapsid containing a double stranded DNA genome.

Adenoviruses represent the largest nonenveloped viruses. They are able to be transported through the endosome (i.e., envelope fusion is not necessary). The virion also has a unique “spike” or fiber associated with each penton base of the capsid that aids in attachment to the host cell via the receptor on the surface of the host cell.

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Adenovirus structure: Adenoviruses are non-enveloped (i.e., they have no external lipid bilayer) and are icosahedral (i.e., shaped like a polyhedron with 20 faces). They have fibers at their vertices that help them attach to host cells.

Replication

Adenoviruses possess a linear dsDNA genome and are able to replicate in the nucleus of vertebrate cells using the host’s replication machinery.

Once the virus has successfully gained entry into the host cell, the endosome acidifies, which alters virus topology by causing capsid components to disband, which in turn destroys the endosome and allows the virion entry into the cytoplasm. It is transported to the nuclear pore, disassembles, and is released into the nucleus. At this point viral gene expression can occur and new virus particles can be generated.

Herpesviruses

Herpesviridae is a large family of DNA viruses that cause diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word herpein (“to creep”), referring to the latent, recurring infections typical of this group of viruses. Herpesviridae can cause latent or lytic infections.

At least five species of Herpesviridae – HSV-1 and HSV-2 (both of which can cause orolabial herpes and genital herpes), Varicella zoster virus (which causes chicken-pox and shingles), Epstein-Barr virus (which causes mononucleosis), and Cytomegalovirus – are extremely widespread among humans. More than 90% of adults have been infected with at least one of these, and a latent form of the virus remains in most people. In total, there are 8 herpesvirus types that infect humans: herpes simplex viruses 1 and 2, varicella-zoster virus, EBV (Epstein-Barr virus), human cytomegalovirus, human herpesvirus 6, human herpesvirus 7, and Kaposi’s sarcoma-associated herpesvirus. There are more than 130 herpesviruses, and some are from mammals, birds, fish, reptiles, amphibians, and molluscs.

Replication

All herpesviruses are nuclear-replicating—the viral DNA is transcribed to mRNA within the infected cell’s nucleus. Infection is initiated when a viral particle contacts a cell with specific types of receptor molecules on the cell surface. Following binding of viral envelope glycoproteins to cell membrane receptors, the virion is internalized and dismantled, allowing viral DNA to migrate to the cell nucleus. Within the nucleus, replication of viral DNA and transcription of viral genes occurs.

Poxviruses

Poxviridae is a family of viruses. Human, vertebrates, and arthropods serve as natural hosts. There are currently 69 species in this family, divided among 28 genera, which are divided into two subfamilies. Diseases associated with this family include smallpox.

Poxviridae viral particles (virions) are generally enveloped (external enveloped virion- EEV), though the intracellular mature virion (IMV) form of the virus, which contains different envelope, is also infectious. The virion is exceptionally large—around 200 nm in diameter and 300 nm in length.

Replication

The replication of poxvirus is unusual for a virus with double-stranded DNA genome (dsDNA) because it occurs in the cytoplasm, although this is typical of other large DNA viruses. Poxvirus encodes its own machinery for genome transcription, a DNA dependent RNA polymerase, which makes replication in the cytoplasm possible. Most dsDNA viruses require the host cell’s DNA-dependent RNA polymerase to perform transcription. These host DNA are found in the nucleus, and therefore most dsDNA viruses carry out a part of their infection cycle within the host cell’s nucleus.

Double-Stranded DNA Viruses: Herpesviruses

Herpes viruses cause a wide range of latent, recurring infections including oral and genital herpes, cytomegalovirus, and chicken pox.

Learning Objectives

Recognize the attributes of herpes viruses

Key Takeaways

Key Points

  • Herpesviridae is a large family of DNA viruses that cause diseases in animals, including humans.
  • The structure of herpes viruses consists of a relatively large double-stranded, linear DNA genome encased within an icosahedral protein cage called the capsid, which is wrapped in a lipid bilayer called the envelope.
  • Notable herpes viruses include herpes simplex viruses 1 and 2, Varicella zoster virus (the causative agent of shingles and chicken pox), cytomegalovirus, and Kaposi’s sarcoma virus.
  • There is no method to eradicate herpes virus from the body, but antiviral medications, such as acyclovir, can reduce the frequency, duration, and severity of outbreaks.

Key Terms

  • tegument: A natural covering of the body or of a bodily organ.
  • capsid: The outer protein shell of a virus.
  • virion: A single individual particle of a virus (the viral equivalent of a cell).

Herpesviridae is a large family of DNA viruses that cause diseases in animals, including humans. The members of this family are also known as herpes viruses. The family name is derived from the Greek word herpein (“to creep”), referring to the latent, recurring infections typical of this group of viruses.

Animal herpes viruses all share some common properties. The structure of these viruses consists of a relatively large double-stranded, linear DNA genome encased within an icosahedral protein cage called the capsid, which is wrapped in a lipid bilayer called the envelope. The envelope is joined to the capsid by means of a tegument. This complete particle is known as the virion. HSV-1 and HSV-2 each contain at least 74 genes within their genomes, although speculation over gene crowding allows as many as 84 unique protein-coding genes by 94 putative pen reading frames. These genes encode a variety of proteins involved in forming the capsid, tegument and envelope of the virus, as well as controlling the replication and infectivity of the virus.

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Herpesviridae: Various viruses from the Herpesviridae family seen using an electron micrograph Amongst these members is varicella-zoster (Chickenpox), and herpes simplex type 1 and 2 (HSV-1, HSV-2).

Types of herpes viruses

There are nine distinct herpes viruses which cause disease in humans:

  • HHV‑1 Herpes simplex virus-1 (HSV-1)
  • HHV-2 Herpes simplex virus-2 (HSV-2)
  • HHV-3 Varicella zoster virus (VZV)
  • HHV-4 Epstein-Barr virus (EBV)
  • HHV-5 Cytomegalovirus (CMV)
  • HHV-6A/B Roseolovirus, Herpes lymphotropic virus
  • HHV-7 Pityriasis Rosea
  • HHV-8 Kaposi’s sarcoma-associated herpesvirus

Of particular interest include HSV-1 and HSV-2, which cause oral and/or genital herpes, HSV-3 which causes chickenpox and shingles, and HHV-5 which causes mononucleosis-like symptoms, and HHV-8 which causes a Kaposi’s sarcoma, a cancer of the lymphatic epithelium.

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Herpes Simplex Virions: This negatively-stained transmission electron micrograph (TEM) revealed the presence of numerous herpes simplex virions, members of the Herpesviridae family. There are two strains of the herpes simplex virus, HSV-1, which is responsible for cold sores, and HSV-2, which is responsible for genital herpes. At the core of its icosahedral proteinaceous capsid, the HSV contains a double-stranded DNA linear genome.

Infection is caused through close contact with an infected individual. Infection is initiated when a viral particle comes in contact with the target cell specific to the individual herpes virus. Viral glycoproteins bind cell surface receptors molecules on the cell surface, followed by virion internalization and disassembly. Viral DNA then migrates to the cell nucleus where replication of viral DNA and transcription of viral genes occurs.

During symptomatic infection, infected cells transcribe lytic viral genes. In some host cells, a small number of viral genes termed latency-associated transcripts accumulate instead. In this fashion, the virus can persist in the cell (and thus the host) indefinitely. While primary infection is often accompanied by a self-limited period of clinical illness, long-term latency is symptom-free.

Reactivation of latent viruses

This has been implicated in a number of diseases (e.g. Shingles, Pityriasis Rosea). Following activation, transcription of viral genes transitions from latency-associated transcripts to multiple lytic genes; these lead to enhanced replication and virus production. Often, lytic activation leads to cell death. Clinically, lytic activation is often accompanied by emergence of non-specific symptoms such as low grade fever, headache, sore throat, malaise, and rash, as well as clinical signs such as swollen or tender lymph nodes, and immunological findings such as reduced levels of natural killer cells.

There is no method to eradicate the herpes virus from the body, but antiviral medications, such as acyclovir, can reduce the frequency, duration, and severity of outbreaks. Analgesics such as ibuprofen and acetaminophen can reduce pain and fever. Topical anesthetic treatments such as prilocaine, lidocaine, benzocaine or tetracaine can also relieve itching and pain.

Attachment and Entry of Herpes Simplex

Herpes simplex virus attaches to a host’s cells with viral envelope glycoproteins, which then allows entry of the viral capsid into the host cell.

Learning Objectives

Illustrate HSV attachment to host cells

Key Takeaways

Key Points

  • The genome encodes for 11 different glycoproteins, four of which, gB, gC, gD and gH, are involved in viral attachment.
  • The sequential stages of HSV entry are analogous to those of other viruses.
  • First, complementary viral and cell surface receptors bring the viral and host cell membranes into close proximity. Next, the two membranes begin to merge, forming a hemifusion state. Finally, a stable entry pore is formed through which the viral envelope contents are introduced to the host cell.

Key Terms

  • glycoprotein: A protein with covalently bonded carbohydrates.
  • hemifusion: Partial fusion, or the first stage in full fusion.
  • heparan sulfate: A polysaccharide found, associated with protein, in all animal tissue; it has a regulatory function in several biological activities.

Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are two members of the herpes virus family, Herpesviridae, that infect humans. Both HSV-1 (which produces most cold sores) and HSV-2 (which produces most genital herpes) are ubiquitous and contagious. They can be spread when an infected person is producing and shedding the virus.

The sequential stages of HSV entry are analogous to those of other viruses. At first, complementary receptors on the virus and the cell surface bring the viral and cell membranes into close proximity. In an intermediate state, the two membranes begin to merge, forming a hemifusion state. Finally, a stable entry pore is formed through which the viral envelope contents are introduced to the host cell.

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Virus replication: Herpes simplex virus attaches to host cell surface receptors using glycoproteins. Following attachment, the viral envelope fuses with the host cell membrane and the viral capsid gains entry into the cell.

The genome encodes for 11 different glycoproteins, four of which, gB, gC, gD and gH, are involved in viral attachment. Initial interactions occur when viral envelope glycoprotein C (gC) binds to a cell surface particle called heparan sulfate. A second glycoprotein, glycoprotein D (gD), binds specifically to at least one of three known entry receptors. These include herpesvirus entry mediator (HVEM), nectin-1 and 3-O sulfated heparan sulfate. The receptor provides a strong, fixed attachment to the host cell. These interactions bring the membrane surfaces into mutual proximity and allow for other glycoproteins embedded in the viral envelope to interact with other cell surface molecules. Once bound to the HVEM, gD changes its conformation and interacts with viral glycoproteins H (gH) and L (gL), which form a complex. The interaction of these membrane proteins results in the hemifusion state. Afterward, gB interaction with the gH/gL complex creates an entry pore for the viral capsid. Glycoprotein B interacts with glycosaminoglycans on the surface of the host cell.

Replication of Herpes Simplex Virus

Herpes replication entails three phases: gene transcription, viral assembly in the nucleus, and budding through the nuclear membrane.

Learning Objectives

Review the herpes simplex viral replication cycle

Key Takeaways

Key Points

  • Upon entry into the host cell nucleus, three distinct phases of gene transcription and protein synthesis are initiated, producing the immediate-early, early, and late proteins.
  • Viral nucleocapsid assembly occurs within the host cell nucleus.
  • The virus acquires its final envelope by budding into cytoplasmic vesicles.

Key Terms

  • nucleocapsid: The core structure of a virus, consisting of nucleic acid surrounded by a coat of protein.

Following infection of a cell, a cascade of herpes virus proteins, called immediate-early, early, and late, are produced. Research using flow cytometry on another member of the herpes virus family, Kaposi’s sarcoma-associated herpesvirus, indicates the possibility of an additional lytic stage, delayed-late. These stages of lytic infection, particularly late lytic, are distinct from the latency stage. In the case of HSV-1, no protein products are detected during latency, whereas they are detected during the lytic cycle.

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Herpes simplex virus: Structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16.

The early proteins transcribed are used in the regulation of genetic replication of the virus. On entering the cell, an α-TIF protein joins the viral particle and aids in immediate-early transcription. The virion host shutoff protein (VHS or UL41) is very important to viral replication. This enzyme shuts off protein synthesis in the host, degrades host mRNA, helps in viral replication, and regulates gene expression of viral proteins. The viral genome immediately travels to the nucleus but the VHS protein remains in the cytoplasm.

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HSV replication: Entry of HSV into the host cell involves interactions of several glycoproteins on the surface of the enveloped virus, with receptors on the surface of the host cell. The envelope covering the virus particle, when bound to specific receptors on the cell surface, will fuse with the host cell membrane and create an opening, or pore, through which the virus enters the host cell. An enzyme shuts off protein synthesis in the host, degrades host mRNA, helps in viral replication, and regulates gene expression of viral proteins.

The late proteins form the capsid and the receptors on the surface of the virus. Packaging of the viral particles — including the genome, core and the capsid – occurs in the nucleus of the cell. Here, concatemers of the viral genome are separated by cleavage and are placed into pre-formed nucleocapsids. HSV-1 undergoes a process of primary and secondary envelopment. The primary envelope is acquired by budding into the inner nuclear membrane of the cell. This then fuses with the outer nuclear membrane releasing a naked capsid into the cytoplasm. The virus acquires its final envelope by budding into cytoplasmic vesicles.

Immunodeficiency

Immunodeficiency occurs when the immune system cannot appropriately respond to infections.

Learning Objectives

Explain the problems associated with immunodeficiency

Key Takeaways

Key Points

  • If a pathogen is allowed to proliferate to certain levels, the immune system can become overwhelmed; immunodeficiency occurs when the immune system fails to respond sufficiently to a pathogen.
  • Immunodeficiency can be caused by many factors, including certain pathogens, malnutrition, chemical exposure, radiation exposure, or even extreme stress.
  • HIV is a virus that causes immunodeficiency by infecting helper T cells, causing cytotoxic T cells to destroy them.

Key Terms

  • phagocyte: a cell of the immune system, such as a neutrophil, macrophage or dendritic cell, that engulfs and destroys viruses, bacteria, and waste materials
  • lysis: the disintegration or destruction of cells
  • immunodeficiency: a depletion in the body’s natural immune system, or in some component of it

Immunodeficiency

Failures, insufficiencies, or delays at any level of the immune response can allow pathogens or tumor cells to gain a foothold to replicate or proliferate to high enough levels that the immune system becomes overwhelmed, leading to immunodeficiency; it may be acquired or inherited. Immunodeficiency can be acquired as a result of infection with certain pathogens (such as HIV), chemical exposure (including certain medical treatments), malnutrition, or, possibly, by extreme stress. For instance, radiation exposure can destroy populations of lymphocytes, elevating an individual’s susceptibility to infections and cancer. Dozens of genetic disorders result in immunodeficiencies, including Severe Combined Immunodeficiency (SCID), bare lymphocyte syndrome, and MHC II deficiencies. Rarely, primary immunodeficiencies that are present from birth may occur. Neutropenia is one form in which the immune system produces a below-average number of neutrophils, the body’s most abundant phagocytes. As a result, bacterial infections may go unrestricted in the blood, causing serious complications.

HIV/AIDS

Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS), is a disease of the human immune system caused by infection with human immunodeficiency virus (HIV). During the initial infection, a person may experience a brief period of influenza-like illness. This is typically followed by a prolonged period without symptoms. As the illness progresses, it interferes more and more with the immune system. The person has a high probability of becoming infected, including from opportunistic infections and tumors that do not usually affect people who have working immune systems.

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Image of HIV: scanning electron micrograph of HIV-1 budding (in green, color added) from cultured lymphocyte: Multiple round bumps on cell surface represent sites of assembly and budding of HIV. During primary infection, the level of HIV may reach several million virus particles per milliliter of blood.

After the virus enters the body, there is a period of rapid viral replication, leading to an abundance of virus in the peripheral blood. During primary infection, the level of HIV may reach several million virus particles per milliliter of blood. This response is accompanied by a marked drop in the number of circulating CD4+ T cells, cells that are or will become helper T cells. The acute viremia, or spreading of the virus, is almost invariably associated with activation of CD8+ T cells (which kill HIV-infected cells) and, subsequently, with antibody production. The CD8+ T cell response is thought to be important in controlling virus levels, which peak and then decline, as the CD4+ T cell counts recover.

Ultimately, HIV causes AIDS by depleting CD4+ T cells (helper T cells). This weakens the immune system, allowing opportunistic infections. T cells are essential to the immune response; without them, the body cannot fight infections or kill cancerous cells. The mechanism of CD4+ T cell depletion differs in the acute and chronic phases. During the acute phase, HIV-induced cell lysis and killing of infected cells by cytotoxic T cells accounts for CD4+ T cell depletion, although apoptosis (programmed cell death) may also be a factor. During the chronic phase, the consequences of generalized immune activation coupled with the gradual loss of the ability of the immune system to generate new T cells appear to account for the slow decline in CD4+ T cell numbers.

Double-Stranded DNA Viruses: Pox Viruses

The poxviruses are a family of large, complex, enveloped DNA viruses that infect a variety of vertebrate and invertebrate hosts.

Learning Objectives

Examine pox viruses for their relevance to human disease and research

Key Takeaways

Key Points

  • The most famous of the poxviruses was smallpox. Smallpox is one of two infectious diseases to have been eradicated, the other being rinderpest, which was declared eradicated in 2011.
  • The most abundant and simplest infectious form of the poxvirus particle, the mature virion, consists of the viral DNA genome encased in a proteinaceous core and an outer lipoprotein membrane.
  • Poxviruses exhibit a temporally-regulated gene expression program: early, intermediate, and late genes drive DNA replication followed by expression of structural proteins necessary for progeny virion assembly.

Key Terms

  • recombinant: This term refers to something formed by combining existing elements in a new combination. Thus, the phrase recombinant DNA refers to an organism created in the lab by adding DNA from another species.
  • lipoprotein: Any of a large group of complexes of protein and lipid with many biochemical functions.

The poxviruses are a family of large, complex, enveloped DNA viruses that infect a variety of vertebrate and invertebrate hosts. Poxviruses are of significance both medically and scientifically due to their wide distribution, pathogenicity, and cytoplasmic replicative life cycle. Several prominent members, including variola virus (causative agent of smallpox), molluscum contagiosum virus (cause of a common skin infection of young children and immunosuppressed adults) and monkeypox virus (agent of a smallpox-like disease in parts of Africa), are of considerable concern for public health and biodefense.

The most famous of the poxviruses was smallpox. Smallpox was an infectious disease unique to humans, caused by either of two virus variants, Variola major and Variola minor. The disease is also known by the Latin names Variola or Variola vera, which is a derivative of the Latin varius, meaning “spotted,” or varus, meaning “pimple. ” The term “smallpox” was first used in Britain in the 15th century to distinguish variola from the “great pox” (syphilis). The last naturally occurring case of smallpox (Variola minor) was diagnosed on October 26, 1977. After vaccination campaigns throughout the 19th and 20th centuries, the World Health Organization (WHO) certified the eradication of smallpox in 1979. Smallpox is one of two infectious diseases to have been eradicated, the other being rinderpest, which was declared eradicated in 2011.

The prototypic and most studied poxvirus, vaccinia virus (VACV), serves as an effective smallpox vaccine, a platform for recombinant vaccines against other pathogens, and an efficient gene expression vector for basic research. Along its approximate 195-kbp double-stranded DNA genome, VACV encodes approximately 200 proteins, ranging in function from viral RNA and DNA synthesis and virion assembly to modulation of host immune defenses.

The most abundant and simplest infectious form of the poxvirus particle, the mature virion (MV), consists of the viral DNA genome encased in a proteinaceous core and an outer lipoprotein membrane with approximately 60 and 25 associated viral proteins, respectively. Following attachment to cell surfaces and fusion with the plasma or endosomal membrane, poxvirus replication is initiated by entry of the viral core into the cytoplasm, where all subsequent steps of the life cycle take place. Poxvirus cores harbor the viral DNA-dependent RNA polymerase and transcription factors necessary for expression of early genes, which constitute nearly half of the viral genome and encode proteins needed for DNA replication and intermediate gene transcription, as well as a large number of immunomodulators.

Poxviruses exhibit a temporally-regulated gene expression program, i.e., expression of early genes encoding DNA replication and intermediate transcription factors triggers the expression of intermediate genes encoding late gene specific transcription factors. Late gene products primarily consist of structural proteins needed for progeny virion assembly, as well as those enzymes destined for incorporation into progeny virions, and used for early gene expression during the next round of infection. Assembly of the MV involves more than 80 viral gene products. In addition, during transit through the cytoplasm, a subset of progeny MVs acquires two additional membrane bilayers, one of which is lost during exocytosis of the particle, to yield the less abundant enveloped virion (EV). Thus, an EV is essentially an MV with an additional membrane in which at least six unique proteins are associated. EVs are antigenically distinct from MVs and are important for efficient virus dissemination in the infected host and protection against immune defenses. In contrast, MVs are released upon cell lysis and may be important for animal-to-animal transmission.

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Girl infected with smallpox. Bangladesh, 1973.: In ordinary type smallpox the bumps are filled with a thick, opaque fluid and often have a depression or dimple in the center. This is a major distinguishing characteristic of smallpox.

Double-Stranded DNA Viruses: Adenoviruses

Adenoviruses are non-enveloped, icosahedral DNA viruses which cause upper respiratory infections, primarily in children.

Learning Objectives

Define the characteristics of adenoviruses

Key Takeaways

Key Points

  • Adenoviruses are medium-sized (90–100 nm), non-enveloped, icosahedral viruses composed of a nucleocapsid and a linear double-stranded DNA (dsDNA) genome.
  • There are 57 described serotypes in humans, which are responsible for 5–10% of upper respiratory infections in children, and many infections in adults as well.
  • Adenoviruses bind cell surface receptors on host cells, resulting in entry of the virion into the host cell within an endosome.
  • The adenovirus life cycle is separated by the DNA replication process into two phases: an early and a late phase. Early genes are responsible for expressing mainly non-structural, regulatory proteins, while late genes produce structural protein necessary for viral replication.

Key Terms

  • endosome: An endocytic vacuole through which molecules are internalized during endocytosis pass, en route to lysosomes.
  • recombinant DNA: DNA that has been engineered by splicing together fragments of DNA from multiple species and introduced into the cells of a host.
  • integrin: Any of many heterodimeric transmembrane proteins that function as receptors in communication between cells.
  • penton: A pentagonal capsomere of an adenovirus capsid.
  • capsid: A capsid is the protein shell of a virus.

Adenoviruses are medium-sized (90–100 nm), non-enveloped, icosahedral viruses composed of a nucleocapsid and a linear, double-stranded DNA (dsDNA) genome. There are 57 described serotypes in humans, which are responsible for 5–10% of upper respiratory infections in children, and many infections in adults as well.

Diversity

Viruses of the family Adenoviridae infect vertebrates, including humans. Among human-tropic viruses classification can be complex; there are 57 accepted human adenovirus types (HAdV-1 to 57) in seven species (Human adenovirus A to G). Different species/serotypes are associated with different conditions:

  • respiratory disease (mainly species HAdV-B and C)
  • conjunctivitis (HAdV-B and D)
  • gastroenteritis (HAdV-F types 40, 41, HAdV-G type 52)

In addition to human viruses, Adenoviridae can be divided into five genera: Mastadenovirus, Aviadenovirus, Atadenovirus, Siadenovirus, and Ichtadenovirus.

Genome

Structurally, adenoviruses represent the largest non-enveloped viruses. They possess non-segmented dsDNA genomes between 26 and 45 Kbp, significantly larger than other dsDNA viruses. The virion also has unique “spike” or fiber associated with each penton base of the capsid that aids in attachment to the host cell via host cell surface receptors.

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Adenovirus Structure: 1) Penton capsomeres 2) Hexon capsomeres 3) Viral genome (linear dsDNA)

Viral Entry and Replication

Entry of adenoviruses into the host cell involves two sets of interactions between the virus and the host cell. First, entry into the host cell is initiated by the knob domain of the fiber protein binding to a host cell receptor, either CD46 for the group B human adenovirus serotypes, or the coxsackievirus adenovirus receptor for all other serotypes. Next, a specialized motif in the penton base protein interacts with αv integrin, stimulating internalization of the adenovirus via clathrin-coated pits, resulting in entry of the virion into the host cell within an endosome.

Following internalization, the endosome acidifies, which alters virus topology, causing capsid components to disassociate. These changes, as well as the toxic nature of the pentons, result in the release of the virion into the cytoplasm. With the help of cellular microtubules, the virus is transported to the nuclear pore complex, where viral gene expression can occur.

The adenovirus life cycle is separated by the DNA replication process into two phases: an early and a late phase. In both, a primary transcript that is alternatively spliced to generate monocistronic mRNAs compatible with the host’s ribosome is generated, allowing for the products to be translated.

The early genes are responsible for expressing mainly non-structural, regulatory proteins. The goal of these proteins is threefold: to alter the expression of host proteins necessary for DNA synthesis; to activate other viral genes (such as the virus-encoded DNA polymerase); and to avoid premature death of the infected cell by the host-immune defenses (blockage of apoptosis, blockage of interferon activity, and blockage of MHC class I translocation and expression).

The late phase of the adenovirus lifecycle is focused on producing sufficient quantities of structural protein to pack all the genetic material produced by DNA replication. Once the viral components have successfully been replicated, the virus is assembled into its protein shells and released from the cell as a result of virally induced cell lysis.

Transmission

Adenoviruses are unusually stable to chemical or physical agents and adverse pH conditions, allowing for prolonged survival outside of the body and water. Adenoviruses are spread primarily via respiratory droplets; however, they can also be spread by fecal routes.

Humans infected with adenoviruses display a wide range of responses, from no symptoms at all to the severe infections typical of Adenovirus serotype 14. In the past, U.S. military recruits were vaccinated against two serotypes of adenoviruses, with a corresponding decrease in illnesses caused by those serotypes. Although the vaccine is no longer manufactured for civilians, military personnel can receive the vaccine as of 2014.

Infections

Viral transmission occurs primarily through expectorate, but can also be transmitted via contact with infected objects. Most adenovirus infections affect the upper respiratory tract. These often show up as conjunctivitis, tonsillitis, ear infection, or croup. Adenoviruses, types 40 and 41 can also cause gastroenteritis. A combination of conjunctivitis and tonsillitis is particularly common with adenovirus infections. Some children (especially small ones) can develop adenovirus bronchiolitis or pneumonia, both of which can be severe.

Utilization in Treatment of Unrelated Diseases

Adenovirus is used as a vehicle to administer targeted therapy in the form of recombinant DNA or protein. Specific modifications on fiber proteins are used to target Adenovirus to certain cell types; a major effort is made to limit hepatotoxicity and prevent multiple organ failure. Adenovirus dodecahedron serves as a potent delivery platform for foreign antigens to human myeloid dendritic cells (MDC), and is efficiently presented by MDC to M1-specific CD8+ T lymphocytes.

Retroviruses and Hepadnavirus

Hepadnaviruses, retroviruses, use virally encoded reverse transcriptase to convert RNA into DNA.

Learning Objectives

Differentiate between retroviruses and hepadnaviruses

Key Takeaways

Key Points

  • Retrovirus RNA serves as a template for reverse transcriptase and is copied into DNA.
  • Hepadnaviruses are a family of viruses which can cause liver infections in humans and animals.

Key Terms

  • endogenous: produced, originating or growing from within
  • episome: A segment of DNA that can exist and replicate either autonomously in the cytoplasm or as part of achromosome, mainly found in bacteria.

A well-studied family of this class of viruses includes the retroviruses. One defining feature is the use of reverse transcriptase to convert the positive-sense RNA into DNA. Instead of using the RNA for templates of proteins, they use DNA to create the templates, which is spliced into the host genome using integrase. Replication can then commence with the help of the host cell’s polymerases. A well-studied example of this includes HIV.

A special variant of retroviruses are endogenous retroviruses, which are integrated into the genome of the host and inherited across generations.

The virus itself stores its nucleic acid in the form of a +mRNA (including the 5’cap and 3’PolyA inside the virion ) genome. This then serves as a means of delivery of that genome into cells it targets as an obligate parasite, and constitutes the infection. Once in the host’s cell, the RNA strands undergo reverse transcription in the cytoplasm and are integrated into the host’s genome, at which point the retroviral DNA is referred to as a provirus. It is difficult to detect the virus until it has infected the host.

In most viruses, DNA is transcribed into RNA, and then RNA is translated into protein. However, retroviruses function differently – their RNA is reverse-transcribed into DNA, which is integrated into the host cell’s genome (when it becomes a provirus), and then undergoes the usual transcription and translational processes to express the genes carried by the virus. So, the information contained in a retroviral gene is used to generate the corresponding protein via the sequence: RNA → DNA → RNA → protein. This extends the fundamental process identified by Francis Crick, in which the sequence is: DNA → RNA → protein. Retroviruses are proving to be valuable research tools in molecular biology and have been used successfully in gene delivery systems.

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Hepatitis B Virus: TEM micrograph showing hepatitis B virions.

Hepadnaviruses are a family of viruses which can cause liver infections in humans and animals. There are two recognized genera:

  • Genus Orthohepadnavirus ; type species: Hepatitis B virus
  • Genus Avihepadnavirus ; type species: Duck hepatitis B virus

Hepadnaviruses have very small genomes of partially double-stranded, partially single stranded circular DNA. The genome consists of two uneven strands of DNA. One has a negative-sense orientation, and the other, shorter, strand has a positive-sense orientation.Hepadnaviruses replicate through an RNA intermediate (which they transcribe back into cDNA using reverse transcriptase). The reverse transcriptase becomes covalently linked to a short 3- or 4-nucleotide primer. Most hepadnaviruses will only replicate in specific hosts, and this makes experiments using in vitro methods very difficult.

HBV infection is initiated through viral attachment to an unknown cell surface receptor. The virally encoded DNA polymerase acts upon the DNA, leaving it fully double-stranded.

Treatment of Animal Viral Infections

Interferons play pivotal roles in shaping the immune responses in mammals.

Learning Objectives

List the treatments we have to combat viruses

Key Takeaways

Key Points

  • Vaccines prime the body’s immune system against specific pathogens, but are not effective for treating an infection.
  • Many animal viruses are also important from a human medical perspective. The emergence of the SARS virus in the human population, coming from an animal source, highlights the importance of animals in bearing infectious agents. Avian influenza viruses can directly infect humans.
  • Immune therapy using immunomodulatory factors, such as interferons, is effective for treatment of hepatitis B and C.
  • Immune therapy using immunomodulatory factors, such as interferons, is effective for treatment of hepatitis B and C.

Key Terms

  • foot and mouth disease: A highly variable and transmissible viral disease. The virus enters the body through inhalation and affects cattle worldwide.
  • interferon: Any of a group of glycoproteins, produced by the immune system, that prevent viral replication in infected cells.

The study of animal viruses is important from a veterinary viewpoint. Many animal viruses are also important from a human medical perspective. The emergence of the SARS virus in the human population, coming from an animal source, highlights the importance of animals in bearing infectious agents. Avian influenza viruses can directly infect humans. In addition research into animal viruses has made an important contribution to our understanding of viruses in general, their replication, molecular biology, evolution, and interaction with the host.

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TEM of the Bluetongue virus: Bluetongue virus (BTV), a member of Orbivirus genus within the Reoviridae family causes serious disease in livestock (sheep, goat, cattle).

Rhabdoviruses are a diverse family of single stranded, negative sense RNA viruses that can successfully utilize a myriad of ecological niches, ranging from plants and insects, to fish and mammals. This virus family includes pathogens such as rabies virus, vesicular stomatitis virus, and potato yellow dwarf virus that are of tremendous public health, veterinary, and agricultural significance. Due to the relative simplicity of their genomes and morphology, in recent years rhabdoviruses have become powerful model systems for studying molecular virology.

Foot and mouth disease virus (FMDV) is the prototypic member of the Aphthovirus genus in the Picornaviridae family. This picornavirus is the etiological agent of an acute systemic vesicular disease that affects cattle worldwide, foot-and-mouth disease. FMDV is a highly variable and transmissible virus. It enters the body through inhalation. Soon after infection, the single stranded positive RNA that constitutes the viral genome is efficiently translated using a cap-independent mechanism driven by the internal ribosome entry site element (IRES). This process occurs concomitantly with the inhibition of cellular protein synthesis, caused by the expression of viral proteases. In depth knowledge of the molecular basis of the viral cycle is needed to control viral pathogenesis and disease spreading.

Pestiviruses account for important diseases in animals such as Classical swine fever (CSF) and Bovine viral diarrhea / Mucosal disease (BVD/MD). The molecular biology of pestiviruses shares many similarities and peculiarities with the human hepaciviruses. Genome organization and translation strategy are highly similar for the members of both genera. One hallmark of pestiviruses is their unique strategy to establish persistent infection during pregnancy.

Coronavirus (CoV) genome replication takes place in the cytoplasm in a membrane-protected microenvironment, and starts with the translation of the genome to produce the viral replicase.

The first line of defense against viral infections is usually antiviral vaccines, which prime the body’s immune system against specific pathogens. Vaccines traditionally consist of an attenuated (weakened or killed) version of the virus, although many vaccines now target specific immunogenic targets unique to a particular pathogen. Both viral and cellular proteins are required for replication and transcription. CoVs initiate translation by cap-dependent and cap-independent mechanisms. Cell macromolecular synthesis may be controlled after CoV infection by locating some virus proteins in the host cell nucleus. Infection by different coronaviruses cause in the host alteration in the transcription and translation patterns, in the cell cycle, the cytoskeleton, apoptosis and coagulation pathways, inflammation, and immune and stress responses. The balance between genes up- and down-regulated could explain the pathogenesis caused by these viruses.

Antiviral drugs are a class of medication used specifically for treating viral infections. Like antibiotics for bacteria, antiviral drugs are usually specific for a particular virus. Unlike most antibiotics, antiviral drugs do not destroy their target pathogen; instead they inhibit their development.

In addition to targeting viral infections directly, some therapeutics work by enhancing the immune responses necessary for viral clearance. One of the best-known of this class of drugs are interferons, which inhibit viral synthesis in infected cells. Interferons (IFNs) play pivotal roles in shaping the immune responses in mammals and are particularly important for the control of viral infections, cell growth, and immune regulation. These proteins rapidly induce an “anti-viral state” in cells that surround infected cells. In order to survive, viruses have evolved multiple strategies to evade the anti-viral effects of IFNs. Elucidating the molecular and cellular biology of the virus-interferon interaction is key to understanding issues such as viral pathogenesis, latency, and the development of novel antivirals.

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Pediatric polio vaccination in India by a Stop Transmission of Polio (STOP) teams (2002): Vaccinations are the best defense against a wide range of viruses, but they are not effective in treating active infections.