Tobacco Mosaic Virus

Introduction:
Tobacco mosaic virus ( TMV ) is a positive-sense single stranded RNA virus,
genus tobamovirus that infects a wide range of plants, especially tobacco and other
members of the family Solanaceae . The infection causes characteristic patterns,
such as " mosaic "-like mottling and discoloration on the leaves (hence the name).
TMV was the first virus ever to be discovered. Although it was known from the late
19th century that an infectious disease was damaging tobacco crops, it was not until
1930 that the infectious agent was determined to be a virus. It is the first pathogen
identified as a virus.

Classification:
Group: Group IV ( (+)ssRNA )
Order: Unassigned
Family: Virgaviridae
Genus: Tobamovirus
Species: Tobacco mosaic virus

Structure:

Schematic model of TMV: 1. nucleic acid(RNA), 2. capsomer protein

(protomer)3. capsid
Tobacco mosaic virus has a rod-like appearance. Its capsid is made from 2130
molecules of coat protein (see image to the left).The coat protein self-assembles into
the rod-like helical structure (16.3 proteins per helix turn) around the RNA, which
forms a hairpin loop structure (see the electron micrograph above). The protein
monomer consists of 158 amino acids which are assembled into four main alpha-
helices, which are joined by a prominent loop proximal to the axis of the virion.
Virions are ~300 nm in length and ~18 nm in diameter.Negatively stained electron
microphotographs show a distinct inner channel of ~4 nm. The RNA is located at a
radius of ~6 nm and is protected from the action of cellular enzymes by the coat
protein. There are three RNA nucleotides per protein monomer.X-ray fiber diffraction
structure of the intact virus was studied based on an electron density map at 3.6 Å
resolution.Inside the core helix, coiled RNA molecule is present, which is made up of
nearly 6500 nucleotides.

Genome:
The TMV genome consists of a 6.3-6.5 kb single-stranded (ss) RNA . The 3’-
terminus has a tRNA-like structure, and the 5’ terminus has a methylated nucleotide
cap. (m7G5’pppG). The genome encodes 4 open reading frames (ORFs), two of
which produce a single protein due to ribosomal readthrough of a leaky UAG stop
codon . The 4 genes encode a replicase (with methyltransferase [MT] and RNA
helicase [Hel] domains), an RNA-dependent RNA polymerase a so-called movement
protein (MP) and a capsid protein (CP).

Disease cycle:
TMV does not have a distinct overwintering structure. Rather, it will over-
winter in infected tobacco stalks and leaves in the soil, on the surface of
contaminated seed (TMV can even survive in contaminated tobacco products for
many years). With the direct contact with host plants through its vectors (normally
insects such as aphids and leafhoppers), TMV will go through the infection process
and then the replication process.

Infection and Transmission:

After its multiplication, it enters the neighboring cells through plasmodesmata
. The infection spreads by direct contact to the neighboring cells, For its smooth
entry, TMV produces a 30 k Da movement protein called P30 which enlarges the
plasmodesmata. TMV most likely moves from cell-to-cell as a complex of the RNA,
P30, and replicate proteins.It can also spread through phloem for longer distance
movement within the plant. Moreover, TMV can be transmitted from one plant to
another by direct contact. Although TMV does not have defined transmission
vectors, the virus can be easily transmitted from the infected hosts to the healthy
plants, by human handling.

Replication:
Following entry into its host via mechanical inoculation, TMV uncoats itself to
release its viral [+]RNA strand. As uncoating occurs, the MetHel:Pol gene is
translated to make the capping enzyme MetHel and the RNA Polymerase. Then the
viral genome will further replicate to produce multiple mRNAs via a [-]RNA
intermediate primed by the tRNAHIS at the [+]RNA 3' end. The resulting mRNAs
encode several proteins, including the coat protein and an RNA-dependent RNA
polymerase (RdRp), as well as the movement protein. Thus TMV can replicate its
own genome. After the coat protein and RNA genome of TMV have been
synthesized, they spontaneously assemble into complete TMV virions in a highly
organized process. The protomers come together to form disks or 'lockwashers'
composed of two layers of protomers arranged in a helix. The helical capsid grows
by the addition of protomers to the end of the rod.As the rod lengthens, the RNA
passes through a channel in its center and forms a loop at the growing end. In this
way the RNA can easily fit as a spiral into the interior of the helical capsid.

Sign and Symptoms:

Tobacco mosaic virus symptoms on Tobacco mosaic virus

tobacco symptoms on orchid
 The first symptom of this virus disease is a light green coloration between the
veins of young leaves. This is followed quickly by the development of a "mosaic" or
mottled pattern of light and dark green areas in the leaves. Rugosity may also be
seen where the infected plant leaves display small localized random wrinkles. These
symptoms develop quickly and are more pronounced on younger leaves. Its Lower
leaves are subjected to "mosaic burn" especially during periods of hot and dry
weather. In these cases, large dead areas develop in the leaves.Infected leaves may
be crinkled, puckered, or elongated.

Treatment and Management:

One of the common control methods for TMV is sanitation, which includes
removing infected plants and washing hands in between each planting. Crop rotation
should also be employed to avoid infected soil/seed beds for at least two years. As
for any plant disease, looking for resistant strains against TMV may also be advised.
Furthermore, the cross protection method can be administered, where the stronger
strain of TMV infection is inhibited by infecting the host plant with mild strain of TMV,
similar to the effect of a vaccine.The application of genetic engineering on a host
plant genome has been developed to allow the host plant to produce the TMV coat
protein within their cells. It was hypothesized that the TMV genome will be re-coated
rapidly upon entering the host cell, thus it prevents the initiation of TMV replication.
Later it was found that the mechanism that protects the host from viral genome
insertion is through gene silencing.

Cotton Leaf Curl Geminivirus

Introduction:
Cotton leaf curl virus (CLCuV) is a plant pathogenic virus of the
family Geminiviridae.In Asia and Africa the major disease of cotton is caused by the
Cotton leaf curl geminivirus (CLCuV). Leaves of infected cotton curl upward and bear
leaf-like enations on the underside along with vein thickening. Plants infected early in
the season are stunted and yield is reduced drastically. (A. Nadeem and Z. Xiong,
University of Arizona) This virus devastated the Pakistan cotton industry in early
1990s where it caused an estimated yield reduction of 30-35%.
Classification:
Group
Group: II (ssDNA)

Family: Geminiviridae

Genus: Begomovirus

Species: Cotton leaf

curl virus

Structure:

Non-enveloped, about 38 nm in length and 22 nm in diameter (for MSV),

twinned (geminate) incomplete T=1 icosahedral symmetry capsid that contains 22
pentameric capsomers made of 110 capsid proteins (CP). Each geminate particle
contains only a single circular ssDNA.

Genome:
All begomovirus species causing cotton leaf curl disease have geminate
particles, approximately 18-20 nm in diameter and 30 nm long and a circular, single-
stranded DNA genome. All except Cotton leaf crumple virus have a monopartite
genome, with all viral products required for replication, systemic movement and
whitefly transmission encoded on a single DNA component of c. 2.75 kB (DNA A).
The genome of CLCrV is bipartite. Two smaller, circular, single-stranded DNA
molecules, named DNA 1 and DNA β, are associated with a range of monopartite
begomoviruses from the Old World including the cotton leaf curl viruses.
Symptoms:

Upward carling Vein thickening Downward carling

Cotton leave’s downward curling, their cup like structure formation

called enations and swollen veins of leaves are few of the symptoms
regarding CLCuD (Figure 1-4). Two types of thickenings of veins are observed
on cotton plant; i) Major vein’s thickening ii) Minor vein’s thickening. Initaly the
thickening is at leaf margins but with the increase in disease intensity it
extends inward and form thickened veins network (Watkins, 1981). Young
leaf’s fine veins thickens and turn pale this depicts presence of minor type of
vein thickening (Nour and Nour, 1964), Chloroplast deposited tissues get
proliferated thus CLCuV effected genotypes appear darker than normal one’s.
(Sattar et al., 2013).

Effects of CLCuV on Cotton Plant:

CLCuV has devastating Effects on the growth of cotton plant. It
causes Reduction in Plant height (40.6%), Boll weight (33.8%) ginning outturn
3.9% and number of bolls(72.5%) per plant of Cotton (Mahmood et al .,1996).
A savior decrease in staple length, up to 3.44%, staple strength up to 10% and
staple elongation %age occurs due to CLCuV (Ahmed .,1999).It has devastating
effects on yield as yield is reduced at great extent. In 1991_1992 cotton production
of Pakistan were maximum 12.4 million bales (MB) but in 1994 due to CLCuV cotton
production reduced to 7.9 million bales from 12.4 million bales (Mahmood et
al.2013). After it highly tolerant/resistant varieties against this disease got developed.
CLCuV disease loses were minimized while cotton yield was also maintained
between 8-11.5 MB.

Way of Transmission:
Geminivirus are 2700–3000 nt weighing 1 or more components of
single stranded circular DNA containing organisms which are usually
transported through insect pest. (Moffat, 1999). Gemini viruses damage the
crops and they are mainly spread due to the weak quarantine measures, lack
of control of insect vectors and poor sanitation (Gray & Benerjee, 1999). On
Structural, Host and insectal range Gemini viruses are alienated in 4 genera
i.e. Begomovirus, Topocuvirus, Curtovirus & Mastrevirus (Rybicki et al., 2000,
Fauquet & Stanley, 2003, Stanley et al., 2005).Monocotyledons infecting
Mastrevirus’s genome is monopartite having leaf hopper as a virus transmitting
vector (Palmer and Rybicki, 1998). Curtovirus’s monopartite genome use leaf-
hopper as its vector while infecting dicotyledons only (Mansoor et al., 2003).
Similarly monopartitte genomic Topocovirus infect dicotyledons only but are of
2800 bp with similar vector as curtovirus (leaf hopper) (Briddon et al.,
1996).Begomovirus have both monopartite and bipartite genome. CLCuV is
undoubtedly monopartite begomovirus having white fly as vector. A variety of
crops are infected by these four genera of gemini viruses (Morales &
Anderson, 2001 ; Mansoor et al., 2003 b). Genus Begomovirus undoubtedly is
most variable, most economically devastating and extremely geographically
distributed genus among viruses (Muhammad Aslam* and Atif Ali Gilani., 2000).

Replication:

1. Virus penetrates into the host cell.

2. Uncoating, the viral ssDNA genome penetrates into the nucleus.
3. The ssDNA is converted into dsDNA with the participation of cellular factors.
4. bidirectional dsDNA transcription from the IR promoter produces viral mRNAs
and translation of viral proteins.
5. Replication is initiated by cleavage of the(+)strand by REP, and occurs
by rolling circle producing ssDNA genomes.
6. These newly synthesized ssDNA can either
a) be converted to dsDNA and serve as a template for
transcription/replication
b) be encapsidated by CP and form virions released from the cell by budding
c) be transported outside the nucleus, to a neighboring cell through
plasmodesmata (cell-cell movement) with the help of viral movement proteins.

Prevention and Control:

1. Use resistant or tolerant cultivars

2. Protect seedlings from whiteflies

3. Use only good seeds and healthy transplants

4. Control whiteflies

5. Immediately remove infected-looking plants and bury them

6. Control weeds
 7. Do not plant cotton near tomato and/or other crops susceptible to whiteflies
or vice

8. Use acephate- imidacloprid at 50% - 1.8% respectively, at every seven

days.

9. Plow-under all plant debris after harvest or burn them when possible

10. Practice crop rotation by planting crops that are not susceptible to whitefly.

Potato Virus Y

Introduction:

Potato virus Y(PVY) is also known as Solarium virus 2, potato virus 20 and
potato leaf drop streak virus. It is distributed throughout the world on a wide range of
hosts in Solanaceae, for example tomato, potato etc. Several strains of PVY have
also been reported which differ in physical features. The thermal death point is 52°C
for 10 minutes and longevity 24-48 hours at the laboratory conditions.

Classification:

Group IV
Group:
((+)ssRNA)
Family: Potyviridae
Genus: Potyvirus
Potato virus Y
Species:
(PVY)

Structure of PVY:

The virions of a potyvirus consist of a non-enveloped capsid with helical

symmetry. Virion is flexuous, filamentous, 720-850 nm long and 12-15 nm in
diameter (Fig. 16.10 A). The axial canal can be distinct or indistinct but 2.5-3 nm in
diameter. The basic helix is obvious or obscure and the pitch of the helix is 3.3-3.4
nm.
The definitive morphological structure is composed of approximately 2000 copies of
capsid protein (CP) (B). Characteristic inclusion bodies are found within the infected
plant cells. It is cytoplasmic virus but some have nuclear inclusions. It is not
persistent in aphid vectors. It is the major virus of potatoes because it spreads easily
and reduces the yield.

There are three types of strains of PVY viz., PVY° (common strains), PVN n (tobacco
vein necrosis strains), PVYC (stipple streak strains). These strains are identified
according to severity of symptoms in tobacco, potato, etc.

PVY is divided into three subgroups:

(i) Potyvirus (aphid-transmitted virus),

(ii) Bymovirus (fungus-transmitted virus), and

(iii) Rymovirus (mite-transmitted virus).

Genome Organization of PVY:

The R genome of potyvirus is mnonopartite and contains only one linear,

(+) sense single-stranded RNA. The genome is sequenced and the complete
sequence is about 9.000-10,080-12,000 nucleotides long. The genome has a base
ratio of 21-23.51-26% guanine; 23-30.15-44% adenine; 14.9-22.41-28% cytosine;
15.6-24.41-30.9% uracil.

The 5′-end of the genome has a genome-linked protein (VPg). The 5′ non-coding
region functions as an enhancer of translation. The 3′-terminus has a poly (A) tract
and the genome has an intergenic poly (A) region. The genome organisation of a
typical member is shown in Fig. 16.11 which indicates 10 mature proteins and the
nine cleavage sites (see arrow).
The potyvirus contains one long open reading frame (ORF) which encodes one large
polyprotein precursor of 350 kDa that is subsequently processed by 3 different virus-
encoded proteases (all encoded by the virus itself) into 10 different mature functional
proteins denoted as proteinase P1, helper component (HC), proteinase P3,
cylindrical inclusion (CI), nuclear inclusion A (NIa), nuclear inclusion B (Nib), capsid
protein (CP), as well as two small putative proteins known as 6K1 and 6K.2.

There are conserved and variable regions within the potyvirus genome. The
conserved regions incorporate the helper component proteinase (HC-Pro) and
nuclear inclusion B (Nib), whereas the variable regions consist of P1. P3, and the
coat protein (CP). It has been reported that P3 displays low homology between
species but despite the variation observed between P3 proteins of distinct poty
viruses.

Symptoms of PVY:

Symptoms caused by PVY vary according to environment and host

varieties. It ranges from weak mosaic to foliage necrosis. The common symptoms
are leaf drops streak or acropetal necrosis. Secondary infected plants show less
necrosis but are dwarfed with brittle, crinkled and branched leaves. In combination
with PVX, it causes rugose mosaic of potato. This disease causes a severe damage
to the plants.

Upper side of leaf Lower side of leaf Infected potato by PVY

shows variable symptoms in different varieties of potato. The foliage is mottled which
in turn becomes wrinkled, punctured and remarkably reduced in size too. The margin
of leaflets gets rolled downwardly and plant is stunted.
Abnormal hairiness of leaves and dwarfing of whole plant occur. When the plants are
severely infected they die before producing tubers. Host range of PVY is mainly
Solanaceae but the virus also causes disease in Chenopodiaceae and
Leguminosae.

Replication of PVY:

Virus penetrates into the host cell. Uncoating and release of the viral
genomic RNA occur into the cytoplasm. The virion RNA is infectious and serves as
both the genome and viral messenger RNA. The genomic RNA is translated into
poly-proteins which are subsequently processed by the action of three viral-encoded
proteinases into functional products.

The viral genome replicates within the cytoplasm; hence replication is cytoplasmic
one. During transcription, the sub- genomic RNA is absent from infected cells.
Virions may provide helper functions to dependent virus during replication. The virion
acts a helper for another virus.

A negative-sense complementary ssRNA is synthesized by using the genomic RNA

as a template. Thereafter, new genomic RNA is synthesized by using the negative-
sense RNA as a template. Consequently, new virus particles are formed after
assembly of genomic RNA and coat protein.

Disease Cycle of PVY:

Transmission:

PVY can be spread by many species of aphids (small, soft-bodied insects

that feed on plant sap). Within minutes of starting to feed on a PVY-infected plant,
the PVY particles get stuck in the aphid’s stylet (its piercing-sucking mouthpart). If
the aphid then moves to a healthy plant and soon starts to feed, the virus particles
are transmitted to the healthy plant. This process, termed “non-persistent”
transmission, is similar to contaminating a glass of pure water with a straw you
previously used to drink lemonade—a small amount of lemonade will taint the pure
water. Of course, the difference is, the trace amount of lemonade does not have the
ability to start replicating in the water like the PVY virus particles do in the healthy
plant.

Control of PVY:

There are three key IPM principals for managing PVY-

1) Reduce the level of initial PVY inoculum in the crop. This greatly reduces the
final disease incidence in the disease epidemic, in other words, fewer infected plants
at harvest and improved yield. This occurs because the start of the epidemic is
delayed by slowing or eliminating the appearance of the first PVY-infected plants in
the field.

2) Use resistant cultivars. These can minimize or prevent the disease epidemic in
a number of ways, including

 reducing final disease incidence, mainly by delaying the start of the epidemic
because plants are slow to become infected,
 slowing the rate of the disease epidemic, the number of infected plants over
time in the field, mainly by disrupting PVY’s ability to replicate and then be
spread,
 masking the disease epidemic, by growing and yielding normally despite being
infected, or
 combinations of the above.

3) Reduce on-farm spread of PVY by aphids. This slows the rate of the disease
epidemic, in other words fewer of infected plants over time in the field, mainly by
interfering with the spread of PVY from diseased to healthy plants by aphids. This
results in fewer infected plants at harvest and improved yield.