Text

The structure of the text of this module is presented in the form

of the following flow diagram:

Discovery
and history
Nomenclature
and Glossary
classification

Origin and References

evolution

Structure and
composition Quiz
Module
Structure
Isolation
and Assignments
purification

Replication
FAQs
and
transmission

Economic Nobel laureates

importance in virology
 A historical overview of viruses

Viruses have been infecting humans as well as other

organisms for thousands of years, thereby causing millions of
deaths and inflicting huge impact on the course of human history.
These viral outbreaks and the costs associated with them have
made man conscious about them from the very early times.
However, history of the science of virology is not too ancient,
mainly because of lack of tools and techniques to deal with these
infitismally small agents untill recent past. The course of
development of this field of microbiological science witnessed
some abrupt changes. In the dynamic and rapidly progressing
field of contemporary virology, todays discovery is tomorrows
history, and it is beyond the scope of present module to present a
complete history of this discipline. While some of the pioneer and
landmark contributions are listed in this brief historical account of
viruses, many others may not find their place herein.

Discovery of viruses can not be attributed to a single person,

but to the joint contribution of a team of Dutch, German and
Russian scientists. After Louis Pasteur and Robert Koch
discovered that infectious diseases were caused by minute living
organisms or 'germs', it was expected that the germs for all
infectious diseases would be discovered. However, bacteriological
techniques failed to demonstrate the causative organisms for
many diseases like measles, small pox, rabies and mumps. It was
the Russian pathologist Ivanovsky who in 1892 used the filter
devised by Charles Chamberland in 1884 to trap smallest possible
bacteria to demonstrate that the juice from tobacco plants
infected with the 'mosaic' disease contain disease causing agent
smaller than any known bacterium, though he still considered it a
bacterium. Beijerinck (1851-1931) deserves the credit for first
realizing that contagions of tobacco mosaic differed essentially
from micro-organisms. This mosaic causing agent was later called
a virus, but untill 1930 viruses were considered as extremely
small bacteria or even enzymes or proteins. But in 1935 Stanley
purified and crystallized the virus causing tobacco mosaic
disease, and demonstrated that the crystals retain their
infectivity when inoculated into the healthy plants. He thus
showed that viruses were not like typical cells thereby openening
a debate on living and non living nature of viruses, which is as
yet unsettled for many practical purposes. Some people argue
that viruses are neither totally inert nor completely alive and may
better be regarded as active (when multiplying) or inactive (not
multiplying). Stanley for his unprecedented discovery was duly
rewarded with Noble Prize in Chemistry in 1946. Bacteriophages
(viruses that parasitise bacteria) were discovered by the French
scientist d'Herelle (1917), while noticing that some agent was
destroying his cultures of bacilli.While Schelsinger (1933) first
determined the composition of a virus and showed that a
bacteriophage consists of only protein and DNA, Hershey and
Chase (1952) studied the T2 bacteriophage and demonstrated
that (i) the genetic information is carried in the phage DNA, (ii)
infection is the result of penetration of viral DNA into cells. The
pioneering contributions by these microbiologists guided the way
forward for the recent advances in virology.

Classification of viruses

The classification of viruses is more or less problematic and

relatively less satisfactory, mainly due to their ultramicroscopic
size, presence of both living and non-living features, absence of
fossil records and lack of proper knowledge of their origin and
evolutionary history. Earlier, viruses were generally classified by
the organisms they infect, such as animal viruses, plant viruses,
or bacteriophages. While a flawless and widely acceptable
classification system of viruses is yet to emerge, recently the
International Committee on Taxonomy of Viruses (ICTV)
attempted to develop a uniform classification system and divided
viruses into 73 families, mainly on the basis of their nucleic acid
type and strandedness and presence or absence of the envelope.
The ICTV, which was established in 1966 and meets after every
four years, published its seventh report in October 2000, which is
considered as the official reference for virus taxonomy and
nomenclature and covers more than 4000 viruses, arranged by
families. The ICTV considers Family as the highest taxonomic
category and accepts Van Regenmortels (1990) definition of
virus species as a polythetic class of viruses that constitutes a
replicating lineage and occupies a particular ecological niche.

The important taxonomic criteria for classification of viruses

include:

a. Nature of the host: animal, plant, bacteria, fungi, etc.,

b. Nucleic acid characteristics: DNA or RNA, single or double
strandedness, molecular weight, segmentation and number
of pieces or segments,
c. Capsid symmetry: Icosahedral, helical, complex or binal,
d. Presence or absence of the envelope and its sensitivity,
e. Diameter of the virion or the nucleocapsid,
f. Number of capsomers in icosahedral viruses,
g. Immunological properties,
h. Intracellular location of the viral replication: cytoplasm or
nucleus,
i. Mode of transmission, and
j. The type of disease caused.

The abovementioned criteria can be categorized into:

i. Primary characteristics (such as chemical nature,

structure, site of replication), or
 ii. Secondary characteristics (such as host range, mode of
transmission, antegenecity etc.)

Origin and evolution of viruses

While the origin of viruses is still an intriguing question, the

following three major theories have been advanced to explain
their origin and evolution:
Viruses, because of simplicity of their genome, might
represent the direct descendents of the self-replicating units
(in primordial soup) from which the first cells evolved and
then coevolved with more complex life forms.
Viruses evolved from the free living organisms that invaded
other life forms and gradually lost functions, also known as
Retrogressive evolution.
Viruses are escaped nucleic acids no longer under control of
the cell. This is also known as the Escaped Gene Theory.

While all these hypotheses (Fig.1) contribute partly to our

uderstanding of viral origin, a unifying concept of their origin is
yet to emerge. It is believed that viruses have arisen and
probably continue to arise, by multiple origins. Besides, viruses
act as agents of evolution by their participation in lateral gene
transfer. Notwithstanding the debate on the origin of viruses,
their rapid evolutionary potential stems from their key attributes
including:
 Extremely small genome size
Enormous population sizes
Short generation times, and
High mutation rates.

Retrogressive
Direct
evolution due to
descendence
loss of functions
from primitive
upon invasion
self-replicating
of other life
units
forms

Escaped Gene
Theory (Escaped
nucleic acids no
longer
controlled by
cells)

Fig.1 : An integrated framework for the possible origin and

evolution of viruses.

Structure and composition of viruses

Viruses lack cellular organization and do not possess plasma

membranes, cytoplasm with ribosomes and enzymes necessary
for protein synthesis and energy production. Viruses range in size
from as large as 250 nm (e.g. Poxviruses) to as small as 20 nm
(e.g. Parvoviruses). Thus, on the lower side they have the same
diameter as a DNA molecule, on the higher side they are of the
size of of the smallest bacteria, such as Chlamydeae and
Mycoplasmas.

All viruses consist of two two basic components:

i. A core of nucleic acid- the genome, and

ii. A surrounding coat of protein- the capsid.

Genome and capsid together comprise the nucleocapsid or

genocapsid. However, many viruses possess a typical
lipoprotenaceous bimembrane outside their capsids and are
known as enveloped viruses.

Viral Genome

Viral genome, unlike genomes of rest of the life forms,

contains either DNA or RNA, but never both. As in cells, the
nucleic acid of each virus encodes the genetic information for the
synthesis of important viral proteins. The nucleic acids may be
double-stranded or single-stranded. In fact, viruses are
exceptionally flexible with respect to the nature of their genetic
matrerial, and employ all the four possible nucleic acid types:
 i. Single stranded DNA (ssDNA), e.g. Parvoviruses, M13
bacteriophages
ii. Double stranded DNA (dsDNA), e.g. Lambda phages
iii. Single stranded RNA (ss RNA), e.g. TMV, Brome mosaic
virus
iv. Double stranded RNA (ds RNA), e.g. Retroviruses.

While plant viruses are largely ssRNA viruses, all the above
four types of nucleic acid types are found in animal viruses.
However, three types of plant viruses, namely Geminiviruses,
Badnaviruses and Caulimoviruses, have DNA as their genetic
material. There are two types of RNA-based viruses. In most, the
genomic RNA is termed a plus (+) strand because it acts as
messenger RNA for direct synthesis (translation) of viral protein.
A few, however, have negative (-) of RNA. In these cases, the
virion has an enzyme, called RNA-dependent RNA polymerase
(transcriptase), which must first catalyze the production of
complementary messenger RNA from the virion genomic RNA,
before viral protein synthesis can occur.

Not only the type, but also the size of genome, in viruses
varies greatly. While the smallest genome of the order of 1X106
Daltons (e.g. MS2 and QB viruses) can code for just 3 to 4
protiens only, the largest genomes of the size of 1.0 to 1.6 X 108
Dalton (e.g. Herpesvirus and Vaccinia virus) is large enough to
direct the synthesis of over 100 proteins. In shape also the viral
nucleic acids may vary from linear through circular to segmented
or fragmented. Due to the advances in molecular biology
techniques, the entire nucleic acid sequences have recently been
determined in hundreds of viruses. These molecular comparisons
have shown considerable similraity in viruses infecting apparently
different hosts.

Capsid

Capsid is a proteinaceous coat, or shell-like covering, of

nucleic acids in viruses. This shell is composed of protein
organized in subunits known as capsomers. The number of
capsomers is species specific and is used as a taxonomic
character. It is closely associated with the nucleic acid and reflect
its configuration, either a rod-shaped helix or a polygon-shaped
sphere. Under the appropriate conditions, viral RNA in a liquid
suspension of protein molecules will self-assemble a capsid to
become a functional and infectious virus. The important functions
of the capsids include:

Protection of the viral genome,

Determining shape of the viruses, and
Facilitation of attachment and penetration of viruses into
the host.
Envelope

Envelope is a membraneous covering found on some virus

capsids that allow the virus to enter a host cell by fusing with its
cell membrane. Surrounding nucleocapsids, many viruses have a
typical bimembrane, composed of glycolipids and protiens, and
are referred to as enveloped (Fig.2). Viruses lacking such
envelopes are referred to as naked or non-enveloped. The
envelope is predominatly acquired from the host cells during the
replication process and is unique to each type of viruses. While
the lipids and carbohydrates are normal host constituants,
envelope protiens are usually coded by viral genes. These viral
coded proteins project as spikes, known as peplomers, which, in
combination with glycogen moities, determine viral host
specificity. The main adventages of having envelopes in viruses
include:

i. Prevention from attack by hosts immune system because

envelopes are acquired from and are therefore similar to
host cell membranes.
ii. Facilitation of infecting new cells through membrane
fusion with host cell membrane.

Enveloped viruses, damaged easily in comparison to naked

viruses, because the membranes are destroyed easily by the
harsh environmental factors, such as increased temperatures,
freezing and thawing, highly acidic or alkaline conditions, or other
chemical disinfectants.

Fig. 2. HIV virus with its lipid envelope

Morphological types of viruses

While the ultrastructural details of viruses remained unclear for

a long period of time after their discovery, mainly due to lack of
proper techniques, the advent and use of electron microscopy, X-
ray differaction, biochemical analysis and immunological
techniques have provided useful insights into their structure and
composition. Viruses are broadly classified into the following
morphological types:

i. Icosahedral,
ii. Helical,
iii. Enveloped and
iv. Complex.

Icosahedral

In view of the exceptionally small genome size of viruses,

efficient ways of enclosing and encoding maximum information in
minimum space of this small genome is inevitable. Icosahedron is
one of the natures most favourite shapes to accomplish this in
case of viruses. The sphere shaped virus is actually a 20-sided
polygon (icosahedron). A typical icosahedron is a polyhedron with
12 vertices in 20 equilateral triangles as faces (Fig. 3). The
capsomers in the capsids of icosahedral viruses are composed of
protomers with 5 (pentamers) or 6 (hexamers) subunits. While
pentamers are found on the vertices of the icosahedron,
hexamers form the edges of its triangular faces. Most icosahedral
capsids apparently contain both pentamers and hexamers, except
in Simian virus 40 (SV 40), a small dsDNA virus, which has only
pentamers. The examples of icosahedral viruses include
Adenoviruses, Polioviruses and Canine Parvoviruses.
 Fig. 3. Icosahedron

Helical

Helical viruses are the rod shaped, long, hollow cylinders

with linear array of the nucleic acid and the protein subunits
making up the capsid. In such viruses, e.g. TMV, the protein
subunits are arranged in helical spiral with genome fitted into a
groove on the inner portion of the protein. The helical viruses are
narrow (15-20nm) and may be quite long (300-400nm). They
may be very rigid (e.g. TMV) or flexible (e.g. Influenza virus)
depending upon the nature of the constituant proteins. The size
of the helical capsid is influenced by both its protomers and the
nucleic acid enclosed within the capsid.
 Fig.4. Helical virus

Complex viruses

These are the viruses that are assembed from parts that are
synthesised separately (head, tail, capsomer), and do fit neither
in icosahedral nor in helical capsid symmetry, but have
complicated morphology. The Poxviruses and large
bacteriophages are two important examples. Complex bacterial
viruses with both head and tail are said to have binal symmetry,
because they possess a combination of icosahedral (the head)
and helical (the tail) symmetry.
 Viral replication

Viral replication refers to the means by which virus particles

make new copies of themselves. Viruses replicate by infecting the
host cells and overtaking their synthetic capabilities to produce
more viruses. The newly formed virions may leave the host cell
either without causing any damage to the host cells (Lysogenic
cycle) or sometimes killing them in the process (Lytic cycle).
 Fig.6. Lytic
and lysogenic cycles of viral replication.

Although precise mechanisms of viral replication may vary,

viruses of animals, plants and bacteria exhibit essentially similar
sequence of major events in the process of replication. Viral
replication can be principally divided into several stages as
follows:

1. Adsorption

Adsorption is the first step in viral replication, which

generally takes place through rendom collision of virion
particles with host cell surfaces. Distribution of specific
receptor proteins on the host cell membrane plays a crucial
role in dtermining the host-specificity of viruses. Attachment is
via ionic interactions, which are temperature-independent. The
viral attachment protein recognizes specific receptors, which
may be protein, carbohydrate or lipid, outside of the cell. Cells
without appropriate receptors are not susceptible to viruses.
Bacteriophages and animal viruses have attachment sites
facilitating them to attach to complementry receptor sites on
host cell surfaces. However, unlike bacteriophages which have
tails as attachment sites, in animal viruses the receptor sites
are distributed over th entire capsid surface.

2. Penetration and uncoating

Depending upon presence or absence of the envelope,

viruses enter the cell in a variety of ways according to their
nature. In enveloped viruses entry may be:

i. by fusing with the plasma membrane. Some enveloped

viruses fuse directly with the plasma membrane. Thus, the
internal components of the virion are immediately delivered to
the cytoplasm of the cell, or

ii. through endosomes at the cell surface.

 Some enveloped viruses require an acid pH for fusion to occur
and are unable to fuse directly with the plasma membrane. These
viruses are taken up by invagination of the membrane into
endosomes. As the endosomes become acidified, the latent fusion
activity of the virus proteins becomes activated by the fall in pH
and the virion membrane fuses with the endosome membrane.
This results in delivery of the internal components of the virus to
the cytoplasm of the cell.

The non-enveloped viruses may cross the plasma membrane

directly or may be taken up into endosomes. They then cross (or
destroy) the endosomal membrane.

Uncoating

The process in which protein coats of animal viruses that

have entered cells, are removed by proteolytic enzymes, is called
uncoating. Nucleic acid has to be sufficiently uncoated so that
virus replication can begin at this stage. When the nucleic acid is
uncoated, infectious virus particles cannot be recovered from
the cell. There is an ECLIPSE phase which lasts until new
infectious virions are made.

3. Synthesis of viral nucleic acids and protein

Many strategies are used by viruses for synthesising

nucleic acids and proteins, and many variations occur between
DNA viruses and RNA viruses. While DNA replication usually
occurs in the host cell nucleus, Pox viruses are an exception,
where it takes place in the cytoplasm. RNA viruses replicate their
nucleic acid by a greater variety of ways than DNA viruses on the
basis of which they have been categorized into four classes. A
detailed description of these mechanisms is beyond the scope of
present module. All proteins in a mature virus particle are said to
be structural proteins - even if they make no contribution to the
morphology or rigidity of the virion - non-structural proteins are
those viral proteins found in the cell but not packaged into the
virion.

4. Assembly/maturation

Once abundant viral genomes, enzymes and other proteins

have been synthesised, assembly of these components in the
complete virions starts. This process, in which new virus
particles are assembled, constitutes maturartion. There may
be a maturation step that follows the initial assembly process.

5. Release

Mechanism of virus release differ between naked

and enveloped vruses. Virus may be released due to cell lysis,
or, if enveloped, may bud from the cell. Budding viruses do
not necessarily kill the cell. Thus, some budding viruses may
 be able to set up persistent infections. Not all released viral
particles are infectious. The ratio of non-infectious to infectious
particles varies with the virus and the growth conditions.

Transmission of viruses

Transmission refers to the transfer of viruses from one host to

the other through different carriers or agencies. Since viruses are
inactive outside their hosts, they must undergo passive transfer
from one plant to the other. They transmit either by direct
contact with infected individuals, carriers or plants or indirect
contact with inanimate objects such as contaminated food and
water, etc. Most common ways and means of viral transmission in
plants include:
i. Mechanical transmission (natural or artificial),
ii. By grafting,
iii. With dodder,
iv. Through plant propagules,
v. Via insects and mites, and
vi. Through soil inhabiting organisms.

Isolation and purification of viruses

Isolation of viruses from their hosts and subsequent

purification assume pivotal significance for understanding their
physico-chemical nature, composition, replication and mode of
penetration. Isolation techniques, however, depend on several
viral characteristics, such as:
i. Larger size of viruses relative to proteins,
ii. More stability than normal host cell components, and
iii. Presence of surface proteins.

Various techniques employed for virus isolation and

purification include:
a. Centrifugation (differential and density gradient)
b. Precipitation
c. Denaturation
d. Enzymatic digestion
e. Filtration
f. Electrophoresis
g. Chromatography

After successful isolation, the objective of purification is high

yield of viruses with lowest amount of contaminants and with
highest degree of purity or integrity and infectivity. Purification
usually requires repetition of above techniques at different
intensities for different periods.

Economic importance of viruses

Well over 2,000 kinds of plant diseases are known to be

caused by more than 600 different kinds of identified plant
viruses. Viral diseases greatly reduce the productivity of many
kinds of agricultural and horticultural crops. Worldwide losses due
to viral diseases are estimated at about $15 billion annually.
Besides, more than 400 different viruses can infect humans,
thereby causing myriad of diseases with no or just prophylactic or
supportive treatment, except in a few cases. Most common
human diseases caused by viruses include pox, hum, polio,
influenza and AIDS. The commonly occuring viral diseases in
cattle iclude, foot and mouth disease of cow, sheep, goat, and
buffalo.
Losses incured by viruses may be:
a. Biological (Damage inflicted upon the organism)
b. Economic (What finally counts through reduced production)
The losses are estimated in terms of reduction in growth,
vitality, quality and the market value of the organisms infected.
Three parameters that may be considered as quantitative
indicators for assesment of losses include:
i. Disease incidence,
ii. Disease severity, and
iii. Duration of infection.

Beneficial aspects of viruses

 While viruses are generally considered harmful for the
reasons stated above, yet some viruses can play positive role in
human welfare, such as:

i) Different vaccines, like small pox, jaundice etc. vaccines are

produced from viruses.

ii) Viruses comprise the significant experimental models and tools

for scientific studies in molecular biology and genetic engineering.

iii) Variegated foliage of some plants, especially ornamentals,

caused by viruses has aesthetic appeal.

Viroids

Infectious RNA molecules that function independently

without encapsidation by any protein coat are called as viroids.
Their discovery was made by a team of scientists led by
T.O.Diener (1971) of USDA who found that nothing destroyed the
Potato Spindle Tuber Disease Causing Agent (PSTV) except the
RNAase, the RNA degrading enzymes. Thus, viroids are very
different from viruses and each viroid is solely a small RNA
molecule. Subsequently it was established that RNA is the
causative agent for PSTV and currently more than a dozen of
plant diseases are known to be caused by viroids.They are said to
cause many plant diseases and are also referred to as subviral
pathogens. Viroids cause plant diseases by interfering with mRNA
processing.
 Prions

Proteinaceous infectious particles are called as prions.

Research indicates that prions are normal proteins that become
folded incorrectly. Prions cause neurological degenerative
diseases, including Creutzfeldt-Jakob disease, kuru, scrapie and
Mad Cow disease by an entirely novel mechanism. However, the
best studied prions are the ones that cause degenerative
disorders of the central nervous system (called as scrapie) in
sheep and goat. Named by Stanley Prusiner, prions are suceptible
to protein-digesting enzymes, but not to the nucleases. Prions
provide the only example were genetic information flows from
proteins to nucleic acids, and not the otherway round. While
knowledge about prions has profound implications for studies of
the structural plasticity of proteins, investigations of prion
diseases suggest that new strategies for the prevention and
treatment of these disorders may also find application in the
more common degenerative diseases.

Virusoids
Virusoids are circular single-stranded RNAs dependent
on plant viruses for replication and encapsidation. The genome of
virusoids consist of several hundred nucleotides, and it only
encodes structural proteins. Virusoids are similar to viroids in
size, structure and means of replication (rolling-circle replication).
They, while being studied in virology, are not considered as
viruses but as subviral particles. Since they depend on helper
viruses, they are classified as satellites. The term virusoid is also
sometimes used more generally to refer to all the satellites.
Virusoid genomes are 220 to 388 nucleotides long and do
not code for any proteins, but instead serve only to replicate
themselves. Virusoids can replicate in the cytoplasm and possess
ribozyme activity. RNA replication is similar to that of viroids, but
each requires that the cell be infected with a specific "helper"
virus. Five virusoids are known, and the helper viruses for these
are all members of the Sobemovirus family. An example of a
"helper" virus is the subterranean clover mottle virus, which has
an associated virusoid. Virus enzymes may aid replication of the
virusoid RNA. The virusoid is incorporated into the virus particle
and transmitted as a "satellite," a separate nucleic acid not part
of the viral chromosome. Replication of the helper virus is
independent of the virusoid.
 Noble prizes awarded in virology

Year Prize Topic Studied

of Winner(s)
Prize

1946 Stainley Crystallization of

viruses
1951 Theiler Vaccine for yellow
fever
1954 Enders, Weller Cultivation of poli
& Robbins virus

1966 Rous Viruses and cancer

1969 Delbruck, Mechanism of virus

Harshey & Luria infection in living cells

1975 Baltimore, Interaction between

Temin & tumour viruses and
Dulbecco genetic material of
 the cell

1996 Doherry & Recognition of virus

Zinkernagel infected cells by
immune defenses

1997 Stanley Prions

Prusiner
2008 Human papilloma
Harald zur viruses causing
Hausen cervical cancer

Franoise Human
Barr-Sinoussi immunodeficiency
and Luc virus
Montagnier