Virus

Virus - Introduction

Viruses are genetic elements that cannot replicate independently of a living cell, called the host cell. However, viruses do possess their own genetic information and are thus independent of the host cell’s genome. Viruses rely on the host cell for energy, metabolic intermediates, and protein synthesis. Viruses are therefore obligate intracellular parasites that rely on entering a suitable living cell to carry out their replication cycle. However, unlike genetic elements such as plasmids, viruses have an extracellular form, the virus particle, that enables them to exist outside the host and that facilitates transmission from one host cell to another. To multiply, viruses must enter a cell in which they can replicate, a process called infection. Viruses can replicate in a way that is destructive to the host cell, and this accounts for the fact that some viruses are agents of disease.

Extracellular state: Outside the host cell, the virus is a minute particle containing nucleic acid surrounded by protein, which is referred as virions or virus particles. Virions are inert and no biosynthetic and metabolic functions occur.

Intracellular state: The active state in which the virus replicate in the host cell. When the virus nucleic acid is introduced to host cell and replication starts, the process is referred as infection. The cell in which infection of virus and replication takes place is referred as host cell.

Chemistry of virus: All the living cells have double strand DNA as their genetic material. In contrast, viruses can have either DNA or RNA as their genetic material and it can be either single strand or double strand. The third group of virus which contain RNA as genome, but replicate by DNA intermediate, used both DNA and RNA as their genetic material in their reproductive stage. The viruses can be divided into following groups based on their nucleic acid and their form (single/double strand)

DNA containing virus (Single strand DNA virus and Double strand DNA virus)
RNA containing virus (Single strand RNA virus and Double strand RNA virus)
RNA to DNA virus

Viruses are also divided into three major groups based on their host as 1. Plant viruses 2. Animal viruses and 3. Bacteriophages

Structure of virions: The structure of virus varies to spherical, rod, complex structures and the size of virus is in nanometers (nm). The size ranges from 20 to 200 nm. Ex. Small pox virus – 200 nm (smaller than smallest bacterium – Nanobacterium); Polio virus – 28 nm (about the ribosome size)

The genome (genetic material in terms of base pairs of either DNA or RNA) size of each virus also varies.

Herpes virus – ds DNA – 150 kbp (1 kbp = 1000 bp)
Polio virus – ss RNA – 7 kbp
Cow pea mosaic virus – ss RNA – 9 kbp
Lambda Bacteriophage – ds DNA – 48 kbp

The structure of virions is quite diversified. The nucleic acid of virion is always located within the particle and surrounded by protein coat called capsid. (Protein coat / shell / capsid are often used interchangeably). The protein coat is always formed of a number of individual sub units referred as capsomeres. Capsomeres are arranged in a precise and highly repetitive pattern around the nucleic acid. These morphological sub-units can be seen under electron microscope.

The complete complex of nucleic acid and protein packed as virus particle is called as nucleocapsids.

Some viruses are covered with lipid bilayer which are referred as envelopes. Such viruses are referred as enveloped viruses and without envelopes as naked viruses.

Virus Symmetry : Symmetry refers the way in which protein sub units are arranged in the virus coat. The rod shaped viruses are called as helical symmetry and the spherical shaped viruses are with icosahedral symmetry. Ex. for helical symmetry – Tobacco mosaic virus; Icosahedral symmetry – adeno virus

Envelopes: Complex membrane structures surrounding the nucleocapsid are referred as envelopes. Enveloped viruses are common in animal viruses (HIV is an enveloped virus). Usually, the envelopes are of lipoprotein nature. The lipid portion is derived from host cell and the protein portion is synthesized by virus. They provide the shape of the virus.

Complex viruses: Some groups of viruses have complex structures with several shapes. They provide head, tail, end plates and tail fibres. The maximum of 20 different proteins will be present in these viruses.

Viral Enzymes: As extracelluar particle, virions are metabolically inert. When infect the host cell, they can able to produce some enzymes which are essential for their replication.

Nucleic acid polymerase – either DNA polymerase or RNA polymerase depends upon their genome.
Reverse transcriptase – Some RNA viruses (ex. HIV like retrovirus) have this enzyme to produce DNA from RNA.
Neuraminadase – To break down the glycosidic bonds of host cell to enter and to rapture the host cell
Lysozyme – Especially bacteriophages produce lysozyme to make a hole in the bacterial cell wall for entry

Virus replication:

Since, virus doesn’t have any system for replication by itself, it should induce the host cell to synthesize all essential components needed for complete virus. Then, these components must assemble into proper structure, and new virions must escape from the cell and infect the other cells. The sequence of virus replication is as follow:

Attachment (adsorption) of virion to a susceptible host cell
Penetration (injection) of virion or its nucleic acid into cell
Early steps in replication
Replication of virus nucleic acid and protein sub-units
Assembly (Packing) and Escape or release

Attachment: Attachment of virus particle with host cell is mainly based on the specific interaction between host and virus. The virus has one or two specific proteins on the outside of the virion with specific activity. This protein will recognize some host cell surface components such as proteins, polysaccharides, lipoproteins etc. These compounds are referred as receptors. If the receptor is removed in the host cell, the attachment of virus is not possible on the host cell.

Ex. Some bacterial flagella or pili act as receptors; For influenza virus, glycoprotein of red blood cell acts as receptor; For T2 bacteriophage, core polysaccharide of outer membrane of E. coli acts as receptor. The resistant host will have no receptor for virus or the receptor is protected by some physical means (Ex. Capsules of bacteria gave resistance by blocking the receptors).

Penetration: The penetration of virus into the host cell is mainly based on the surface morphology of the host cell. The penetration varies from host to host (plant and bacteria have cell wall and animals don’t have cell wall). The bacteriophages (T2 phage) first attached its tail fibres with receptor (core protein); By means of lysozyme, the phage made a hole in the cell wall and injected the nucleic acid by the help of tail. The animal viruses as a whole virion penetrate into the host cell through phagocytosis. Plant viruses enter into host cell by mechanical injuries or by some insect’s action.

Early stages of replication: When the viral nucleic acid enters to cytoplasm of the host cell, as a protective mechanism host cell can able to digest the nucleic acid by means of restriction endonuclease (for DNA) or by RNAse (in case of RNA). To avoid that, the viral nucleic acid or genome modifies its base pairs so that the restriction enzymes cannot react on it. By addition of glucose (glucosylation) or by addition of methyl group (methylation), the modification of viral genome is possible.

Replication of viral nucleic acid and proteins: New viral proteins and nucleic acids should be synthesized with the help of host DNA. The genetic system of host is used by the viral nucleic acid to produce capsid and nucleic acid. Nucleic acids were synthesized by means of DNA or RNA replication using the enzymes DNA polymerase or RNA polymerase respectively. The protein part of virions is synthesized as protein synthesis. The genetic informations of virus (DNA or RNA) should be converted into mRNA (called as transcription). The mRNA synthesis shows diversity among the viruses. Following diagram shows how the mRNA synthesis occurs from different viral genomes namely ssDNA, dsDNA, ssRNA and dsRNA. After mRNA synthesized, viral protein sub-units were synthesized. The early proteins – synthesized soon after infection (enzymes) and late proteins – synthesized later part (coat protein). The latent period refers the period which the presence of virus in the host cell cannot be detected. During that period, the synthesis of enzymes, nucleic acid and protein synthesis take place.

Assembly and release: After the protein coat and nucleic acid synthesis, the assembly takes place leads to completion of viral particle which will lyse the host cell; escape and infect the next host cell. Above diagram shows the one step growth curve (means one lytic cycle) of virus against time. The population of virus is expressed as plaque forming units.

The growth curve of virus has three distinct phases as:

Latent period: The latent period is the shortest time required for virus reproduction and release.
Eclipse period: The initial part of the latent period in which infected host bacteria do not contain any complete virions.
Rise or bust period: The period during the onestep growth experiment when host cells lyse and release phage particles
burst size: The number of phages released by a host cell during the lytic life cycle.

These types of viruses, which kill the host cell during release, are referred as lytic viruses and the cycle is referred as lytic cycle. But some bacteriophages will multiply inside the host cell and release to the environment after assembly without killing the host cell are referred as temperate phages and the cycle is referred as lysogenic cycle.

One-step growth curve of virus replication

Virus classification

The virologist David Baltimore, who along with Howard Temin and Renato Dulbecco shared the Nobel Prize for Physiology or Medicine in 1975 for the discovery of retroviruses and reverse transcriptase, developed a classification scheme for viruses. The Baltimore classification scheme is based on the relationship of the viral genome to its mRNA and recognizes seven classes of viruses.

Bacteriophages

Bacteriophages: The viruses which attack the bacteria and multiply are referred as bacteriophages. Most of the bacteriophages studied so far are belonged to the virus affecting E. coli and Salmonella.

The characteristic features of bacteriophages are:

Most of the bacteriophages are naked
Most of them structurally complex nature
Head, tail, tail fibres, base plates are some parts of these viruses
Most of these viruses are used as molecular tool for genetic engineering
The shape, size, chemistry and replication method are diversified.
ssRNA, dsRNA, ssDNA and dsDNA are as genomes.

Bacteriophage diversity: Most known bacteriophages contain dsDNA genomes and this type of bacteriophage is thought to be the most common in nature. However, many other kinds are known, including those with ssRNA genomes, dsRNA genomes, and ssDNA genomes.

Double strand DNA lytic phage: T3, T7;
Double strand DNA temperate phage: Lambda phage;
Single strand DNA lytic phage: PaiX174;
Single strand DNA temperate phage: M16;
Double strand RNA phage: Pai6;
Single strand RNA phage: MS2

Replication: As studied earlier, bacteriophage replication has five major steps:

1. Attachment (adsorption) of the virion to a susceptible host cell.

2. Penetration (entry, injection) of the virion or its nucleic acid into the host cell.

3. Synthesis of virus nucleic acid and protein by host cell metabolism as redirected by the virus.

4. Assembly of capsids (and membrane components in enveloped viruses) and packaging of viral genomes into new virions. This whole process is called maturation.

5. Release of mature virions from the cell.

Replication methods of bacteriophages

T2,T4, T3,T7 phages – They are ds DNA phages which are lytic phages and the cycle is lytic cycle. (25 minutes per cycle). The lytic cycle of these phages occurs as discussed earlier.
Lambda phage – This dsDNA phage is a temperate phage. After penetration, the lambda phage DNA will integrate with the bacterial DNA and will persist for ever. This state of phage is referred as prophage. When the prophage is induced (either by chemical or physical means) it become lytic phage and replicate in the host cell and by killing the host the virions will escape.
M13 – This ssDNA phage has linear DNA. The DNA synthesized in cytoplasm and protein coats are synthesized and accumulated in the cytoplasmic membrane. The linear DNA when released from host covered by protein coat and released. This is a temperate phage which will not kill the host cell during replication. (A slight decline in the growth of bacteria will occur). The cycle is referred as lysogenic cycle and the phage is temperate phage and host bacterium is lysogen.
MS2 - This single strand RNA phage uses its RNA as mRNA and protein synthesized. The complimentary RNA also synthesized from which viral RNAs synthesized.
PaiX174 – This ssDNA phage has single strand circular DNA which duplicate by rolling circle replication.
Mu Phage – This dsDNA phage is also a temperate phage like lambda phage. It has the unusual property like transposable elements (which can move from one portion of genomic DNA to another part) and thereby cause mutation. They are referred as biological mutagens.

Animal virus

Animal viruses: The animal viruses are both DNA and RNA viruses. Retro virus is a RNA virus but can have DNA as an intermediate (referred as RNA to DNA virus). The animal viruses enter into host cell as whole virion through phagocytosis. The viral nucleic acid will be produced at the nucleus of host cell and the protein coat will be produced at cytoplasm and assembly takes place. Most of the animal viruses are enveloped. The animal viruses vary their infection pattern on their host.

Types of infection

lytic infection: destroys host cells.
persistent infection: host cell continues to shed virus over long time. Cell gradually becomes recognizably poorer (recognized as cytopathic effect, or CPE), eventually "crumps out".
Oncogenes: Infection by certain viruses causes cells to change, become cancerous. Responsible genes are called oncogenes (tumor-producing genes). Viral oncogenes have also been found in uninfected cells. These are genes involved in regulation of cell cycle; when defective, normal regulatory control is lost and cell can become cancerous.
Persistent infection: The viruses released slowly from the host cell without affecting the host cell.
latent infection: virus genes may not be expressed for long time (ex. many Herpes infections).

The animal viruses are grouped in to many families based on nucleic acids, envelopes, etc.

Replication is similar to that of bacteriophages

Retrovirus replication: The structure of Retrovirus (Human Immunodeficiency Virus) which has ssRNA as its genome and surrounded by core protein and envelope. The retrovirus is the RNA containing enveloped virus, has the specialized system of replication in the host cells. The virus temporarily synthesizes DNA by means of reverse transcriptase enzyme and the DNA get integrated into chromosome of host DNA. After some period, the DNA integrated in the genome synthesize the RNA and protein coat. After assembly, while escape from the cell, the cytoplasmic membrane of host cell provides the envelope and the virion escaped the host by lysis.

Plant virus

PLANT VIRUSES: Most of the plant viruses are naked viruses. They don’t have specific mechanism for entering the host plants. The injuries, insect vectors are the means of entry. The cell wall and cuticle layers of plant are the barrier for the entry of virus. The virus diseases on plants are very rare because infection is not strong enough to kill the plant. Mostly the virus infection can be recognized by mosaic like leaf pattern, in which the loss of chlorophyll leads to yellow in colour. Some viruses multiply in the host plant without showing the symptom referred as latent infection.

There are four important groups of plant viruses.

Single strand RNA virus: Tobacco mosaic virus; Turnip crinkle virus; Cucumber mosaic virus
Double strand RNA virus: Wound tumor virus
Single strand DNA virus (They are referred as Gemini virus (Usually found as pair)]: Maize streak virus; Tomato golden mosaic virus
Double strand DNA virus: Cauliflower Mosaic virus (CaMV) (This virus can modify the plant genome. So used as molecular tool in the field of plant biotechnology.)

viroids and Prions

A virus is defined as a genetic element that subverts normal cellular processes for its own replication and that has an infectious extracellular form. There are several infectious agents that resemble viruses but whose properties are at odds with this definition and are thus not considered viruses. Defective viruses are clearly derived from viruses but have become dependent on other, complete, viruses to supply certain gene products. In contrast, two of the most important subviral entities, viroids and prions, are not viruses at all, but differ in fundamental ways from viruses. They both illustrate the unusual ways that genetic elements can replicate and the unexpected ways they can subvert their host cells. However, prions stand out among all the entities we have considered in this chapter because the infectious transmissible agent lacks nucleic acid.

Viroids: Viroids are the smallest infectious agents which are having a circular RNA alone as genome (they don’t have even protein coat too). They use DNA dependent RNA polymerase of host plant for their multiplication. The viroids infect the plants and cause diseases. Ex. Potato spindle tuber viroid. (It consists of 359 ribonucleotides and is characterized by numerous intra molecular base-pairings that lend stability to the structure.)

Prions: Prions are infectious protein particles that cause several diseases in animals and humans. Prions are the only infectious agents that do not contain any nucleic acids. Prion diseases are often called spongiform encephalopathies because of the post mortem appearance of the brain with large vacuoles. They cause brain diseases in sheep (scrapie disease), cows ("mad cow disease"), humans (Kuru and Creutzfeld-Jakob disease) and other animals.

Creutzfeldt-Jakob disease

occurs worldwide and usually becomes evident as dementia.
Very rare; afflicts one person in a million. 10 to 15 percent of cases are inherited.
Typically begins in 60's with a loss of memory.
Over several weeks the mental deterioration progresses to dementia, abnormalities of vision or coordination, rigidity, and involuntary.
Death usually occurs within six months, and at necropsy the brain shows a "spongy" texture

Mad Cow Disease

Cows become uncoordinated and unusually apprehensive.
Disease traced to use of sheep tissue as food supplement for cows over long period of time in United Kingdom. Practice was begun in late 1970s.

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