Virus

•Viruses are infectious pathogens that are too small to be seen

with a light microscope, despite of their small size they can
cause chaos.
•Viruses consist of genetic material—either deoxyribonucleic
acid (DNA) or ribonucleic acid (RNA)—surrounded by a
protective coating of protein, called a capsid, with or without
an outer lipid envelope. As is the case with other organisms,
viruses carry genetic information in their nucleic acid which
typically specifies three or more proteins.
•All viruses are obligate parasites that depend on the cellular
machinery of their hosts to reproduce.
•Viruses are not active outside of their hosts, and this has led
some people to suggest that they are not alive.
 Virus
• All types of living organisms including animals,
plants, fungi, and bacteria are hosts for viruses,
but most viruses infect only one type of host.
• Viruses cause many important plant diseases and
are responsible for losses in crop yield and
quality in all parts of the world.

• The study of viruses is called virology.

Virus classification (Systematic position)
A universal system for classifying viruses, and a unified taxonomy, has been
established by the International Committee on Taxonomy of Viruses (ICTV) in
early 1990s .
The ICTV system shares many features with the system used for classifying
cellular organisms.
Viruses are generally classified by the organisms they infect, animals, plants,
or bacteria.
There are several differences however; the classification of cellular organisms
starts with the Kingdom, while viruses start with Order.
The systemic position of viral taxa is therefore:

Order- Virales
Family- Viridae
Superfamily-Virinae
Genus- Virus
Species- tobacco mosaic virus
 Virus classification
• The names of like all taxonomic groups - orders, families,
subfamilies, genera - are written in italics with the first letter
capitalised. Species names are italicised and have the first
letter of the first word capitalized, but virus names are not .
• The names of orders must be single word end with the
suffix -virales.
• A family name must be a single word end with the suffix -
viridae
• A Sub-family name must be a single word end with the
suffix - virinae.
• A genus name must be a single word ending in ...virus.
• Virus and virus taxon nomenclature are not based on
proposed International Code of Bionomenclature(BioCode).
 Virus classification
• Currently, 5 orders, 84 families and 2,083 species of virus
have been defined and many families have not yet been
classified into orders. 5orders are Caudovirales,
Herpesvirales, Mononegavirales, Nidovirales,
Picornavirales.
• Today, the primary criteria used to differentiate virus
orders, families, and genera are as follows:
• The type and organization of the viral genome
• the strategy of viral replication
• the structure of the virion
 Virus classification
• Classification by genome type :- seven groups are:-
• DNA viruses:-
• Group I - dsDNA viruses (double stranded DNA)such as the herpes
virus and the chickenpox virus.
• Group II - ssDNA viruses (single stranded DNA)viruses such as the
parvo virus. RNA viruses:-
• Group III, - dsRNA viruses (double stranded RNA)
• Group IV, - (+)ssRNA viruses (positive single stranded RNA or
mRNA like) such as the Sars virus, the yellow fever virus and many
other well known viruses
• Group V - (-)ssRNA viruses (negative single-stranded RNA) such
as the measles virus, the mumps virus and the rabies virus. DNA and
RNA Reverse Transcribing viruses:-
 Shape of viruses
• There are mainly two types of shapes found amongst
viruses: rods, or filaments, and spheres. The rod shape is
due to the linear array of the nucleic acid and the protein
subunits making up the capsid. The sphere shape is actually
a 20-sided polygon (icosahedron).
• Filamentous (tubular); e.g., tobacco mosaic virus
• Polyhedral (roughly spherical); e.g., adenovirus (causes
respiratory infections, different than rhinovirus which
causes colds)
• Combined (polyhedral head attached to a filamentous tail);
e.g., E. coli bacteriophage T4.
 Virus classification
• Group VI - ssRNA-RT viruses (single stranded RNA)such
as HIV
• Group VII - dsDNA-RT viruses (double stranded DNA)
such as the hepatitis B virus.
• The Group VI viruses use the enzyme to reverse-transcribe
their RNA into DNA and then insert the transcribed DNA
into the host organism's DNA, where it is replicated
whenever a cell divides.
• The Group VII viruses transcribe their DNA into an RNA
form, then transcribe the RNA back into DNA to be inserted
into the host's DNA and replicated.
 Morphology of Virus
The protein shells of plant viruses (capsids)
are assembled in accord with one of the two
fundamental types of symmetry.

The first type of virion is helical (roughly

elongated). The elongated viruses come in Figure 1
two major variants, rigid rods (Figure 1)
and flexuous filaments (Figure 2).

In both of these variants, the nucleic acid is

highly ordered.
(Figure 2).
It assumes the same helical conformation as the
proteinaceous capsid.
 Morphology of Virus
The second type of virus particle is icosahedral
(roughly spherical; Figure 3).
Figure 3
The variations of this basic shape include
bacilliform virions (Figure 4) and twin virions
composed of two joined incomplete icosahedra
(Figure 5).
In the icosahedral virions, the genomic nucleic acid Figure 4
forms a partially ordered ball inside the
proteinaceous capsid. The icosahedral and
elongated virions alike can self-assemble in a test
tube if the nucleic acid and protein subunits are
incubated under proper conditions.

Figure 5
 Size of Virus
• Usually, the size of viruses ranges from 20-300(or 350
nm).The smallest virus is Coliphage F2 measuring about 2
nm.

• The longest known plant virus is Citus Tristeza virus - rod

shapes measuring 2000 X 12 nm.

• The smallest plant virus is satellite tobacco necrosis virus

measuring 17 nm which can replicate in the host cell only if
Tobbacco necrosis virus is also present.
 Reproduction
• Although the genetic material for most organisms is double-stranded
(ds) DNA, only a minority of plant viruses possess dsDNA genomes.

• Some of the plant viruses have genomes that are composed of single-
stranded (ss) DNA. However, the majority of plant viruses do not use
DNA at all. Instead, the genomes of nearly all plant viruses are made
of RNA. Most of these genomes are composed of ssRNA that is the
same (positive-sense) polarity as the messenger RNAs of the cell.
Some of the RNA viruses use ssRNAs of negative polarity, and yet
others have genomes made of dsRNA.

• Due to this enormous variation in the very nature of the genetic

material of viruses, the reproductive cycles and life styles of different
viruses are often very distinct from each other.
 Reproduction
• Plant viruses are obligate, biotrophic parasites, their life cycles start by
penetration of the virion into the cell.
• Plant viruses are unable to penetrate the plant cuticle and cell wall. It is
believed that the virion enters the cytoplasm of the cell passively
through wounds caused by mechanical damage to the cuticle and cell
wall.
• Partial or complete removal of the coat protein shell of the virion in the
cytoplasm. Expression of the viral genome by providing a transcription
apparatus (for DNA viruses) and a translation apparatus (for all
viruses).
• The DNA viruses must be transported to the nucleus for transcription in
order to gain access to the cell proteins required for the production of
messenger RNA from viral DNA. Translation of viral RNA in the
cytoplasm produces viral proteins that are required for completion of
the virus life cycle.
 Reproduction
• All viruses must direct the formation of at least three types of
proteins:
a) Replication proteins that are essential for nucleic acid production,
b) Structural proteins that form the protein shell and other components
contained in the virions.
c) Movement proteins that mediate virus transport between plant cells
• The viral replication proteins combine with cellular proteins to
produce a complex of proteins that manufactures multiple copies of
the virus genome.
• (Follow the hand for diagram)
• Depending on the virus, the viral genomes or the virions are
transported into neighboring cells through small channels called
plasmodesmata that form connections between cells. Many viruses
produce movement proteins that modify the plasmodesmata channels
and facilitate viral movement into neighboring cells.
 Survival and Dissemination
• Few viruses, such as TMV, rely on long-term (up to decades) survival
in the environment and on passive mechanical transmission from
plant to plant.
• Most plant viruses are actively transmitted from infected to healthy
plants by a living organism called a vector.
• Plant-feeding arthropods, nematodes and plant-parasitic fungi are the
major types of vector organisms for plant viruses.
• Among these, aphids and whiteflies are capable of transmitting the
largest number of virus species.
• Most viruses are actively transmitted to healthy plants in a matter of
seconds, hours, or days by vectors.
• In addition, some viruses are transmitted from infected plants when
these plants are vegetatively propagated, for example, through tubers
or grafting, or ‘vertically’ through seeds or pollen from infected
plants. This type of transmission is particularly important for virus
survival during the winter
 Survival and Dissemination
• Transmission of viruses by a vector is a very specific process. Each
particular virus can be transmitted by only one vector type (e.g.,
aphid), and not by another (e.g., whitefly).
• Each vector species (e.g., green peach aphid Myzus persicae), can
transmit some viruses (e.g., Beet yellows virus) but not others (e.g.,
Citrus tristeza virus), despite the fact that these viruses are genetically
very similar to each other.
• Relationships between viruses and their vectors are complex and of
considerable interest to plant virologists because vectors provide the
main method of spread for many viruses that cause severe economic
losses. For some virus/vector combinations, the interaction between a
virus and its vector is very superficial and is the result of attachment
to the external surfaces of the vector mouthparts. For example, viruses
in the Potyvirus genus produce a special protein called helper
component that “glues” the virions to aphid stylets.
 Survival and Dissemination
• In this case, acquisition of the virus from infected plants and
inoculation of virus to healthy plants takes from seconds to minutes.
• In contrast, viruses in the family Luteoviridae circulate in their aphid
vector moving through the gut wall, into the body cavity, and then
into the saliva of the aphid (Figure 11).
• It takes at least 12 hours for these viruses to circulate in their aphid
vector before they can be transmitted to another plant.
• For other plant virus vectors, the relationship is very intimate and the
viruses actually multiply in the cells of their insect vectors.
• For example, Tomato spotted wilt virus multiplies in cells of its thrips
vector, and once thrips acquire this virus, they can transmit it for the
rest of their life.
 Survival and Dissemination
• Such viruses that multiply in their insect vectors are considered to be
both plant and insect viruses. Because management practices for plant
diseases are often directed at the virus vectors, an understanding of
the virus transmission process is critical for development of effective
management strategies for diseases caused by plant viruses
 Diagnosis of Plant Virus Diseases
• Different viruses may elicit similar symptoms therefore disease
phenotype can provide only limited, although important, information
for disease diagnosis. More specific and reliable methods of virus
identification are based on various properties of the virus.
1. Pathogenicity: Bioassays using indicator plants. Some plant genera,
such as Nicotiana (tobacco) and Chenopodium (lambsquarters) are
hosts for a number of viruses. Since the responses of these plants to
viral infections under greenhouse conditions are consistent and
distinctive, they are commonly used as indicator plants. Two major
types of responses are local lesions, which are confined to inoculated
leaves (local lesion hosts), and systemic infections which produce
symptoms on leaves distant from the inoculation site (systemic hosts).
Many plant viruses are transmissible to indicator plants by means of
mechanical transmission or grafting.
 Diagnosis of Plant Virus Diseases
• Transmissibility – Vector transmission assays. Because of vector
specificity, identification of the organism that transmits the virus may
provide important information for virus identification.
• Architecture of virus particles – Electron microscopy. The shape and
size of virions distinguish rod-shaped, filamentous, icosahedral, or
large enveloped particles.
• Presence of virus-specific structures in infected cells – Electron
microscopy. Because of their intimate association with components of
the cell, viruses often form unusual structures within plant cells as a
result of virus infection. For example, viruses in the family Potyviridae
produce ‘pinwheel’ inclusions that are characteristic of viruses in this
family and are not found in healthy cells or cells infected with other
viruses.
 Diagnosis of Plant Virus Diseases
• Properties of the protein coat – Immunological procedures. These
tests rely on identification of a virus (the antigen) through its reaction
with specific antibodies. One of the most widely used diagnostic tests
for plant viruses is an antibody-based procedure called the Enzyme-
Linked Immunosorbent Assay (ELISA) which is by far the most
widely used immunological technique for virus identification.

• Properties of viral nucleic acid – PCR amplification. Polymerase

Chain Reaction (PCR) is a very sensitive and specific technique for
virus detection that is based on the presence of unique nucleic acid
sequences in the genome of a virus. The viral DNA sequence that a
researcher wants to amplify undergoes about thirty cycles of copying
in a small test tubes
 Management of Plant Virus Diseases
• Although there are virtually no antiviral compounds available to cure
plants with viral diseases, efficient control measures can greatly
mitigate or prevent disease from occurring.
• Virus identification is a mandatory first step in the management of a
disease caused by a virus.
• The subsequent strategy for management will depend on the means by
which a particular virus enters a crop, how the virus is transmitted
between plants within a crop, and how the virus survives when the
crop is not being grown.
• Preventative measures may include use of certified virus-free seed or
vegetative stocks, elimination of the virus reservoirs in the
surrounding wild vegetation, and modification of planting and
harvesting practices.
• If the virus is known to be transmitted by a particular vector, control
or avoidance of this vector is of paramount importance.
 Management of Plant Virus Diseases
• Alternative strategy for virus control is utilization of natural or
engineered resistance to virus infection.
• If available, natural virus resistance genes can be introduced into crop
cultivars by conventional breeding. These natural resistance genes are
often found among the many cultivars that are available for a
particular crop, or the resistance genes are found in related plants that
have been identified near the centre of origin for that crop plant.
• Genetic engineering, the transfer of genes between specific organisms
using enzymes and laboratory techniques rather than biological
hybridization, allows cross-species introduction of such genes.
Furthermore, virus resistance can be designed by pre-setting the plant
RNA silencing defense system. This is achieved by introduction of
fragments of viral nucleic acid into the plant chromosomes. Such
transgenic resistance confers immunity to infection by the virus from
which the nucleic acid was derived.