Viruses have existed for thousands of years.

The first evidence comes from

historical records showing evidence of small pox like disease in Asia. In the
19th century, germ theory was developed, which states that all infections are
caused by a particular microbe that can be grown, are microscopic and can be
retained by filters.

The term virus has originated from a Latin word which means poison, and was
given by Louis Pasteur, a French chemist who suggested that something smaller
than the bacterium could cause the disease rabies. The Oxford English
Dictionary describes virus as a ‘morbid poison, a poison of contagious disease,
as smallpox.’
Iwanowski, a Russian botanist in 1892 found that sap from diseased tobacco
plant was capable of inducing mosaic disease in healthy plants even after the
sap was made sterile and was passed through bacteria proof filters. He
concluded that the disease causing agent was smaller than the bacterium. Later,
a German scientist Adolf Mayer also innoculated the sap from an infected plant
into healthy ones, observing the onset of mosaic disease in the healthy plant.
Both of them believed that either bacteria (very small in size and were
submicroscopic) or toxin were the cause of the disease.

In 1898, Martinus Beijernick (1851-1931) confirmed Iwanowski's results on

tobacco mosaic virus. He rejected the idea of the causative organism being a
bacteria and developed the term "contagium vivum fluidum" which means
“contagious living fluid” as first the idea of the virus. He placed some sap from
the infected plant on an agar plate for several days. He expected the causative
organism to penetrate into the agar. After a few days, the upper layer of agar
was removed and healthy plants were infected by two successive
underlying layers of agar. The inoculated plants gradually developed the disease
and thus convincing Beijernick of a liquid or soluble nature of the causative
agent.
Bacteriophages were first described by Frederick Twort (1915) and Felix D
Herelle (1917). In 1935, W Stanley was able to crystallize the virus causing
Tobacco Mosaic Virus disease. These crystals could produce disease in healthy
plants. The crystals had the property of self replication and could be stored like
any other chemical.
Viruses are minute, infectious agents, smaller than the smallest bacteria. They
do not have a cellular structure or any metabolic activity and cannot reproduce
outside living cells. The reproduction of viruses is dependent on the host cells
that they infect. They cannot perform functions on their own. When present
outside a host cell they exist as protein coat or capsid. The capsid encloses
either RNA or DNA.

Origin
There are three theories to explain the origin of viruses:
Regressive evolution

The first hypothesis is the theory of ‘‘regressive evolution’’, which proposes

that viruses descend from free-living and more complex parasites. According to
this theory viruses were dependent on host cell machinery through evolution but
retained the ability to auto replicate. Viruses are degenerate life-forms which
have lost many functions that other organisms possess & have only retained the
genetic information essential to their parasitic way of life.
Cellular origins
The second hypothesis is the theory of ‘‘cell origin’’, which assumes that
viruses originate from cell DNA and/or messenger RNA, which acquired the
ability to auto-replicate, create extracellular virions, exist and function
independently.
Independent entities

The theory of ‘‘independent’’ or ‘‘parallel’’ evolution of viruses and other

organisms, which assumes that
viruses appeared at the same time as the most primitive organisms.

General Properties of Viruses

Viruses are a unique group of infectious agents whose distinctiveness resides in
their simple, acellular organization and pattern of reproduction. A complete
virus particle or virion consists of one or more molecules of DNA or RNA
enclosed in a coat of protein, and sometimes also in other layers. These
additional layers may be very complex and contain carbohydrates, lipids, and
additional proteins. Viruses can exist in two phases: extracellular and
intracellular. Virions, the extracellular phase, possess few if any enzymes and
cannot reproduce independent of living cells. In the intracellular phase, viruses
exist primarily as replicating nucleic acids that induce host metabolism to
synthesize virion components; eventually complete virus particles or virions are
released. In summary, viruses differ from living cells in at least three ways: (1)
their simple, acellular organization; (2) the presence of either DNA or RNA, but
not both, in almost all virions (human cytomegalovirus has a DNA genome and
four mRNAs); and (3) their inability to reproduce independent of cells and carry
out cell division as procaryotes and eucaryotes do. Although bacteria such as
Chlamydia and rickettsia (see sections 21.5 and 22.1) are obligately intracellular
parasites like viruses, they do not meet the first two criteria.
General Structural Properties
All virions, even if they possess other constituents, are constructed around a
nucleocapsid core (indeed, some viruses consist only of a nucleocapsid). The
nucleocapsid is composed of a nucleic acid, either DNA or RNA, held within a
protein coat called the capsid, which protects viral genetic material and aids
in its transfer between host cells.
Nucleic Acids
Viruses are exceptionally flexible with respect to the nature of their genetic
material. They employ all four possible nucleic acid types: single-stranded
DNA, double-stranded DNA, single-stranded RNA, and double-stranded RNA.
All four types are found in animal viruses. Plant viruses most often have single-
stranded RNA genomes. Although phages may have single-stranded DNA or
single-stranded RNA, bacterial viruses usually contain double-stranded DNA.

The Structure of Viruses

Virus morphology has been intensely studied over the past decades because of
the importance of viruses and the realization that virus structure was simple
enough to be understood. Progress has come from the use of several different
techniques: electron microscopy, X-ray diffraction, biochemical analysis, and
immunology.
Although our knowledge is incomplete due to the large number of different
viruses, the general nature of virus structure is becoming clear.
Virion Size
Virions range in size from about 10 to 300 or 400 nm in diameter (figure 16.10).
The smallest viruses are a little larger than ribosomes, whereas the poxviruses,
like vaccinia, are about the same size as the smallest bacteria and can be seen in
the light microscope. Most viruses, however, are too small to be visible in the
light microscope and must be viewed with the scanning and transmission
electron microscopes.

The Morphology

The morphological characteristics of a virus can be studied using an electron

microscope. Viruses display a wide diversity of shapes and sizes. A virus
particle capable of infecting a host is called virion. The size of the virion varies
from 20 to 300 nm. Viruses are composed of a central core of nucleic acid
surrounded by a protein coat called a capsid.
According to their shape, the viruses are classified into the following types:
• Icosahedral (the viral particle appears spheroidal)
• rod like
• Mixed or combination particles with shapes of both spheroidal and rod like
(Complex virus)
Capsid
The protein shell that encloses the nucleic acid is called capsid. It consists of
several protein subunits known as capsomeres. When the nucleic acid is
enclosed by protein shell then it is called nucleocapsid.
The capsid has three functions:
i. it protects the nucleic acid from digestion by enzymes,
ii. contains special sites on its surface that allow the virion to attach to a host
cell,
iii. provides proteins that enable the virion to penetrate the host cell membrane.
Figure: Structure and Electron Micrograph of a Bacteriophage

Envelope
In some viruses the capsid is enclosed with a lipid membrane called the
envelope. The envelope is lipoproteinaceous in nature. It has a lipid bilayer with
interspersed protein molecules. The envelope has the lipid molecules of the
membrane of the host cell. The proteins maybe derived both from the virus and
the host cell. The host proteins are present in the envelope. Most viruses have
glycoproteineceous spikes on their envelope which help them to attach to
specific cell surfaces at the time of initiation of infection in a new host cell.
The proteins are of two types: Glycoproteins and Matrix proteins. Glycoproteins
are integral membrane proteins which have enzymatic activity. They are
exposed on the outer surface of the membrane. Matrix proteins are found on
inner face of envelope.

Functions of the Envelope

1. It assists in viral attachment to the host cell through External Glycoproteins

2. It provides the virus with the ability to infect.

3. It maintains the structural integrity of the virus.

Nucleic Acid (Genome)

Chemically viruses are basically nucleoproteinaceous. The protein coat

surrounds the nucleic acids. The property of viruses to multiply is because of its
nucleic acid content. The nucleic acid may either be DNA or RNA. The DNA
may either be circular or linear whereas RNA mostly exists only as linear
double or single stranded molecules.
Depending on the presence of DNA or RNA it may be called a DNA virus or an
RNA virus respectively. The length of nucleic acid in a virus varies from virus
to virus. Larger the size of virus particle more will be the content of nucleic acid
and vice versa.

Table: Shapes and sizes of some animal viruses

Classification
Viruses can be classified on the basis of their geometry, presence or absence of
envelopes, type of genome, mode of replication of the genome, mode of
transmission, or by the type of disease they cause.
Approximately 80 families and 4000 species of viruses are known. Nobel Prize
winner David Baltimore classified viruses on the basis of the type of nucleic
acid a virus contains and the way it expresses and replicates. Viruses must
generate positive stranded mRNA from their genomes to produce proteins and
replicate themselves. The RNA strand of a single stranded genome is either a
sense strand (plus strand), which functions as mRNA (messenger RNA) or an
antisense strand (minus strand). This is complimentary to the sense strand and
cannot function as mRNA and undergo protein translation.

The taxonomy of viruses is similar to that of cellular organisms:

Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species

This classification places viruses into seven groups:

I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)

II: ssDNA viruses (+) sense DNA (e.g. Parvoviruses)
III: dsRNA viruses (e.g. Reoviruses)
IV: (+)ssRNA viruses with (+)sense RNA (e.g. Picornaviruses, Togaviruses)
V: (-)ssRNA viruses with (-)sense RNA (e.g. Orthomyxoviruses,
Rhabdoviruses)
VI: ssRNA-reverse transcribing viruses with (+) sense RNA that replicates via
DNA intermediate in life-cycle (e.g. Retroviruses)
VII: dsDNA-reverse transcribing viruses that replicates via RNA intermediate
in life-cycle (e.g. Hepadnaviruses)

Baltimore Classification

Viruses are also classified on the basis of morphology, chemical composition,

and mode of replication. The viruses that infect humans are grouped into 21
families.

a. Based on Morphology
Shape
Helical Symmetry

In this type, similar protein subunits self assemble into helical form surrounding
the nucleic acid. The nucleic acid also follows a spiral path. These
nucleocapsids are rigid, highly elongated rods or filaments. Tobacco Mosaic
Virus (TMV) is a helical virus.

Icosahedral Symmetry
An icosahedron has 20 equilateral triangular faces and 12 vertices. In viruses
which show this type of shape the protein sununits called capsomeres are
arranged in a hollow spherical shell that encloses the genome of the virus.. Such
a symmetry shows a polyhedron structure.
Adenovirus is a DNA virus with a polyhedral capsid. T – even bacteriophage is
a DNA virus with a polyhedral head and a helical tail (tadpole shaped).
There are four general morphological types of capsids and virion structure.
1. Some capsids are icosahedral in shape. An icosahedron is a regular
polyhedron with 20 equilateral triangular faces and 12 vertices. These capsids
appear spherical when viewed at low power in the electron microscope.
2. Other capsids are helical and shaped like hollow protein
cylinders, which may be either rigid or flexible (figure
16.10m).
3. Many viruses have an envelope, an outer membranous layer surrounding the
nucleocapsid. Enveloped viruses have a roughly spherical but somewhat
variable shape even though their nucleocapsid can be either icosahedral or
helical.
4. Complex viruses have capsid symmetry that is neither purely icosahedral nor
helical (figure 16.10a,d,f,g). They may possess tails and other structures (e.g.,
many bacteriophages) or have complex, multilayered walls surrounding the
nucleic acid (e.g., poxviruses such as vaccinia). Both helical and icosahedral
capsids are large macromolecular structures constructed from many copies of
one or a few types of protein subunits or protomers. Probably the most
important advantage of this design strategy is that the information stored in viral
genetic material is used with maximum efficiency. For example, the tobacco
mosaic virus (TMV) capsid contains a single type of small subunit possessing
158 amino acids. Only about 474 nucleotides out of 6,000 in the virus RNA are
required to code for coat protein amino acids. Unless the same protein is
used many times in capsid construction, a large nucleic acid, such as the TMV
RNA, cannot be enclosed in a protein coat without using much or all of the
available genetic material to code for capsid proteins. If the TMV capsid were
composed of six different protomers of the same size as the TMV subunit, about
2,900 of the 6,000 nucleotides would be required for its construction, and
much less genetic material would be available for other purposes. Once formed
and exposed to the proper conditions, protomers usually interact specifically
with each other and spontaneously associate to form the capsid. Because the
capsid is constructed without any outside aid, the process is called self-assembly
Some more complex viruses possess genes for special factors that are not
incorporated into the virion but are required for its assembly.
Helical Capsids
Helical capsids are shaped much like hollow tubes with protein walls. The
tobacco mosaic virus provides a well-studied example of helical capsid structure
A single type of protomer associates together in a helical or spiral arrangement
to produce a long, rigid tube, 15 to 18 nm in diameter by 300 nm long. The
RNA genetic material is wound in a spiral and positioned toward the inside of
the capsid where it lies within a groove formed by the protein subunits. Not all
helical capsids are as rigid as the TMV capsid. Influenza virus RNAs are
enclosed in thin, flexible helical capsids folded within an envelope ).
The size of a helical capsid is influenced by both its protomers and the nucleic
acid enclosed within the capsid. The diameter of the capsid is a function of the
size, shape, and interactions of the protomers. The nucleic acid determines
helical capsid length because the capsid does not seem to extend much beyond
the end of the DNA or RNA.
Icosahedral Capsids
The icosahedron is one of nature’s favorite shapes (the helix is probably most
popular). Viruses employ the icosahedral shape because it is the most efficient
way to enclose a space. A few genes, sometimes only one, can code for proteins
that selfassemble to form the capsid. In this way a small number of linear genes
can specify a large three-dimensional structure. Certain requirements must be
met to construct an icosahedron. Hexagons pack together in planes and cannot
enclose a space, and therefore pentagons must also be used. When icosahedral
viruses are negatively stained and viewed in the transmission electron
microscope, a complex icosahedral capsid structure is revealed.The capsids are
constructed from ring- or knob-shaped units called capsomers, each usually
made of five or six protomers. Pentamers (pentons) have five subunits;
hexamers (hexons) possess six. Pentamers are at the vertices of the
icosahedron, whereas hexamers form its edges and triangular faces (figure
16.13). The icosahedron in figure 16.13 is constructed of 42 capsomers; larger
icosahedra are made if more hexamers are used to form the edges and faces
(adenoviruses have a capsid with 252 capsomers as shown in figure 16.12g,h).
In many plant and bacterial RNA viruses, both the pentamers and hexamers of a
capsid are constructed with only one type of subunit, whereas adenovirus
pentamers are composed of different proteins than are adenovirus hexamers.

Protomers join to form capsomers through noncovalent bonding. The bonds

between proteins within pentamers and hexamers are stronger than those
between separate capsomers.

Empty capsids can even dissociate into separate capsomers. Recently it has been
discovered that there is more than one way to build an icosahedral capsid.
Although most icosahedral capsids appear to contain both pentamers and
hexamers, simianvirus 40 (SV-40), a small double-stranded DNA
polyomavirus, has only pentamers (figure 16.14a). The virus is constructed of
72 cylindrical pentamers with hollow centers. Five flexible arms extend from
the edge of each pentamer (figure 16.14b). Twelve pentamers occupy the
icosahedron’s vertices and associate with five neighbors, just as they do when
hexamers also are present. Each of the 60 nonvertex pentamers associates with
its six adjacent neighbors as shown in figure 16.14c. An arm extends toward the
adjacent vertex pentamer (pentamer 1) and twists around one of its arms. Three
more arms interact in the same way with arms of other nonvertex pentamers
(pentamers 3 to 5). The fifth arm binds directly to an adjacent nonvertex
pentamer (pentamer 6) but does not attach to one of its arms. An arm does not
extend from the central pentamer to pentamer 2; other arms hold pentamer 2 in
place. Thus an icosahedral capsid is assembled without hexamers by using
flexible arms as ropes to tie the pentamers together

b. Based on Chemical Composition and Mode of Replication

RNA Virus Genomes
70% of all viruses are RNA viruses. The viral RNA maybe single stranded (ss)
or double stranded (ds)..
DNA Virus Genomes
DNA viruses generally contain a single genome of linear dsDNA. Some,
however, have a circular DNA for eg. Papova virus.
Single-stranded linear DNA, is found with the members of the Parvovirus
family that comprises the parvo-, the erythro- and the dependoviruses. The
virion contains 2–4 structural protein species which are differently derived from
the same gene product.
Figure: Diversity in shape of viruses

Detailed study of special type of viruses

RNA VIRUS – Tobacco Mosaic Virus
Tobacco mosaic virus (TMV) is one of the simplest viruses known. TMV is the
classical example of a rod-shaped virus. Its rod shape results from its basic
design, namely a regular helical array of identical protein subunits, in which
frame- work is embedded a single molecule of RNA wound as a helix.

TMV is a positive-sense single stranded RNA virus that infects plants,

especially tobacco and other members of the family Solanaceae.
It has a capsid made of 2130 molecules of coat protein. There are about 134
turns to one TMV protein coat and 16.3 proteins per helix turn. 158 amino acids
form a protein. Its RNA is 6400 bases long.

Viruses enter plant cells through wounds, grafting, seed, pollen and insects.
Tobacco mosaic virus is most commonly introduced into plants through small
wounds caused by handling and by insects chewing on plant parts. The most
common sources of virus inoculum for tobacco mosaic virus are the debris of
infected plants that remains in the soil and certain infected tobacco products that
contaminate workers hands.

Symptoms
Symptoms induced by Tobacco mosaic virus (TMV) are dependent on the host
plant. These include mosaic, mottling; necrosis, stunting, leaf curling and
yellowing of plant tissues. The symptoms are dependent on the age of the
infected plant, virus strain, genetics of host plant and environmental conditions.

Structure of Tobacco Mosaic Virus (TMV):

TMV is a simple rod-shaped helical virus (Fig. 13.20) consisting of
centrally located single- stranded RNA (5.6%) enveloped by a protein coat
(94.4%). The rod is considered to be 3,000 Å in length and about 180 Å in
diameter.

The protein coat is technically called ‘capsid’. R. Franklin estimated 2,130

sub-units, namely, capsomeres in a complete helical rod and 49
capsomeres on every three turns of the helix; thus there would be about
130 turns per rod of TMV.

The diameter of RNA helix is about 80 Å and the RNA molecule lies
about 50 Å inward from the outer-most surface of the rod. The central core
of the rod is about 40 Å in diameter. Each capsomere is a grape like
structure containing about 158 amino acids and having a molecular weight
of 17,000 dalton as determined by Knight.
The ssRNA is little more in length (about 3300 Å) slightly protruding from
one end of the rod. The RNA molecule consists of about 7300 nucleotides;
the molecular weight of the RNA molecule being about 25,000 dalton.

Life-Cycle (Replication) of Tobacco Mosaic Virus (TMV):

Plant viruses like TMV penetrate and enter the host cells in to and their
replication completes within such infected host cells (Fig. 13.21). Inside
the host cell, the protein coat dissociates and viral nucleic acid becomes
free in the cell cytoplasm.

Although the sites for different steps of the viral multiplication and
formation of new viruses have not yet been determined with absolute
certainty, the studies suggest ha alter becoming free in the cell cytoplasm
the viral-RNA moves into the nucleus (possibly into the nucleolus).

The viral-RNA first induces the formation of specific enzymes called

‘RNA polymerases’ the single-stranded viral-RNA synthesizes an
additional RNA strand called replicative RNA.

This RNA strand is complementary to the viral genome and serves as

‘template’ for producing new RNA single strands which is the copies of
the parental viral-RNA. The new viral-RNAs are released from the nucleus
into cytoplasm and serve as messenger-RNAs (mRNAs). Each mRNA, in
cooperation with ribosomes and t-RNA of the host cell directs the
synthesis of protein subunits.
After the desired protein sub-units (capsomeres) have been produced, the
new viral nucleic acid is considered to organize the protein subunit around
it resulting in the formation of complete virus particle, the virion.

No ‘lysis’ of the host cell, as seen in case of virulent bacteriophages, takes

place. The host ells remain alive and viruses move from one cell to the
other causing systemic infection. When transmitted by some means the
viruses infect other healthy plants.

Viruses and disease

Viruses are incapable of replication without a host cell thus the process of
transmission from one host to another is necessary for viruses. Ecological,
cultural, and genetic factors are responsible for incidence and prevalence of
viral diseases. Viral infections may be localized, systemic or those that are not
detectable easily.

The symptoms of viral diseases vary to a great extent. Symptoms may appear at
the site of infection or at certain distant areas not related to point of infection. A
particular virus is capable of producing different symptoms on entering different
hosts.

PLANT VIRAL DISEASES

Plant diseases caused by virus are generally systemic in nature. Even though the
virus spreads throughout the plant but only a few organs exhibit the symptoms.
Leaves show the most prominent features of viral diseases. In certain cases,
shoots, floral organs or even roots can show symptoms. The most important
feature of viral plant disease is the general retardation of growth, vigor and
cropping power of plant.

DNA VIRUS – T Phages

DNA Viruses
• DNA Viruses are the viruses which consist of DNA genome. They complete
their activities by transcription and most of them attack on organisms of similar
genome.

Viruses with Capsids of Complex Symmetry

Although most viruses have either icosahedral or helical capsids, many viruses
do not fit into either category. The poxviruses and large bacteriophages are two
important examples. The poxviruses are the largest of the animal viruses (about
400 _ 240 _ 200 nm in size) and can even be seen with a phasecontrast
microscope or in stained preparations. They possess an exceptionally complex
internal structure with an ovoid- to brickshaped exterior. The double-stranded
DNA is associated with proteins and contained in the nucleoid, a central
structure shaped like a biconcave disk and surrounded by a membrane.Two
elliptical or lateral bodies lie between the nucleoid and its outer envelope, a
membrane and a thick layer covered by an array of tubules or fibers. Some large
bacteriophages are even more elaborate than the poxviruses. The T2, T4, and T6
phages that infect E. coli have been intensely studied. Bacteriophages
attacking Escherichia coli are called coliphages or T-phages. Max
Delbruck (1938) numbered coliphages as T-even phages (T2, T4, T6 etc.)
and T-odd phages (T1, T3, T5 etc.).

Their head resembles an icosahedron elongated by one or two rows of hexamers

in the middle and contains the DNA genome. The tail is composed of a collar
joining it to the head, a central hollow tube, a sheath surrounding the tube, and a
complex baseplate.
In T-even phages, the baseplate is hexagonal and has a pin and a jointed
tail fiber at each corner. The tail fibers are responsible for virus attachment
to the proper site on the bacterial surface. There is considerable variation in
structure among the large bacteriophages, even those infecting a single host. In
contrast with the T-even phages, many coliphages have true icosahedral heads.

T1, T5, and lambda phages have sheathless tails that lack a baseplate and
terminate in rudimentary tail fibers. Coliphages T3 and T7 have short,
noncontractile tails without tail fibers. Clearly these viruses can complete their
reproductive cycles using a variety of tail structures. Complex bacterial viruses
with both heads and tails are said to have binal symmetry because they possess
a combination of icosahedral (the head) and helical (the tail) symmetry.

The viruses that attack bacteria are called bacteriophages. The first clue
regarding these viruses was given by Twort (1915) in England and Felix de
Herelle (1917) in France who also coined the term bacteriophage (i.e., bacteria
eater commonly called as phages). Bacteriophages attacking Escherichia coli
are called coliphages or T-phages. Max Delbruck (1938) numbered
coliphages as T-even phages (T2, T4, T6 etc.) and T-odd phages (T1, T3,
T5 etc.).

So to sum up the genetic material of the phages can be dsDNA, ssDNA, dsRNA
or ssRNA. The bacteriophages occur in three common forms: Tailed, cubic and
filamentous. The tailed bacteriophages named T-phages (include the T-even and
T-odd phages) form the largest group.
T-Phages
A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4;
(BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent"
because they cause cessation of all bacterial metabolism on infection. Phages T1, T3;
(BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent"
because they depend on continued bacterial metabolism during the lytic cycle. The T-even
phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.

Coliphage T2 (Bacteriophage)
The structure of T2 bacteriophage consists of a head, a tail, a basal plate and tail
fibers. In the centre of the head there is a linear double stranded DNA. The tail
is hollow and cylindrical. In the tail the molecules of protein are spirally
arranged. There is a basal plate at the end of the tail, which bears tail fibers. The
tail fibers help the virus for absorption into a bacterium. All these parts are
formed of proteins.
Alfred Hershey and Martha Chase showed that DNA of viruses is injected into
the bacterial cells while most proteins remain outside. Their discovery
supported that DNA rather than proteins is the hereditary material.

1. Structure:
The virion of T-even phage is binal or tadpole like structure with a
polyhedral head connected to a helical tail through a short collar. The head
composed of about 2000 capsomeres arid encloses a tightly packed
dsDNA (50 nm long). The tail has an inner hollow tube called core,
surrounded by a contractile sheath which consists of 24 annular rings. The
distal end of the tube is connected to a hexagonal basal plate with spike or
tail spin at each corner. Six long, flexible tail fibers also arise from the
basal plate which helps in adsorption to bacteria (Fig. 10.5).
2. Reproduction (Replication cycle):
Bacteriophages exhibit two types of replication cycle – virulent or lytic
cycle and temperate or lysogenic cycle (Fig. 10.6).

I. Virulent or lytic cycle:

The phages undergoing lytic cycle are called lytic phages or virulent
phages, e.g., T-series bacteriophages. In lytic cycle, a lytic phage infects
and kills the host cell to release progeny virions.
The whole process involves following steps:
(a) Adsorption or infection

(d) Virion assembly

(b) Penetration or injection

(e) Lysis or release

(c) Synthesis of phage components

Step-1. Adsorption or infection:

The lytic cycle begins with a collision between T-phage virion and a
susceptible host cell i.e. Escherichia coli. The process of attachment of a
virion on the host cell surface is called adsorption. The tips of tail fibers
bind or adsorb to specific receptors on the surface of E. coli.

The viral receptors may be F-pili, lipoproteins, iron transport proteins etc.
The T-phage virion adsorb to specific receptors by the tip of tail fibers. For
example, T4 and T7 coliphages bind to lipopolysaccharides.

Step-2. Penetration or Injection:

The tail fibers of virion bend to bring the spikes and basal plate in contact
with the surface of bacterial wall. The tail sheath contracts so that the
hollow tail core (inner tube) penetrates the bacterial wall and injects the
viral genome into the cytoplasm. After penetration, the empty capsid that
remains outside the bacterium is called the ghost or doughnut.

Step-3. Synthesis of phage components:

Immediately after penetration, the phage DNA (genome) synthesizes early
proteins. Some early proteins break down the bacterial (host) DNA and
take the control of the bacterial cell machinery. The other early proteins
used as enzymes for replication of phage DNA. The newly synthesized
phage DNAs produces late proteins, which are the protein subunits of the
phage capsid (head and tail).

Step-4. Virion assembly:

The capsid proteins assemble to form empty head and a condenced viral
DNA is packed inside it. Finally the separately assembled tail joins to head
to form a daughter or progeny virion.

Step-5. Lysis or release:

During assembly of progeny virions, the bacterial cell becomes spherical.
The phage enzymes weaken the cell wall which ultimately burst or lyse to
release about 100-200 progeny virions.

II. Temperate or lysogenic cycle:

The phages that exhibit lysogenic cycle are called temperate phages or
non-virulent phages. For example, λ, (Lambda)- phages attacking, E. coli.
During lysogenic cycle, the phage DNA integrates into the bacterial DNA
and is now called as prophage. The host bacterium containing prophage is
called a lysogenic bacterium or lysogen. The prophage passively replicates
along with the host DNA for many generations. When a lysogenic
bacterium exposed to UV-light or a chemical, the prophage withdraw from
the host DNA to undergo lytic cycle. This conversion of a prophage into a
lytic phage is called induction.
• The lytic cycle: The phage infects a bacterium, hijacks the bacterium
to make lots of phages, and then kills the cell by making it explode (lyse).
• The lysogenic cycle: The phage infects a bacterium and inserts its
DNA into the bacterial chromosome, allowing the phage DNA (now called
a prophage) to be copied and passed on along with the cell's own DNA.
Let's take a closer look at each of these cycles.
•

Bacteriophage infections
Bacteriophages, just like other viruses, must infect a host cell in order to
reproduce. The steps that make up the infection process are collectively
called the lifecycle of the phage.

Some phages can only reproduce via a lytic lifecycle, in which they burst
and kill their host cells. Other phages can alternate between a lytic
lifecycle and a lysogenic lifecycle, in which they don't kill the host cell
(and are instead copied along with the host DNA each time the cell
divides).

Let's take closer look at these two cycles. As an example, we'll use a phage
called lambda (\lambdaλlambda), which infects E. coli bacteria and can
switch between the lytic and lysogenic cycles.

Lytic cycle
In the lytic cycle, a phage acts like a typical virus: it hijacks its host cell
and uses the cell's resources to make lots of new phages, causing the cell
to lyse (burst) and die in the process.
1. Attachment: Proteins in the "tail" of the phage bind to a specific
receptor (in this case, a sugar transporter) on the surface of the bacterial
cell.
2. Entry: The phage injects its double-stranded DNA genome into the
cytoplasm of the bacterium.
3. DNA copying and protein synthesis: Phage DNA is copied, and
phage genes are expressed to make proteins, such as capsid proteins.
4. Assembly of new phage: Capsids assemble from the capsid proteins
and are stuffed with DNA to make lots of new phage particles.
5. Lysis: Late in the lytic cycle, the phage expresses genes for proteins
that poke holes in the plasma membrane and cell wall. The holes let water
flow in, making the cell expand and burst like an overfilled water balloon.
 Cell bursting, or lysis, releases hundreds of new phages, which can find
and infect other host cells nearby.

Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). The modified image is licensed under
a CC BY-SA 3.0 license. Based on similar diagram in Alberts et al.^66start superscript, 6, end superscript

The stages of the lytic cycle are:

1. Attachment: Proteins in the "tail" of the phage bind to a specific

receptor (in this case, a sugar transporter) on the surface of the bacterial
cell.
2. Entry: The phage injects its double-stranded DNA genome into the
cytoplasm of the bacterium.
3. DNA copying and protein synthesis: Phage DNA is copied, and
phage genes are expressed to make proteins, such as capsid proteins.
4. Assembly of new phage: Capsids assemble from the capsid proteins
and are stuffed with DNA to make lots of new phage particles.
5. Lysis: Late in the lytic cycle, the phage expresses genes for proteins
that poke holes in the plasma membrane and cell wall. The holes let water
flow in, making the cell expand and burst like an overfilled water balloon.
Cell bursting, or lysis, releases hundreds of new phages, which can find
and infect other host cells nearby. In this way, a few cycles of lytic
infection can let the phage spread like wildfire through a bacterial
population.
Lysogenic cycle
The lysogenic cycle allows a phage to reproduce without killing its host.
Some phages can only use the lytic cycle, but the phage we are following,
lambda (\lambdaλlambda), can switch between the two cycles.

In the lysogenic cycle, the first two steps (attachment and DNA injection)
occur just as they do for the lytic cycle. However, once the phage DNA is
inside the cell, it is not immediately copied or expressed to make proteins.
Instead, it recombines with a particular region of the bacterial
chromosome. This causes the phage DNA to be integrated into the
chromosome.

Lysogenic cycle:
1. Attachment. Bacteriophage attaches to bacterial cell.
2. Entry. Bacteriophage injects DNA into bacterial cell.
3. Integration. Phage DNA recombines with bacterial chromosome and
becomes integrated into the chromosome as a prophage.
4. Cell division. Each time a cell containing a prophage divides, its
daughter cells inherit the prophage.
Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). The modified image is licensed under
a CC BY-SA 3.0 license. Based on similar diagram in Alberts et al.^66start superscript, 6, end superscript

The integrated phage DNA, called a prophage, is not active: its genes
aren't expressed, and it doesn't drive production of new phages. However,
each time a host cell divides, the prophage is copied along with the host
DNA, getting a free ride. The lysogenic cycle is less flashy (and less gory)
than the lytic cycle, but at the end of the day, it's just another way for the
phage to reproduce.

Under the right conditions, the prophage can become active and come
back out of the bacterial chromosome, triggering the remaining steps of
the lytic cycle (DNA copying and protein synthesis, phage assembly, and
lysis).
1. Prophage exits chromosome and becomes its own circularized DNA
molecule.
2. Lytic cycle commences.
Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). The modified image is licensed under
a CC BY-SA 3.0 license.

To lyse or not to lyse?

How does a phage "decide" whether to enter the lytic or lysogenic cycle
when it infects a bacterium? One important factor is the number of phages
infecting the cell. Larger numbers of co-infecting phages make it more
likely that the infection will use the lysogenic cycle. This strategy may
help prevent the phages from wiping out their bacterial hosts (by toning
down the attack if the phage-to-host ratio gets too high

What triggers a prophage to pop back out of the chromosome and enter the
lytic cycle? At least in the laboratory, DNA-damaging agents (like UV
radiation and chemicals) will trigger most prophages in a population to re-
activate. However, a small fraction of the prophages in a population
spontaneously "go lytic" even without these external cues.

Virion:
A complete viral particle, consisting of RNA or DNA surrounded by a
protein shell capsid and constituting the infective form of a virus. It is also
known as virus is ready for infection. The capsid protects the interior core
that includes the genome and other proteins. All virions have genomic
nucleic acid: this maybe either RNA or DNA, ss (single stranded) or
ds(double stranded). After the virion binds to the surface of a specific host
cell, its DNA or RNA is injected into the host cell and viral replication
occurs with eventual spread of the infection to other host cells.

Virusoids:
Virusoids are circular single-stranded RNAs dependent on plant viruses
for replication and encapsidation. The genome of virusoids consists of
several hundred nucleotides and only encodes structural proteins.
Virusoids are similar to viroids in size, structure and means of replication
.Virusoids while being studied in virology, are not considered as viruses
but as subviral particles.

Prion:
It is an infectious protein particle similar to a virus but lacking nucleic
acid; thought to be the agent responsible for scrapie and other degenerative
diseases of the nervous system. The term Prion was coined in 1982 by
Neurologist Stanley Prusiner. Prions are infectious proteinaceous particles
that lack nucleic acid. Prions are said to be in the border zone between
nonliving and living things because they have no need to metabolize or the
capacity to reproduce but they are capable of replication within the body
of a human or of some mammals.

Prions can gain entry into the body mainly by ingestion, e.g. of
contaminated human. Growth Hormone or of contaminated blood or blood
products. Prions may also arise from a mutation in the gene that encodes
the protein. They not only fold into unusual shapes but also seem to have
the ability to cause other (normal) proteins to alter their shape as well.

Viroid:
Viroid an infectious agent that consists solely of a single strand of RNA
and causes disease in certain plants. It was discovered by T.O .Diener in
1971 .Viroids lack the protein coat (known as capsid) of viruses and are
the smallest known infectious agents containing only about 250 to 375
base pairs. They are much smaller than the smallest genomes of viruses
and have no genes for encoding proteins. Viroids are believed to cause
disease by interfering with the host cell’s gene regulation. They are
destructive to many important commercial plants, including potatoes,
Lycopersicom, Cucumis, Cocos, and Chrysanthemum etc.
Economic importance of viruses

Viruses are common human pathogens causing a number of deadly diseases like
AIDS, Herpes, Cancer etc.

Viruses have been primarily identified as pathogens but they also have
significant economic importance.

Viruses act as simple systems, which can be used as tools for research and
analysis. Studies on recombinant DNA technology were developed using
bacteriophages (Bacterial Viruses).
In addition, the viral genomes were the first ones to be sequenced (øx174 and
MS 2).
The lysogenic life cycle of certain viruses allows easy manipulation of the
viral genome. Viruses are used as vectors to deliver therapeutic genes into
humans in gene therapy. They are also used to cure cancer in a number of ways
like virotherapy and VDEPT (virus directed enzyme pro drug therapy).
Viruses are also the primary sources of vaccines used to prevent the viral
infections.
Some of the viruses can also be used for the control of insect pests of our
crop plants. However, in contrast a number of viruses are important plant
pathogens as will be discussed in the subsequent text.

Medicine and Diagnostics

Vaccine production: Viral vaccines confer immunity against infection by the
pathogenic strains of the same viruses. The initial research on vaccines by
Edward Jenner (1796) started with a virus. Jenner used the cowpox virus (now
known as vaccinia virus) as a live vaccine for preventing smallpox. The
conventional vaccines synthesized using live attenuated viruses or killed viruses
are easy to produce and economic but have a number of disadvantages.
Gene therapy:The introduction of functional genes into human cells to correct
defective genes by replacing them is known as Gene therapy. Initially gene
therapy was used for treatment of patients with genetic disorders, however the
applications of gene therapy have increased widely now .
Gene therapy is effective in cases where introduction of either a single gene or
limited numbers of genes are required to correct a given disorder.
Ex-vivo somatic gene therapy- It involves removal of cells with defective
genes from the body, followed by introduction of therapeutic gene outside the
body. The treated cells are then re-introduced into the patients.

In-vivo somatic gene therapy involves introduction of therapeutic gene

directly into the target cells of the patient.
Germ line gene therapy includes the introduction of therapeutic genes into
germ cells, aimed at correcting defects in the next generation. Germ line gene
therapy is currently not being used in humans and is restricted only to
laboratory
Viruses act as a very specific and efficient gene carrier systems for both ex-vivo
and in-vivo gene therapy modules. There are a number of viruses which are
being used as vectors in gene therapy. The important ones being Adenovirus,
Adeno-associated viruses , Retroviruses, Vaccinia virus , Poxvirus, Herpes
simplex virus etc.

Cancer therapy: Viruses can be directly used to prevent cancer by being the
source of anti cancer vaccines eg. vaccines against hepatitis B virus (causes
hepatic cancer) and human papillomavirus (cervical cancer) are commercially
available. During carcinogenesis six fundamental properties are altered in cells
to give rise to the destructive phenotype of cancer as illustrated in given anti
viral vaccines are prophylactic in nature and stimulate immune system to
synthesize and recruit specific antiviral molecules and cells. Cancerous cells
express characteristic viral specific proteins, thus these could be targeted using
vector to enhance the specificity of the vaccines. Such therapeutic vaccines are
under clinical trials and are still not approved for human use.

Viruses, especially the RNA viruses have been found to have an inherent anti-
cancer effect. They have been found to have a direct cytotoxic effect on cancer
cells without involving the immune system. The direct therapeutic approach of
cancer treatment using viruses is called virotherapy.

Virus-directed enzyme prodrug therapy (VDEPT) uses viruses to deliver an

enzyme into target cancer cell. This enzyme can alter an inactive precursor of a
cytotoxic drug into an active form. This treatment module is in research stages
and is being evaluated for its therapeutic efficacy.

Bacteriophage therapy

The use of bacterial viruses to infect and destroy pathogenic bacteria is known
as bacteriophage therapy. This bacteriophage can be used as biocontrol agents
to destroy their host bacteria. The bacteriophages undergo two types of life
cycles lytic and lysogenic, which have an important bearing on their
pathogenesis. The role of bacteriophages as therapeutic agents is known since
earlier times. Bacteriophage preparations were used against bacterial dysentery,
staphylococcal skin infections etc. However, with the discovery of antibiotics,
the bacteriophage therapy was ignored. Resistance to antibiotics and emergence
of methicillin-resistant Staphylococcus aureus(MRSA) , vancomycin –resistant
Enterococcus (VRE) etc again opened the doors for research in bacteriophage
therapy. This therapy has been used to control the bacterial pathogen Listeria
monocytogenes in food products. The clinical trials for human pathogens have
been conducted for Enterococcus, E.coli, Pseudomonas aeruginosa, MRSA etc.
Bacteriophages are highly promising as therapeutic agents, however intensive
systematic studies are required in this subject.

Role of Viruses in diagnosis

Viruses play a pivotal role in diagnostic procedures commonly employed in
various biological sciences viz. microbiology, molecular Biology, immunology,
genetic engineering etc. Besides diagnosis and treatment of disease viruses have
contributed significantly to research and development of various scientific
disciplines.
Most of the diagnostic techniques like southern blotting, northern blotting , dot
blot, DNA and RNA sequencing, construction of genomic libraries etc. require
probes for identification of DNA/RNA molecules. These probes are
oligonucleotides [10-30 bases ] of DNA or RNA used to detect the presence of
complementary sequence in clinical or research samples.
The enzyme reverse transcriptase produce by retroviruses has been extensively
used in the generation of cDNA which is very frequently required both in
research and clinical diagnosis. Viruses T4 phage also produce the enzyme
ligase which can be used either in recombinant DNA technology or even in
technique such as ligase chain reaction.
Bacteriophage typing is a technique, which employs bacterial viruses for
identification of pathogenic bacteria in the clinical samples as well as for
research purposes. The pathogenic bacterium to be identified is cultured on a
nutrient medium contained in a petridish. The plate is then marked into squares
and each square is inoculated with a specific phage. This is followed by
incubation for 24 hours after which plates are observed for plaque formation.
Results of phage typing are recorded according to phage sensitivity of the
bacterium.
Role of viruses in research
These are a number of ways in which viruses have been used for research. Some
of the applications are as under. Viruses are commonly used as vector in
recombinant DNA technology because of their ability to insert their content into
host cells. A vector is an autonomously replicating DNA fragment into which
genes of interest can be integrated for cloning. Vector should be DNA
molecules which are amenable to manipulation, i.e., they should be easy to
isolate and insert into host. They should carry target sites for restriction
endonucleases as well as selectable markers for easy identification.
Viruses have been sources of number of enzymes that are routinely used in
molecular biology and genetic engineering. Reverse transcriptase an enzyme
coded by the retroviruses is used for the generation of cDNA which is
extensively required for construction of genomic libraries etc.
Viruses are routinely used in research in the field of animal and plant
biotechnology for production of transgenics. Gene of interest from animal is
initially cloned in bacterium E.coli and then expressed in animal cell culture or
embroys using shuttle vectors derived from viruses e.g. pc DNA1.1/Amp. The
animal cell cultures are transfected with viruses for research on gene therapy
and vaccine production.

Research on plant genomes also uses plant viruses as vectors. The virus vector
are used to produce specific products from plants.

Viruses as biopesticides

The most commonly used microbial biopesticide is produced from the

bacterium Bacillus thuringiensis. However, viruses are also used as a pesticide
for killing a number of insect species like moths,bollworms,fruitworms etc. The
Biopesticidal agents can either prey on pests , be parasitic on them,compete
with insects or are insect pathogens .Viruses usually are pathogenic on various
insect species.

Viruses as causal organism of plant disease

Plant diseases cause by viruses lead to massive agronomic losses .Viruses
causes a number of diseases in plants, however there are limited studies in this
field because it is difficult to cultivate and purify viruses. Some plant viruses
like tobacco mosaic virus can be grown on plants protoplasts but most of the
other viruses have to be cultured on either whole plant or tissue preparations,
thus making it difficult to study their life cycle.
Most of the viruses infecting plants are rod shaped or spherical.They are usually
RNA viruses , containing single stranded RNA in a protein coat .However ,there
are a few exceptions like cauliflower mosaic virus ,which is a double stranded
DNA viruses. Penetration of viruses into plant cell is difficult because of the
presence of complex and thick cell wall .Therefore mechanical damage of plant
cell wall is important which can be

caused by either insects or animals .Thus the most common mode of

transmission of plants viruses is by insects like aphids, leafhoppers etc they pick
up viruses on their mouth parts and transmit it to plants. There are basically two
kinds of infections caused by plant viruses- the mosaic disease and the curling
and dwarfing disease.
The mosaic diseases are the most prevalent type of diseases caused by plant
viruses .This is characterized by spoiling of leaves by production of either
yellowish or necrotic spots on leaves .Tobacco mosaic disease caused by
Tobacco mosaic virus is the most common example of such type of disease
pattern. The curling and dwarfing disease of plants also include symptoms like
tumor formation, yellowing etc.
Few of the plant disease caused by plant viruses are discussed below:
Tobacco mosaic virus (TMV)
TMV is a thermal resistant virus which infects tobacco and other plants as well.
It is transmitted through cell sap injury caused during clipping of the shoot .It
has a positive sense RNA and codes for protein like RNA polymerase,
replication proteins and movement protein etc. The symptoms of TMV infection
are mosaic and even blisters on leaves. Control of this disease can be carried out
by crop rotation, sanitation and use of resistant varieties. This plant virus is
present worldwide and has a wide host range vizpotato ,tomato etc. The
symptoms include mosaic and necrosis associated with dwarfing .Genome is
composed of single stranded positive sense RNA .The virus is transmitted
through infected tubers and insects like aphids .Infection of crops with this virus
cause huge economic losses.

Cauliflower mosaic virus

These viruses are the only group of plant virus with double stranded DNA as
genetic material. This virus infects no. of plant species. The symptoms of this
plant disease include leaf mottling and curling of edges .The fruits also show
mottling with yellow and white patches. Cauliflower mosaic virus is transmitted
by insects.
Besides viruses, viriods are cause number of plant disease. Viroids are smaller,
circular RNA molecule with a rod like secondary structure with notable absence
of a protein coat. They do not code for any protein and use the host cell
enzymatic machinery

Summary
Viruses are extremely small sized infectious agents which are obligate parasitic.
They are important as pathogens but have a number of benefits also. Viruses
have a major role in medicine research and diagnostics . They are also important
in environment management

Vaccine production: Viral vaccines confer immunity against infection with the
pathogenic strains of same virus. The conventional vaccines synthesized using
live attenuated viruses or killed viruses are easy to produce and economic.
Gene therapy: The introduction of functional gene into human cells to correct
defective genes by replacing them is known as Gene Therapy. Gene therapy is
largely used in cancer treatment.
Cancer therapy: Viruses can be directly used to prevent cancer by being the
source of anti cancer vaccines, e.g., vaccines against hepatitis B virus (causes
hepatic cancer) and human papillomavirus (cervical cancer) are commercially
available.
Bacteriophage therapy: This is involve the use of bacterio phages for
destruction of bacterial pathogens. This therapy has been used to successfully
treat staphylococcal and E.coli infections and appears to be very promising .
Virus based diagnosis: virus play a pivotal role in diagnostic procedure
commonly employed in various biological sciences viz. Microbiology,
Molecular Biology, Immunology, Genetic Engineering etc.
Role of viruses in research: These are a number of ways in which viruses have
been used for research. Viruses are commonly used as vector in recombinant
DNA technology research procedure because of their ability to insert content
into host cells. Bacteriophages are the routinely used viral vectors in genetic
engineering. The lambda and M13 phage are the most commonly used E.coli
phages.
Viral bio pesticides: They are much less significant than bacterial pesticides
still research and development on various viruses as potential bio-control agents
is going on. Baculoviruses are the most important group of viruses used as
biopesticides
Plant viruses caused by viruses lead to massive agronomic losses. Viruses cause
a number of diseases in plants. Few of the plant disease caused by plant viruses
are- Tobacco mosaic virus, Potato virus and cauliflower mosaic virus.

Discuss the significance of viruses in Research and Diagnostics.