Science Fair Project on Viruses

Do you want to create an amazing science fair project on viruses ? You are in the right place. Read the below given article to get a complete idea on viruses: 1. Origin of Viruses 2. History of Viruses 3. Occurrence 4. Morphology 5. Classification 6. Isolation and Cultivation.

Contents:

1. Science fair Project on the Origin of Viruses
2. Science fair Project on the History of Viruses
3. Science fair Project on the Occurrence of Viruses
4. Science fair Project on the Morphology of Viruses
5. Science fair Project on the Classification of Viruses
6. Science fair Project on the Isolation and Cultivation of Viruses

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Science Fair Project # 1. Origin of Viruses:

There are following three main theories of the origins of viruses:

i. Regressive Theory (Degeneracy Theory):

This theory holds that viruses may have once been small cells that parasitized larger cells. During the course of time, genes not required by their parasitism were lost.

The bacteria, rickettsia and chlamydia are living cells that can reproduce only inside host cells like viruses. They lend credence to this theory as their dependence on parasitism has caused the loss of genes that enabled them to survive outside a cell. This is also called degeneracy theory.

ii. Cellular Origin Theory (Vagrancy Theory):

According to this theory, some viruses have evolved from bits of DNA or RNA that escaped from the genes of a larger organism. The escaped DNA could have come from plasmids i.e. pieces of naked DNA that can move between cells or transposons. These DNA molecules replicate and move around to different positions within the genes of the cell. These are also called jumping genes and could be the origin of some viruses.

iii. Co-Evolution Theory:

Viruses may have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on earth. They would have been dependent on cellular life for many millions of years. Computer analysis of viral and host DNA sequences is giving a better understanding of the evolutionary relationships between different viruses and may help identify the ancestors of modem viruses.

Such analyses have not helped till date to decide which of the theories are correct. However, it seems unlikely that all currently known viruses have a common ancestor and they have probably arisen numerous times in the past by one or more mechanisms.

There are different opinions whether viruses are a form of life, or organic structures that interact with living organisms. They have been described as ‘organisms at the edge of life’, since they resemble organisms in that they possess genes and evolve by natural selection, and reproduce by creating multiple copies of themselves through self-assembly.

Although they have genes, they do not have a cellular structure which is often seen as the basic unit of life. In addition, viruses do not have their own metabolism; therefore, they require a host cell for their multiplication.

Hence, they cannot reproduce outside a host cell (though bacterial species such as rickettsia and chlamydia are considered living organisms despite the same limitation). The living organisms undergo cell division for reproduction.

But viruses spontaneously assemble within cells which is analogous to the autonomous growth of crystals. Virus self-assembly within host cells has implications for the study of the origin of life, as it lends further credence to the hypothesis that life could have started as self-assembling organic molecules.

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Science Fair Project # 2. History of Viruses:

In 1774, a farmer named Benjamin Jesty had vaccinated his wife and two sons with cowpox taken from the udder of an infected cow and had written about his experience. In 1796, Edward Jenner used cowpox to vaccinate against smallpox.

He was the first person to deliberately vaccinate against any infectious disease i.e. to use a preparation containing an antigenic molecule or mixture of such molecules designed to elicit an immune response.

Although, Jenner is commonly given the credit for vaccination, variolation i.e. the practice of deliberately infecting people with smallpox to protect them from the worst type of the disease, had been practiced in China at least two thousand years earlier.

In 1885, Louis Pasteur experimented with rabies vaccination by using the term virus (Latin, poison) to describe the agent. Although Pasteur did not discriminate between viruses and other infectious agents, he originated the terms ‘virus’ and ‘vaccination’ (in honour of Jenner) and developed the scientific basis for Jenner’s experimental approach to vaccination. In 1884, Charts Chamberland developed a porcelain filter that allowed the passing of fluid but not bacteria. The filter was useful in sterilization of liquids.

A. Mayer (1886) working in Holland demonstrated that the sap of mosaic leaves of tobacco plant developed the mosaic symptom when injected into the healthy plants. However, the infectivity of the sap was destroyed when it was boiled. He thought that the causal agent was the bacteria. However, after inoculation with a large number of bacteria, he failed to develop a mosaic symptom.

In 1892, for the first time a Russian botanist Dmitri Iwanowski filtered the sap of diseased tobacco plant through the Chamberland filter designed to obtain bacteria but the infectious agent was filtered through the pores of porcelain.

After injections of filtered sap he found the development of mosaic symptom. He concluded that the infectious agent was the bacterium but smaller than it. The infectious agent was called filtrable virus i.e. poisonous fluid.

In 1898, Martinus W. Beijerinck, a Professor of Microbiology at the Technical University the Netherlands, put forth his concepts that viruses were small and infectious. He defined the infectious agent as a contagium vivum. fluidum, after he discovered that the virus readily passed through a porcelain filter, suggesting that it was smaller than bacteria.

He also observed that the ‘agent’ could diffuse through agar that retained bacteria, and furthermore, that the virus could not be cultured except in living, growing plants. The virus was Tobacco mosaic virus (TMV). This report, suggesting that ‘microbes’ need not be cellular, was to forever change the definition of pathogens.

In 1898, two Germans, Loeffler and Frosch (former students of Koch) also used a porcelain filter for the isolation of the causal agent of foot and mouth disease of cattle, but they suggested that it was a very small microbe. Beijerinck was almost alone in his forward thinking to conclude that he had a filterable, invisible in fectious agent that differed from small microbes.

By the end of third decade of 20th century, two major technical break through occurred:

(ii) Development of technique of ultracentrifugation, and

(ii) Electron microscopy.

An American chemist, Wendell M. Stanley (1935) crystallized the virus causing mosaic on tobacco plant. He found that the crystals were also infectious when inoculated on healthy tobacco plants. He concluded that the viruses were not like a typical cells of the living organism. For this work Stanley was awarded the Nobel Prize in 1946.

The two British biochemists, F.C. Bawden and N.W. Pirie (1938) analysed the crystallized particles and demonstrated that these were made of protein and ribonucleic acid (RNA), for which Pirie was awarded the Nobel Prize. Gieirer and Schramm (1956) proved the real nature of nucleic acid as infectious agent and genetic material.

Inside the infected cells virus uses the nitrogenous and the other compounds and replicates its genome. Later on it was confirmed by Fraenkel-Conrat (1956) that the genetic material of tobacco mosaic virus (TMV) is the RNA.

In fact, it took 50 years to prove that TMV was an infectious nucleoprotein. In that time, TMV was the first virus to be purified in pure crystal form, the first pathogen to be passed through filter candles, and the first virus to be identified as composed of an infectious nucleic acid.

Since then many viruses have been discovered in plants, animal fungi, and bacteria. TMV would continue to play a leading role in the development of fundamental concepts in virology. In the 1960s and 1970s, TMV was a key component in the shift to molecular work in viruses, particularly with regard to the understanding of genetic information and the biological role of virus encoded proteins.

One of the interesting historical phenomena related to the virus was the use of broken tulip. During 16th and 17th century a variety of tulip (an ornamental plant cultivated for its flower) was very popular due to the presence of striations and different shades on petals.

Such tulip plants were called broken tulip. In Holland and France, people were very crazy for broken tulip which was much prized and thought as status symbol. The development of striations and shades was due to the infection of a virus.

Frederick W. Twort (1915) in England and Felix d’Herelle (1916) in Pasteur Research Institute (Paris) observed independently that in cultures the bacterial colonies were lysed by some agent and this effect could be transmitted from colony to colony.

The highly diluted material from a lysed colony, even after passing through a bacterial filter, transmit the lytic effect. After heating the filtrate lytic property was destroyed.

Twort suggested that the lysis would have been due to a virus. d’Herelle (1917) rediscovered the phenomenon (commonly known as Twort – d’Herelle phenom­enon) and coined a term bacteriophage i.e. bacteria eater. Hershey and Chase (1952) studied in detail T₂ bacteriophage and demonstrated that the phage DNA carries the genetic information, and infection occurs upon penetration of phage DNA into living cells.

Moreover, in 1894 a Japanese worker Hashimoto discovered the relationships between an insect, Nephotettix apicalis var cinticeps and virus associated with rice dwarf disease.

The other development includes the discovery of mycoviruses in the cultivated button mushroom by Hollings (1982), discovery of cyanophages (viruses eating upon blue-green algae) by Safferman and Morris (1963), satellite virus by Kassanis (1966), viroids by Diener and Raymer (1967), prion by Prusiner (1982), and HIV by LuC Montagnier (1983).

During the last few decades much information’s have gathered on isolation and culture of viruses, replication processes, preparation of maps, immunization processes, genetic engineering, molecular biology, vaccine development, etc..

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Science Fair Project # 3. Occurrence of Viruses:

Viruses occur on a very wide hosts such as plants (angiosperms, gymnosperms, ferns, algae, fungi) and animals (protozoans, insects, fish, amphibians, birds, mammals, humans). They cause very serious diseases in crop plants, ornamental plants and forest trees resulting in decreased growth, yield and mortality.

In animals like dogs, cats, and humans several serious diseases are known since the time immemorial. Total number of viruses in different host taxa according to their genome types is given in Table 15.1.

Table 15.1 : Number of viruses in different host taxa according to genome type.

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Science Fair Project # 4. Morphology of Viruses:

i. Shape:

Viruses are of different shapes such as spheroid or cuboid (adenoviruses), elongated (potato viruses), flexuous or coiled (beet yellow), bullet shaped (rabies virus), filamentous (bacteriophage M13), pleomorphic (alfalfa mosaic), etc.

ii. Size:

Viruses are of variable sizes. Initially their sizes were estimated by passing them through membranes of known pore diameter. In recent years, their size is determined by ultracentrifugation and electron microscopy. Size vary from 20 nm to 300 nm in diameter.

They are smaller than bacteria; some are slightly larger than protein and nucleic acid molecules and some are about of the same size (small pox virus) as the smallest bacterium and some virus (virus of lymphogranuloma, 300-400 um) are slightly larger than the smallest bacterium.

iii. Viral Structure:

The complete assembly of the infectious particle is known as virion. A virion consists of a nucleic acid core surrounded by a protein coat or capsid. The complete set of virion is known as nucleocapsid. In turn the nucleocapsid may be naked or enveloped by a loose covering. The capsid is composed of a large number of subunits known as capsomers.

Chemically the envelope is made up of proteins and glycoproteins. Due to the presence of lipid the envelope seems flexible and loose. Envelope is composed of both the host and viral components i.e. protein (virus specific) and carbohydrates (host specific).

There are certain projections on the envelope known as spikes which are arranged into distinct units.

The morphological types of virus observed through electron microscopy and crystallography have been categorized into the following three groups:

(i) Helical (Cylindrical) Viruses:

(a) Naked capsids e.g. TMV and the bacteriophage M13, etc.

(b) Enveloped capsid e.g. influenza virus, etc.

(ii) Polyhedral (Icosahedral) Viruses:

(a) Naked capsid e.g. adenovirus, polio viruses, etc.

(b) Enveloped capsids e.g. herpes simplex viruses, etc.

(iii) Complex Viruses:

(a) Capsids not clearly identified e.g. vaccinia virus, etc.

(b) Capsids to which some other structures are attached e.g. some bacteriophages,etc.

(i) Helical Viruses:

The helical viruses are elongated, rod-shaped, rigid or flexible. Their capsid is a hollow cylinder with a helical structure. Capsid consists of monomers arranged helically in a rotational axis. The helical capsids may be naked (e.g. TMV) or enveloped (e.g. influenza virus).

(a) Naked viruses:

One of the examples of naked viruses is the TMV. For the first time Stanley (1935) isolated TMV in the crystalline form from leaf sap of the infected tobacco plants. Thereafter, a lot of work was done on TMV. This virus is rod shaped measuring about 280 x 150-180 µm.

It consists of a protein tube with a lumen of 20Å which encloses a single stranded (ss) helix of coiled RNA. Protein coat of the virus contains a number of identical subunits (monomers) which are arranged in helical manner.

A capsid consists of several capsomers each composed of a few monomers. Forty nine monomers (each with molecular weight 12,000) take three turns of the helix and give a total of 2,130 subunits of the rod. Each subunit is made up of 150 amino acid residues forming a single polypeptide chain. Genetic material i.e. ssRNA has the molecular weight of 2.06 × 10⁶ Dalton.

The RNA consists of 6,500 nucleotides in total and coiled to form a helix with a radius of 80Å which is enclosed in a helix of 85Å radius of similar pitch (23Å) formed by monomers of protein. Each turn of the RNA helix consists of at least 49 nucleotides. There is a cylindrical hole of 20Å radius. The capsid protects the RNA molecule.

(b) Enveloped Viruses:

When the helical viruses are enclosed within an envelope they are known as enveloped helical viruses, for example influenza virus. The envelope is composed of a viral protein and the host cell components i.e. lipid and carbohydrates. The envelope consists of numerous spikes. The helical capsid exists in folded form inside the envelope and sometimes may show pleomorphic appearance.

(ii) Polyhedral (Icosahedral) Viruses:

There are several animal, plant and bacterial viruses which have either naked or enveloped icosahedral shape. Polyhedral structure has the three possible symmetries such as tetrahedral, octahedral and icosahedral. The viruses are more-or-less spherical. Therefore, icosahedral symmetry is the best one for packaging and bonding of subunits.

Several inter molecular bonds of low free energy is formed. An icosahedron is a regular polyhedron with 20 triangular faces and 12 comers. The capsomers of each face form an equatorial triangles and 12 intersepting points or comers (Fig. 15.1 A-C).

Basically, there are two types of capsomers, the pentamers and hexamers. The pentamer is a clusture of 5 monomers and the hexamer is a clusture of 6 monomers (C). The monomers are linked together by bonds. Thus, the capsomers are also linked together by bonds which are weaker than those of monomers due to their breaking into the capsomers during the purification of viral particles.

However, certain capsomers only in certain number may be present in icosahedral capsid, theoretically the minimum number may be 12. Therefore, in different viruses the number of capsomers differ, for example 12 capsomers in ØX174, 32 in poliovirus, 72 in polyomaviras, 92 in reovims, 162 in herpesvirus, 252 in adenoviras and 812 in tipula iridescent viras.

(a) Naked Icosahedral Viruses:

Naked icosahedral viruses are turnip yellow mosaic virus (TYMV), poliovirus, adenovirus and bacteriophage ØX174, QB, etc. Adenoviruses are large (80 nm diameter), icosahedral containing dsDNA.

The capsid has the ring like capsomers each containing pentamers and hexamers. A total of 32 hexamers and 12 pentamers are found in the capsid. The hexamers are polygonal discs of 8 nm diameter with a hole of 2.5 nm diameter in the centre.

At the surface of capsid these spike like structures form 12 points of the five fold symmetry. The capsomers are assembled to construct the capsid in a specific geometrical pattern where the pentamers form the comers of the icosahedron and the hexamers occupy the internal space.

(b) Enveloped Icosahedral Viruses:

There are some of the enveloped icosahedral viruses, for example herpes virus where the capsid is enclosed inside an envelope of 30nm thickness that is made up of a glycoprotein-lipid complex. The envelope consists of spikes on its surface.

The capsid is spherical and of about 100 nm diameter enclosing a dense core of dsRNA molecule. The capsid contains 162 capsomers, (12 pentamer capsomers at apices and 150 hexamer capsomers at the faces).

(iii) Complex Viruses:

The viruses which have the unidentifiable capsids or have the capsids with additional structures are called complex viruses, for example, vaccinia virus and T-even bacteriophages.

In addition, the other variations in the structure of complex viruses are also found such as:

(i) A definite capsid absent (e.g. vaccinia virus),

(ii) Capsid present and consists of a tail.

The second group consists of different types, for example, tadpole shaped viruses (with head and tail, e.g. T-even phage), viruses with tail less head (phage λ, T₁, T₅), virus with brick shaped and devoid of flattened cylinder (pox virus), and bullet shaped capsid viruses (e.g. nuclear polyhedrosis or cytoplasmic polyhedrosis viruses).

iv. Viral Envelope:

There are certain plant and animal viruses and bacteriophages, both icosahedral and helical, which are surrounded by a thin membranous envelope. This envelope is about 10-15 µm thick. It is made up of protein, lipids and carbohydrates which are combined to form glycoprotein and lipoprotein.

Lipids provide flexibility to the shape; therefore, viruses look of variable sizes and shapes. Protein component of the envelope is of viral origin, and lipid and carbohydrates may be the features of host membrane i.e. nuclear or cytoplasmic.

The ssRNA viruses after replication in hosts cytoplasm are released by budding through plasma membrane. During release these are enveloped by a part of membrane of host cell which resembles a typical membrane. The membrane is made up of phospholipid bilayer in which proteins are embedded. The spikes attached to the outer surface of the envelope is made up of glycoproteins. Spikes have agglutination proteins.

In other group of viruses e.g. dsDNA bacteriophage, PM2, dsRNA bacteriophage Ø6, iridescent dsDNA insect viruses and the pox viruses, the lipid bilayer is not derived from the host membrane.

The lipids present in viral envelope fall under the Herce classes:

(i) Phospholipids (e.g. sphingomyelin, phosphatidyl choline, phophatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol),

(ii) Cholesterol,

(iii) Glycolipids (e.g. glycosphingohpids made up of sphingosine, fatty acid and carbohydrate).

v. Nucleic Acids:

Viruses contain either single or double stranded DNA or RNA molecules. The nucleic acids may be in linear or circular form, and have plus or minus polarity. Nucleic acids of several plant viruses occur in their respective particles in one piece. However, the reovirus is known to contain the nucleic acid in 10 segments. The segmented nucleic acid is also found in wound tumour virus and influenza virus.

vi. Proteins:

Proteins found in viruses may be grouped into the four categories:

(i) Envelope protein,

(ii) Nucleocapsid (structural) protein,

(iii) Core protein, and

(iv) Viral enzymes.

(i) Envelope Protein:

Envelope of the viruses consists of proteins specified by both virus and host cell. Structure of a typical enveloped virus is given in Fig. 15.2.

In several viruses, its capsids are covered by a smooth and unbroken lipid bilayer. Such a coating is effectively inert and acts as a protective layer to prevent the desiccation or enzymatic damage of the particles. Moreover, the receptor molecules present on the host cell cannot be recognized. Viruses can also change their lipid envelopes through the synthesis of several classes of proteins.

These proteins get associated in one of three ways with the envelope:

(a) Matrix Proteins:

Basically, these are the internal virion proteins that link the assem­bly of the internal nucleocapsid.

(b) Glycoproteins:

Glycoproteins are such proteins that contain oligosaccharide chains (glycans) covalently attached to their polypeptide side-chains. The carbohydrate is attached to the protein in a co-translational or posttranslational modification. This process is known as glycosylation (Fig, 15.3). The extracellular segments of proteins extending extracellularly are often glycosylated.

These are trans-membrane proteins embedded in the membrane by a hydrophobic domain. Glycoproteins are often important integral membrane proteins where they play a role in cell-cell interactions.

Based on their function, glycoproteins are divided into the following two types:

a. External Glycoproteins:

The external glycoproteins are embedded in the envelope by a single trans-membrane domain. Most of the proteins are present on the outside of the membrane. They have relatively a short internal tail. Mostly individual monomers gets associated to form the spikes which are visible on the surface of many enveloped viruses in the electron microscope. Such proteins act as the major antigens of enveloped viruses.

b. Transport Channels:

This class of proteins contains multiple hydrophobic trans-membrane domains forming a protein-lined channel through the envelope. It helps the virus to change the permeability of the membrane e.g. ion-channels.

Membranes of all class of enveloped viruses contain glycoprotein. In influenza virus the main protein is the carbohydrate-free protein which comprises of 50% of envelope protein and 35-40% of virion protein as a whole. Herpes viruses, poxviruses and leuko-viruses do not contain protein in the envelope specified by them.

It has been found that the envelope proteins are enclosed by the genome of arbo-viruses, rhabdo-viruses and myxo-viruses. In addition, the glycoproteins differ virus to virus. For example, one glycoprotein in rhabdo-viruses, two glycoprotein in paramyxoviruses and four glycoprotein in orthomyxo-viruses have been found.

(ii) Nucleocapsid Protein:

The viral capsids are made up totally of proteins of identical subunits (promoters). The helical capsids contain single type of protein and icosahedral capsid contains several types of protein. For example, TMV contains single protein types, adenovirus contains 14 protein types, T4 bacteriophage contains 30 protein types, etc.

(iii) Core Protein:

Protein found in nucleic acid is known as core protein, for example nucleoproteins of influenza virus, and proteins V and VI of adenoviruses.

(iv) Viral Enzymes:

In animal viruses especially in the enveloped viruses, many virion specific enzymes have been characterized, for example RNase and reverse transcriptase in retrovirus, protein kinase in herpes and adenoviruses, DNA dependent RNA polymerase in poxvirus.

vii. Carbohydrates of Viruses:

A substantial amount of carbohydrate specified by either host cell (e.g. arbovirus) or viral genome (e.g. vaccinia virus) is found in viral envelope. For example galactose, mannose, glucose, fucose, glucosamine, galactosamine are found in influenza virus, para-influenza vims, SV5 and sindbis virus. The carbohydrates are hexoses and hexamines which are present in the form of glycoprotein and/or glycolipids.

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Science Fair Project # 5. Classification of Viruses:

In 1927, Johanson was the first to attempt for the classification of plant viruses. Traditionally, viruses have been named according to the diseases caused by them by adding a suffix virus e.g. poliovirus, influenza- virus, etc.

In addition, the bacteriophages were named after the labora­tory codes e.g. QB, Øx174, M13, etc. The cyanophages were named after the host they lysed and the serologi­cal differences among them e.g. LPP1, LPP2, etc. The bacteriophages and cyanophages.

Holmes (1948) fol­lowed the Linnean sys­tem of bionomial nomen­clature and put the vi­ruses into an order virales and three suborders:

(i) Phaginae: Viruses attacking on bacteria.

(ii) Phytophagine : Viruses attacking on plants.

(iii) Zoophaginae: Viruses attacking on animals.

i. LHT System of Classification:

In 1962, A. Lwoff, R. Home and P. Tournier proposed a system of classification of viruses which is commonly referred to as LHT system of classification. It was adopted by the provisional Committee on Nomenclature of Viruses (PNCV) formed by the International Association of Microbiological society.

The LHT system of classification is based on:

(i) The nature of nucleic acid, (DNA or RNA),

(ii) Symmetry or viral particle (helical, icosaherdal, cubic, cubic-tailed),

(iii) Presence or absence of envelope,

(iv) Diameter of capsid, and

(v) Number of capsomers forming the capsid.

The LHT system of classification is neither a natural classification nor shows any evolutionary phylogenetic relationship. However, it has been widely criticized, besides evoking the considerable interest among the virologists. Now a day, this system of classification is getting much attention.

Bellet (1967) proposed a system of classification.

This system of classification is based mainly on two criteria of the viral particles:

(i) Molecular weight, and

(ii) Percentage of guanine + cytosine of the nucleic acid.

Serological, antigenic and phenotypic properties were also considered. Gibbs (1969) proposed a system of classification for plant viruses which is known as Gibbs system of classification.

The criteria to classify the viruses are:

(i) Shape of capsid,

(ii) Mode of transmission,

(iii) Type of vector,

(iv) Symptoms on host after infection, and

(v) The nature of accessory particles.

He put 135 known viruses into the 6 broad groups.

ii. Casjens and King’s Classification:

Casjens and King (1975) classified the viruses on the basis of nucleic acid types, symmetry, presence or absence of the envelope and site of assembly of the envelope i.e. nuclear cytoplasmic.

The classification of Casjens and King (1975) is given below:

1. ssRNA Viruses:

Helical:

(i) Rigid rods (plants): TMV, tobacco rattle virus, barley stripe mosaic virus.

(ii) Flexous rods (plants): Potato X and Y viruses, clover yellow mosaic virus.

Molecular organization of the tobacco mosalc virus (TMV).

Icosahedral:

(i) Spherical plant viruses.

(a) With 180 identical capsomers (T=3) e.g. cowpea chlorotic mosaic virus,cucumber mosaic virus, turnip yellow.

(b) With 60 subunits of two structural proteins (T=1) e.g. cowpea mosaic virus.

(ii) Bacteriophages: e.g. R17, Fr, F2, QB, MS2

(iii) Picoma Viruses (animal viruses):

(a) Human entroviruses: poliovirus

(b) Rodent cardio-viruses: Encephalomyocarditis virus, mengovirus.

(c) Rhinoviruses: Human respiratory infection viruses.

(d) Foot and mouth disease virus.

Envelope:

(i) Spherical: Togavirus, yellow fever virus.

(ii) Bullet shaped: Rhabdovirus e.g. rabies

(iii) Spherical: Paramyxovirus e.g. measles, or filamentous Myxovirus e.g. influenza virus.

(iv) Spherical: Corona virus e.g. acute upper respiratory tract infection virus, severe acute respiratory syndrome (SARS) virus

: Arena virus e.g. lymphocylic chloromeningitis

: Oncoviruses e.g. leukemia, sacroma

2. dsRNA Viruses:

Segmented genome:

(i) Animal viruses:

Reovirus, blue tongue virus of sheep, cytoplasmic polyhedrosis virus of silk worm.

(ii) Plant viruses:

Wound tumour virus of plants, Maize rough dwarf virus. Rice dwarf virus.

Enveloped:

Bacteriophage Ø6

3. ssDNA Viruses:

Icosahedral:

(i) Bacteriophages: Øx174, S13

(ii) Parvoviruses: Animal and insect viruses

Helical:

Bacteriophages: fd, F1, M13

4. dsDNA Viruses:

Icosahedral complex (tailed):

(i) E. coli phages: T4, P2, T3, T5, T7

(ii) S. typhimurium phage: P22

(iii) B. suhtilis phage: Ø29, cyanophages

Enveloped:

Bacteriophage PM2

Nuclear Assembly:

(i) Papovavirus: Polyomavirus, SV40, human wart virus.

(ii) Adenovirus: Respiratory disease in birds and mammals (icosahedral)

(iii) Herpsvirus (enveloped): Cold sores, shingles, infections mononucleosis cervical sarcoma of uterus, Burkitt’s lymphoma.

Cytoplasmic Assembly:

(i) Poxvirus (enveloped): Variola-small pox, vaccinia-immunity to small pox.

iii. Baltimore Classification:

The Baltimore Classification (2008) of viruses is based on the method of viral mRNA synthesis. The Nobel Prize-winning biologist David Baltimore devised the Baltimore classification system. The ICTV classification system is used in conjunction with the Baltimore classification system in modern virus classification.

The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family (Fig. 15.4). Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase. Additionally, ssRNA viruses may be either (+) sense or (-) antisense.

This classifi­cation places viruses into seven groups:

Group 1: dsDNA viruses (e.g. Adenoviruses, Herpes viruses, Pox­viruses)

Group II: (+) sense ssDNA viruses (e.g. Parvoviruses)

Group III: dsRNA viruses (e.g. Reoviruses)

Group IV: (+) sense ssRNA viruses (e.g. Picornaviruses, Togaviruses)

Group V: (-) sense ssRNA viruses (e.g. Orthomyxo viruses, Rhabdo viruses)

Group VI: (+) sense ssRNA-RT viruses RNA with DNA intermediate in life-cycle (e.g. Retroviruses)

Group VII: dsDNA-RT viruses (e.g. Hepadna viruses)

As an example of viral classification, the chicken pox virus, varicella zoster (VZV), belongs to the order Herpesvirales, family Herpesviridae, subfamily Alphaherpesvirinae, and genus Varicellovirus. VZV has been put in Group I of the Baltimore Classification because it is a dsDNA virus that does not use reverse transcriptase.

iv. International Committee on Taxonomy of Viruses (ICTV):

International Committee on Taxonomy of Viruses (ICTV) is a committee which authorizes and organizes the taxonomic classification of viruses. ICTV began to devise and implement rules for the naming and classification of viruses early in the 1990s, an effort that continues to the present day.

They have developed a universal taxonomic scheme for viruses and aim to describe all the viruses of living organisms. Members of the committee are considered to be world experts on viruses. The committee is governed by the Virology Division of the International Union of Microbiological Societies (IUMS).

The report of ICTV (2005) lists more than 6,000 viruses classified in 1,950 species and in more than 391 different higher taxa. However, GenBank contains an additional 3,142 species which has been unaccounted by the ICTV report.

A number of changes could be made both at ICTV and GenBank to better handle virus taxonomy and classification in the future. The committee also operates a database (ICTVdB) containing taxonomic information for over 6,000 virus species as of 2005. It is open to the public and is searchable by several different means.

The official objectives of the ICTV are:

(i) To develop an internationally agreed taxonomy for viruses

(ii) To develop internationally agreed names for virus taxa, including species and sub-viral agents

(iii) To communicate taxonomic decisions to all users of virus names, in particular the international community of virologists, by publications and via the Internet

(iv) To maintain an index of virus names

(v) To maintain an ICTV database on the Internet that records the data that characterize each named viral taxon, together with the common names of each taxon in all major languages

(i) Principles of Nomenclature:

The ICTV’s essential principles of virus nomenclature are:

a. Stability,

b. To avoid or reject the use of names which might cause error or confusion, and

c. To avoid the unnecessary creation of names.

The ICTV’s universal virus classification system uses a slightly modified version of the standard biological classification system. It only recognises the taxa below kingdom: those of order, family, subfamily, genus, and species. When it is uncertain how to classify a species into a genus but its classification in a family is clear, it will be classified as an unassigned species of that family. Many taxa remain unranked.

(ii) Naming and Changing Taxa:

Proposals for new names, name changes, and the establishment and taxonomic placement of taxa are handled by the Executive Committee of the ICTV in the form of proposals. All relevant ICTV subcommittees and study groups are consulted prior to a decision being taken. The name of a taxon has no status until it has been approved by ICTV, and names will only be accepted if they are linked to the approved hierarchical taxa.

If no suitable name is proposed for a taxon, the taxon may be approved and the name be left undecided until the adoption of an acceptable international name, when one is proposed to and accepted by ICTV.

Names must not convey a meaning for the taxon which would seem to either exclude viruses which are rightfully members of that taxa, exclude members which might one day belong to that taxa or include viruses which are members of different taxa.

Viral classification starts at the level of order and follows with the taxon suffixes given in italics:

Order -virales

Family -viridae

Subfamily -virinae

Genus -virus

Species

So far, five orders have been established by the ICTV:

a. Caudovirales: (It contains tailed dsDNA (Group I) bacteriophages)

b. Herpesvimles: (It contains large eukaryotic dsDNA viruses)

c. Mononegavirales: (It includes non-segmented (-) ssRNA (Group V) plant and animal viruses)

d. Nidovirales: (It is composed of (+) ssRNA (Group IV) viruses with vertebrate hosts)

e. Picomavirales: (contains small (+) ssRNA viruses that infect a variety of plant, insect and animal hosts).

These orders span viruses with varying host ranges. Other variations occur between the orders, for example Nidovirales are isolated for their differentiation in expressing structural and non­structural proteins separately. However, this system of nomenclature differs from other taxonomic codes on several points.

A minor point is that names of orders and families are italicized, as in the International Code of Botanical Nomenclature (ICBN). Most notably, species names generally take the form of [Disease] virus.

The establishment of an order is based on the inference that the virus families contained within a single order have most likely evolved from a common ancestor. The majority of virus families remain unplaced. Up to 2008, 82 families and 2,083 species of virus have been defined.

Sub-Viral Agents:

The following agents are smaller than viruses but have some of their properties:

(i) Viroids:

a. Family Pospiviroidae

i. Genus Pospiviroid; type species: Potato spindle tuber viroid

ii. Genus Hostuviroid; type species: Hop stunt viroid

iii. Genus Cocadviroid; type species: Coconut cadang-cadang viroid

iv. Genus Apscaviroid; type species: Apple scar skin viroid

v. Genus Coleviroid; type species: Coleus blumei viroid 1

b. Family Avsunviroidae:

i. Genus Avsunviroid; type species: Avocado sunblotch viroid

ii. Genus Pelamoviroid; type species: Peach latent mosaic viroid

(ii) Satellites:

Satellites depend on co-infection of a host cell with a helper virus for productive multiplication. Their nucleic acids have substantially distinct nucleotide sequences from either their helper vims or host. When a satellite sub-viral agent encodes the coat protein in which it is encapsulated, it’s then called a satellite virus.

a. Satellite viruses:

1. Single-stranded RNA satellite viruses

i. Subgroup 1: Chronic bee-paralysis satellite virus

ii. Subgroup 2: Tobacco necrosis satellite virus

b. Satellite nucleic acids:

1. Single-stranded satellite DNAs

2. Double-stranded satellite RNAs

3. Single-stranded satellite RNAs

i. Subgroup I: Large satellite RNAs

ii. Subgroup 2: Small linear satellite RNAs

iii. Subgroup 3: Circular satellite RNAs (virusoids)

Prions:

Prions, named for their description as ‘proteinaceous and infectious particles’, lack any detectable (as of 2002) nucleic acids or virus-like particles. They resist inactivation procedures which-normally affect nucleic acids.

a. Mammalian prions:

1. Agents of spongiform encephalopathies

b. Fungal prions:

1. PSI+ prion of Saccharomyces cerevisiae

2. URE3 prion of Saccharomyces cerevisiae

3. RNQ/PIN+ prion of Saccharomyces cerevisiae

4. Het-s prion of Podospora anserina

v. Dimmock Classification:

Dimmock (2001) classified viruses into six sections (on the basis of their host preference) such as infecting animals, plants, fungi, bacteria, and satellite viruses and viroids. Each section is divided into 7 classes (following revised Baltimore scheme), and each class into families.

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Science Fair Project # 6. Isolation and Cultivation of Viruses:

Viruses cannot multiply outside a living host cell; however, their isolation, enumeration and identification become a difficult task. Instead of a chemical medium, they require a living host plant, animal or bacterial cells.

i. Cultivation of Bacteriophages:

The bacteriophages infect the specific bacterial host; hence a defined bacterium is required for the cultivation of bacteriophages. A sample of bacteriophage is mixed with known host bacteria in molten nutrient agar. The nutrient agar contain­ing bacteriophage and its hosts cell is poured into steile Petri dishes.

The mixture of virus and bacteria solidifies into a thin top layer. The Petri plates are incubated at optimum temperature in an incubator. A single virus infects a bacterial cell, multiplies and releases hundreds of new viral particles. The released viruses in turn infect the healthy bacteria in the surroundings. As a result of bacterial lysis, the area where bacterial colonies were growing turns into clearings or plaques.

These plaques are visible against the bacterial lawn. During the course of time the uninfected bacteria multiply rapidly and produce turbid growth in the Petri plate. Theoretically, each plaque represents for the presence of at least a single virus. Hence the total number of viruses present in suspension is expressed as plaque forming units (pfu) (Fig. 15.5).

ii. Cultivation of Cyanophages:

Cyanophages are the viruses that infect cyanobacteria. After the discovery made by Sufferman and Morris in 1963, a large number of cyanophages have been discovered so far including India. Similar to bacteriophages, the cyanophages are also cultivated by plaque assay method. A pure culture of cyanobacterium is mixed with seeded with.

iii. Cultivation of Animal Viruses:

Some of the viruses can be cultured in the living animals such as mice, rabbits, guinea pigs, etc. After incubation, animals are carefully examined for the development of signs or symptoms. The animals may be killed.

(i) Use of Embryonated Eggs:

However, some viruses can be cultivated in the embryonated eggs. If they grow on eggs it will be a cheaper and convenient method. Virus is inoculated through a hole in certain regions only e.g. myxoma virus on chorio-allantoic membrane, while mumps virus in allantoic cavity (Fig. 15.6). The drilled hole is sealed with gelatin and egg is incubated. Infection produces a local lesion called ‘pocks’.

(ii) Use of Animal Cell Culture:

In recent years, use of animal cell culture in vitro as the growth medium for the viruses has replaced the embryonated egg. Cells are cultured artificially in laboratory. The cultured animal cells act as bacterial cells. To start the cell culture, small slice of animal tissue is treated with enzymes which separate each cell.

The cells are suspended in a solution of proper osmotic pressure, nutrients and growth hormones that are required for the cell growth. The cells get attached to the surface of glass and form a layer which is covered with viral inoculation and waited to settle the virions on cell surfaces. Cells are covered with a thin layer of agar to prevent the spread of virions and facilitate cell infection.

Viruses inoculated in the cell suspension destroy the monolayer. The phenomenon is called cytopathic effect which is detected as the plaques formed by bacteriophages. Plaques are formed on infected cells which are detected by staining with specific dyes e.g. neutral red or tryphan blue which differentiate the dead cells from the living cells.

The grown cells obtained from the sliced tissue are known as primary cell lines (Fig. 15.7). Primary cell lines start degenerating after a few generations. Therefore, the diploid cell lines can be established from human embryos. The diploid cell lines can be maintained for about 100 generations. However, for the growth and continuous work on viruses, one requires the continuous cell lines.

Only the transformed cells are used as continuous cell lines because they can be maintained for indefinite generations. Therefore, the trans­formed cells are known as immortal cell lines. HeLa cell line is one of the transformed cell lines which was obtained from the cervix malignant tumours of Henrietta Lacks of 31, who died in 1951 after the spread of cancer throughout her whole body even after intensive irradiation.

After several generations many cell lines lost all the original characters except their support for the viral propagation. Maintenance of cell culture line needs the trained persons; otherwise it gets con­taminated and destroyed.

iv. Cultivation of Plant Viruses:

Viral diseases e.g. tobacco mosaic occurring on plants are first surveyed and diseased parts are brought to the laboratory. About 50 g of TMV-infected diseased leaves are macerated in buffer at optimum pH, and sap is filtered first the with cheese cloth followed by millipore filter paper of 0.45 µ Pore size.

Then a healthy host plant is selected and the leaves are washed with 5% NaOCl solution. Several incisions are made on healthy leaves which are then inoculated with the viral preparation. The inoculated leaves of plants are bagged and tagged properly, and plants are incubated in glass house. Depending on time the viral symptoms develop similar to the original symptoms.

v. Virus Identification:

It is very difficult to identify a virus isolate because they could be observed only under electron microscope and tested serologically by using the human antibodies. They are isolated, purified, crystallized and characterized (particularly the base-sequence of nucleic acid).

In 1966, Gibbs and his associates suggested for the following eight approved characters for the identification of a virus:

(i) The nucleic acid types.

(ii) The number of strands in the nucleic acid.

(iii) The molecular weight of nucleic acid.

(iv) Percentage of nucleic acid in a virion.

(v) The forms of particles.

(vi) The forms of nucleocapsid.

(vii) The host and

(viii) The vector

This proposal was accepted with some modification by the International Committee on Nomenclature of Viruses (ICNV). These parameters are designed in abbreviations while describing a virus. They named the formula as cryptogram.

vi. Viral Multiplication:

A virus needs a living host cell to multiply. It invades the host cell and takes over metabolic machinery of the host. Consequently, depending on virus types, cell death occurs releasing thousands of similar viral particles.

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