Virology_Unit-I (complete Unit).pdf

MMB C-102
VIROLOGY
UNIT- I
GENERAL FEATURES OF VIRUSES
Presented By
Dr. Kalpana Sagar

Virus
Viruses are a unique group of infectious agents that typically consist of nucleic
acid molecules in a protein coat.
Viruses are too small to be seen by light microscopy.
Viruses are able to multiply only within the living cells of a host.
A complete virus particle known as the 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 also known as an envelope.
Viruses vary in shape from the simple helical and icosahedral to more complex
structures.
Viruses range in size from 20 to 300 nm.
Viruses spread in many ways. Many viruses are very specific as to which host
species or tissue they attack.

Viruses can exist in two phases: extracellular and intracellular.
Virions are extracellular, possess few if any enzymes and can not reproduce
independently 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.
Viruses do not have cells that divide; new viruses are assembled in the infected
host cell.
 But unlike still simpler infectious agents viruses contain genes, which give them
the ability to mutate and evolve.
Viruses evolved from plasmids (a piece of DNA that can move between cells,
while others may have evolved from bacteria.
Over 5,000 species of viruses have been discovered.

Discovery of Viruses
In 1884 the French microbiologist Charles Chamberland invented a filter, known
today as the Chamberland filter or Chamberland-Pasteur filter, that has pores
smaller than bacteria. Thus he could pass a solution containing bacteria through
the filter and completely remove them from the solution.
In the early 1890s the Russian biologist Dmitri Ivanovsky used this filter to study
what became known as the tobacco mosaic virus. His experiments showed that
extracts from the crushed leaves of infected tobacco plants remain infectious
after filtration.
In 1899 the Duch microbiologist Martinus Beijerinck observed that the agent
multiplied only in dividing cells. Having failed to demonstrate its particulate
nature he called it a contagium vivum fluidum a soluble living germ.
 In the early 20th century the English bacteriologist Frederick Twort discovered
viruses that infect bacteria.

With the invention of the electron microscope in 1931 by German Engineers
Ernst Ruska and Max Knoll came to the first images of viruses.
In 1935, American biochemist and virologist Wendell Meredith Stanley
examine the tobacco mosaic virus and found it to be mostly made from protein.
A short time later, this virus was separated into protein and RNA parts. The
breakthrough came in 1931 when the American pathologist Ernest William
Goodpasture grew influenza and several other viruses in fertilized chicken’s eggs.

Viruses are different from living cells due to:
1. Their simple, acellular organization.
2. The absence of both DNA and RNA in the same virion.
3. Their inability to reproduce independently of cells and carry out cell
division as prokaryotes and eukaryotes do.

Distinctive properties of viruses
Viruses are obligate intracellular parasites of bacteria, protozoa, fungi, algae,
plants, and animals.
Ultramicroscopic in size, ranging from 20 nm up to 300 nm in diameter.
Not cellular in nature. The structure is very compact and economical.
Do not independently fulfill the characteristics of life.
In active macromolecules outside the host cell and active only inside host cells.
Basic structure consists of a protein shell (capsid) surrounding the nucleic acid
core.
Nucleic acid can be either DNA or RNA but not both.
Nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded
RNA, or double-stranded RNA.

Molecules on virus surface impart high specificity for attachment to host cells.
Multiply by taking control of host cell’s genetic material and regulating the
synthesis and assembly of new viruses.
Lack enzymes for most metabolic processes.
Lack machinery for synthesizing protein.
Most RNA viruses multiply in and are released from the cytoplasm.
Viral infections range from very mild to life threatening.

Nomenclature of Viruses
Various approaches, (do not obey the binomial nomenclature) derived from:
1. Named after the diseases eg. Measles virus, smallpox virus
2. Name after the places where the disease first reported eg. Newcastle disease
virus, Ebola virus, Norwalk virus, Bunyaviridae.
3. Host and signs of disease eg. Tobacco mosaic virus, cauliflower mosaic virus.
4. Latin and Greek words eg. Coronaviridae – “crown” Parvoviridae – “small”
5. Virus discovers eg. Epstein-Barr virus
6. How they were originally thought to be contracted eg. dengue virus (“evil
spirit”), influenza virus (the “influence” of bad air)
7. Combinations of the above eg. Rous Sarcoma virus

Reasons beyond classification
 Classification of virus been determined by the structural and chemical
composition of the virus.
Are applied to all plant viruses, animal viruses, and bacterial viruses.
 Virus is acellular cell – cannot be categorized using taxonomic classification.
 It used International Committee on Taxonomy of Viruses (ICTV) to classify the
viruses.

Classification and Nomenclature of virus
Till 1950, viruses were named based on the diseases they caused or on the
place of their isolation. They were grouped according to assumed tropisms or
affinity to different systems or organs of the body.
Thus human viruses were classified as :
Dermotropic-Viruses those producing skin lesions (smallpox, chicken pox,
measels).
Neurotropic – Viruses those affecting the nervous system (Poliomyelitis, rabies).
Pneumotropic- Viruses those affecting the respiratory tract (influenza, common
cold).
Viscerotropic- Viruses those affecting visceral organs (yellow fever, hepatitis).
Bawden (1941) suggested that viral nomenclature and classification should be
based on the properties of viruses and not upon the host responses.
From the early 1950s, virus began to be classified into groups based on their
physicochemical and structural features.

Classification of viruses
Viruses are not classified as members of the kingdoms.
 Viruses do not obey the biological taxonomy.
The classification of viruses is generally based on:
1. Classical - eg. animal, plant, bacterial virus system - eg. naked or enveloped
virus
2. Genomic - Baltimore classification
3. Serology - classification based on Diagnostic virology - eg. Infectious bronchitis
virus (IBV) of chickens.
(a coronavirus) – 3 different types present, these types have significant
antigenic differences, but perhaps very little genetic or biological difference
between these viruses.

The following criteria are used to classify viruses:
1. Morphology – structure of capsid – presence or absence of envelope
2. Size of the virion
3. Type of host/host structures the virus infected.
• Bacteriophages: infect bacterial cells
• Plant viruses infect plant cells
Animal viruses are subgrouped by the tissues they attack:
(a) Dermotrophic: if they infect the skin
(b) Neurotrophic: if they infect nerve tissue
4. Genome composition – DNA / RNA – ds/ss DNA and ds/ss RNA

Classification of viruses
First time in 1927, Johanson classified the plant viruses. Traditionally, viruses
have been named according to the diseases caused by them by adding the suffix
virus. e.g. Poliovirus, influenza virus etc.
In addition , the bacteriophages werer named after the laboratory codes e.g.
QB, Øx174, M13, etc.
The cyanophages were named after the host they lysed and the serological
differences among them e.g. LPP1, LPP2, etc.
Holmes (1948) followed the Linnean system of binomial nomenclature and put
the viruses into an order virales and three suborders:
(i) Phaginae: Viruses attacking on bacteria.
(ii) Phytophagine: Viruses attacking on plants
(iii)Zoophaginae: Viruses attacking on animals.

1. LHT system of Classification
In 1962, A. Lwoff, R. Horne and P. Tournier proposed a system of classification of viruses
which is commonly referred to as LHT system of classification. It was adopted by the
provisional committee on Nomenclature of viruses (PNCV) formed by the International
Association of Microbiological society. The LHT system of classification is based on:
(i) The nature of nucleic acid (DNA or RNA)
(ii) Symmetry of viral particle ( helical, icosahedral, cubic, cubic tailed)
(iii) Presence or absence of envelope
(iv) Diameter of capsid
(v) Number of capsomers forming the capsid
The LHT system of classification is as :
Phylum: vira
Subphylum: Ribovira (RNA viruses)
Class: Ribohelica (helical symmetry)
Order: Rhabdovirales (rod shaped viruses)
Suborder: Rigidovirales (Plant viruses)
Family: Dolichoviridae (12-13 nm)
Phylum: Vira
Subphylum: Deoxyvira (DNA virus)
Class: Deoxy helica (helical symmetry)
Order: Chitovirales (enveloped)
Family: Pox viridae (poxviruses)

The LHT system of classification is neither a natural classification nor shows any
evolutionary phylogenetic relationship.
However, it has been widely criticized, besides evoking the considerable interest among
the virologists.
Bellet (1967) proposed a system of classification. This system of classification is based
mainly on two criteria of the viral particles:
(i) Molecular weight
(ii) Percentage of guanine+ cytosine (G+C) of the nucleic acid
 Serological, antigenic and phenotypic properties were also considered for this
classification.
 Gibbs (1967) proposed a system of classification for plant viruses which is known as
Gibbs system of classification.
 According to Gibbs the criteria to classify the viruses are:
(i) Shape of capsid
(ii) Mode of transmission
(iii) Type of vector
(iv) Symptoms on host after infection
(v) The nature of accessory particle
Gibbs put 135 known viruses into the 6 broad groups.

2. Casjens and King’s Classification
Casjens and king (1975) classified the viruses on the basis of nucleic acid types,
symmetry, presence or absence of the envelope and site of assembly of the
envelope i.e nuclear or cytoplasmic. The classification of Casjens and king
(1975) is as:
1. ssRNA viruses
(A) Helical
(i) Rigid rods (plants): TMV, Tobacco rattle virus, barley stripe mosaic virus
(ii) Flexous rods (plants): Potato X and Y viruses, clover yellow mosaic virus.
(B) Icosahedral
(i) Spherical plant viruses
(a) With 180 identical capsomers (T=3). e.g. cowpea chlorotic mosaic virus,
cucumber mosaic virus, turnip yellow.
(b) With 60 subunits of two structural proteins (T=1) e.g. cowpea mosaic
virus.

(ii) Bacteriophages: e.g.R17, Fr, F2, QB, MS2
(iii) Picornaviruses (animal viruses)
(a) Human entroviruses- poliovirus
(b) Rodent cardioviruses- Encephalomyocarditis virus, mengovirus.
(c) Rhinoviruses-Human respiratory infection viruses
(d) Foot and mouth disease virus
(C) Envelope
(i) Spherical: Togavirus, yellow fever virus
(ii) Bullet shaped: Rhabdovirus e.g. rabies
(iii) Spherical: Paramyxovirus e.g measles, or filamentous Myxovirus e.g. influenza
virus.
(iv) Spherical : Corona virus e.g. acute upper respiratory tract infection virus,
severe acute respiratory syndrome (SARS) virus, Arena virus e.g. lymphocyclic
chloromeningitis, Oncoviruses e.g. leukemia, sarcoma

2. dsRNA viruses
Segmented genome
(i) Animal viruses- Reovirus, blue tongue virus of sheep, cytoplasmic polyhedrosis
virus of silk worm.
(ii) Plant viruses-Wound tumour virus of plants, Maize rough dwarf virus, Rice
dwarf virus.
Enveloped
Bacteriophage Ø6
3. ssDNA viruses
Icosahedral
(i) Bacteriophages- Øx174, S13
(ii) Parvoviruses-Animal and insect viruses
Helical
Bacteriophage fd, F1, M13

4. dsDNA viruses
Icosahedral complex tailed
(i) E.coli phages-T4, P2, T3, T5, T7
(ii) S. typhimurium phage- P22
(iii) B. subtilis phage- Ø29, cyanophages
Enveloped
Bacteriophage PM2
Nuclear Assembly
(i) Papovavirus- Polyomavirus, SV40, human wart virus
(ii) Adenovirus- Respiratory disease in birds and mammals ( icosahedral)
(iii) Herpsvirus (enveloped)- Cold sores, shingles, infections mononucleosis
cervical sarcoma of uterus, Burkitt’s lymphoma.
Cytoplasmic Assembly
(i) Poxvirus (enveloped)- Variola-small pox, vaccinia-immunity to small pox

3. Baltimore Classification of viruses
The Baltimore classification (2008) of viruses is based on genome type and
mode of replication and transcription.
 Suggested by David Baltimore – Seven Baltimore classes. The Nobel prize
winning biologist David Baltimore devised the Baltimore classification system.
The ICTV classification system is used in conjugation with the Baltimore
classification system in modern virus classification.
Major groups of viruses are distinguished first by their nucleic acid content as
either DNA or RNA.
 RNA and DNA viruses can be single-stranded (ssRNA, ssDNA) or double-
stranded (dsRNA, ssDNA) and may or may not use reverse transcriptase. ssRNA
may be either (+) sense or (-) antisense. This classification places viruses into 7
groups.

4. International Committee on taxonomy of viruses (ICTV)
•International Committee on taxonomy of viruses (ICTV) is a committee which
authorizes and organizes the taxonomic classification of viruses.
•ICTV began to devise and implement rules for the naming and classification of
viruses early in 1990s. ICTV have developed a universal taxonomic scheme for
viruses and aim to describe all the viruses of living organism.
•The committee is governed by the virology division of the International union of
Microbiological societies (IUMS).
•The report of ICTV (2005) lists more than 6,000 viruses classified in 1,950 species
and in more than 391 different higher taxa.
•However, GenBank contains an additional 3,142 species which has been
unaccounted by the ICTV report. A number of changes could be made both at
ICTV and GenBank to better handle virus taxonomy and classification in the
future.
•ICTV also operates a database (ICTVdB) containing taxonomic information for
over 6,000 virus species as of 2005. It is open to the public.

The objectives of ICTV are:
(i) To develop an internationally agreed taxonomy of viruses
(ii) To develop internationally agreed names for virus taxa, including species and
subviral agents.
(iii) To communicate taxonomic decisions to all users of virus names, in particular
the international community of virologists, by publications and via the
internet
(iv) To maintain an index of virus names.
(v) To maintain an ICTV database on the internet that records the data that
characterize each named viral taxon, together with the common names of
each taxon in all major languages.
Principles of Nomenclature
The ICTV essential principles of virus nomenclature are:
 Stability
 To avoid or reject the use of names which might cause error or confusion.
 To avoid the unnecessary creation of names.
ICTV’s universal classification system uses a slightly modified version of the
standard biological classification system. It only recognizes the taxa below
kingdom:those of order, family, subfamily, genus and species.

Viral classification starts at the level of order and follows with the taxon suffixes
given in italics:
Order-virales
Family-viridae
Subfamily-virinae
Genus-virus
Species-
So far, five orders have been established by the ICTV.
1. Caudovirales-It contains tailed dsDNA (Group I) bacteriophages
2. Hepesvirales-It contains large eukaryotic dsDNA viruses
3. Mononegavirales-It includes non-segmented (-) ssRNA (group V) plant and
animal viruses
4. Nidovirales- It is composed of (+) ssRNA (Group IV) viruses with vertebrate
hosts.
5. Picornavirales- contains small (+) ssRNA viruses that infect a variety of plant,
insect and animal hosts.

5. Dimmock et al. classification
On the basis of host preference, Dimmock et al. (2002) classified viruses into six
sections such as infecting animals, plants, fungi, bacteria and satellite viruses
and viroids. Each section is divided into 7 classes following revised Baltimore
scheme and each class into families.
Viruses of vertebrates and Invertebrate Animals
Viruses with double stranded DNA genomes (Class I)
Family: Adenoviridae, Ascoviridae, Asfraviridae, Baculoviridae, Herpesviridae,
Iridoviridae, Papilomaviridae, Polydnaviridae, Polyomaviridae, Poxviridae.
Viruses with ssDNA genomes (Class 2)
Family: Circoviridae, Parvoviridae.
Viruses with dsRNA genomes with virion-associated RNA-dependent RNA
polymerase (Class 3)
Family: Birnaviridae, Reoviridae.

Viruses with positive sense ssRNA genomes (Class 4)
Family: Arteriviridae, Astroviridae, Calciviridae, Coronaviridae, Flaviviridae, Nodaviridae,
Picornaviridae, Tetraviridae, Togaviridae
Viruses with negative-sense/antisense ssRNA genomes and virion-associated RNA-
dependent RNA-polymerase (Class 5)
Family: Arenaviridae, Bornaviridae, Bunyaviridae, Filoviridae, Orthomyxoviridae,
Paramyxoviridae, Rhabdoviridae
Viruses with RNA genomes that replicate through a DNA intermediate (Class 6)
Family: Retroviridae
Viruses with a DNA genome that replicates through an RNA intermediate (Class 7)
Family: Hepadnaviridae
Viruses that multiply in plants
Viruses with ssDNA genomes (Class 2)
Family: Circoviridae, Geminivirus
Viruses with dsRNA genomes and virion-associated RNA-dependent RNA
Family: Partitiviridae, Reoviridae

Viruses with (+) ssRNA genome (Class 4)
Isometric virions (Virures those have same dimensions)
Family: Comovirus, Luteovirus, Sequiviridae, Tombusviridae
Isometric virions and virions that are short rods
Family: Bromovirus
Virions that are rigid rod
Genera: Benyvirus, Furovirus, Hordeviridae, Pecluvirus, Pomovirus, Tobamovirus, Tobravirus
Virions that are flexuous rods
Family: Closteroviridae, potyviridae
Viruses with (-) ssRNA genomes and a virion-associated RNA dependent RNA
Family: Bunyaviridae, Rhabdoviridae
Viruses with DNA Genomes that replicate through an RNA intermediate (Class 7)
Family: Caulimovirodae
Viruses with dsDNA genomes (Class I)
Family: Adenoviridae, Phycodnaviridae

Viruses with dsDNA Genomes and a virion-associated RNA-dependent RNA polymerase
(Class 3)
Family: Hypoviridae, Partitiviridae, Totiviridae
Viruses with (+) ssRNA genomes (class 4)
Family: Barnavirus, Narnaviridae
Viruses (phages) Multiplying in Archaea, Bacteria, Mycoplasma and Spiroplasma
Viruses with dsDNA genome (class 1)
Family (viruses that have head-tail structure): Sipoviridae, Myoviridae, Podoviridae
Family (viruses that do not have head-tail structure): Fuselloviridae, Tectiviridae,
Cortiviridae, Plasmaviridae, Rudiviridae, Lipothrixviridae
Viruses with dsDNA genomes (Class 2)
Family: Inoviridae, Microviridae
Viruses with dsRNA genomes and a virion-associated RNA-dependent RNA polymerase
(Class 3)
Family: Cystoviridae
Viruses with (+) ssRNA Genomes (Class 4)
Family: Leviviridae

Classification of viruses based on DNA and RNA
Viruses are classified into two main divisions depending on the type of nucleic
acid they possess.
1. Ribovirus: viruses containing RNA.
2. Deoxyribovirus: viruses containing DNA.
Further classification is based on other properties such as the strandedness of
nucleic acid, symmetry of nucleocapsid, presence of envelope, size and shape of
virion, and the number of capsomers.
Major groups of viruses are classified as:
1. RNA virus- Picornaviridae family, Orthomyxoviridae family, Paramyxoviridae
Family, Togaviridae Family, Flaviviridae Family, Bunyaviridae Family,
Arenaviridae Family, Rhabdoviridae Family, Reoviridae Family, Retroviridae
Family, Caliciviridae Family, Filoviridae Family
2. DNA virus- Poxviridae family, Herpesviridae Family, Adenoviridae Family,
Papovaviridae Family, Parvoviridae Family, Hepadnaviridae Family

Morphology of Viruses
Shape of Virus
Viruses are of different shapes such as spheroid or cuboid (adenoviruses)
elongated (potato viruses), flexous or coiled (beet yellow), bullet shaped (rabies
virus), filamentous (bacteriophage M13), pleomorphic (alfalfa mosaic) etc.
Size of Viruses
Viruses are of variable sizes.
Initially their sizes were estimated by passing them through membranes of
known pore of diameter.
In recent years, their size is determined by ultracentrifugation and electron
microscopy.
The size of virus vary from 20 nm to 300 nm in diameter.
Viruses are smaller than bacteria and some are slightly larger than protein and
nucleic acid molecules.
Some viruses are the same size as the smallest bacterium e.g. small pox virus
and some viruses are slightly larger than the smallest bacterium e.g virus of
lymphogranuloma (300-400 um).

The structure of Viruses
The structure of viruses has been studied using several different techniques such
as electron microscopy, X-ray diffraction, biochemical analysis, and immunology.
Virion
Virion is a complete virus particle that consists of an RNA or DNA core with a
protein coat sometimes with external envelopes. Virion is the extracellular
infectious form of a virus.
The smallest virus is a little larger than the ribosome.
Poxviruses like vaccinia are about the same size as the smallest bacteria and
can be seen in the light microscope.
Most viruses are too small to be visible in the light microscope and must be
viewed with the scanning and transmission electron microscope.

All virions (if they possess other constituents) are constructed around a
nucleocapsid core (some viruses are consist only of a nucleocapsid).
Nucleocapsid is composed of a nucleic acid, either DNA or RNA, held within a
protein coat called as capsid, which protects viral genetic material and aids in its
transfer between host cells.
Envelope is made up of proteins and glycoproteins. Envelope seems to be
flexible and loose due to presence of lipid.
Envelope is composed of both the host and viral components i.e protein (virus
specific) and carbohydrates (host specific).

The morphological types of virus observed through electron microscopy and
crystallography have been categorised into the following three groups:
1. Helical (cylindrical ) viruses
(a)Naked capsid: TMV, bacteriophage M13
(b) Enveloped capsid: Influenza virus
TMV Influenza virus

2. Polyhedral (icosahedral) viruses
(a)Naked capsid: Adenovirus, Polio virus
(b) Enveloped capsid: Herpes simplex virus
Adenovirus Polio virus

3. Complex Viruses
(a) Capsid not clearly identified: Vaccinia virus
(b) Capsid to which some other structures are attached: some bacteriophages
Vaccinia virus T-even coliphage Flexuous tailed phage

Viroids
Diener a plant pathologist discovered viroid in 1971.
Viroid is an infectious particle smaller than any of the known viruses.
Viroids are 200-400 nucleotide long, circular RNA molecules with a rod-like secondary
structure which possess no capsid or envelope.
Viroid is an agent of certain plant diseases.
Viroids are transmitted mechanically from one cell to another through cellular debris.
Viroids are of much interest because of their sub-viral nature.
In 1967, W. B. Raymer discovered Potato spindle tuber viroids (PSTV) which caused a
disease in potatoes.
Viroids replicate just like viruses as they are also abligate intracellular parasites.
 Till 1970s viruses were considered as the smallest infectious agent but the discovery of
viroids has proved that the infectious entities smaller than virus exist in nature.
Viroids are classified into two families: Pospiviroidae, Avsunviroidae

Properties which differs viroid from conventional viruses
The pathogen exists in vivo as an encapsulated in the RNA.
Virion like particles are not detected in the infected tissues.
The infectious RNA is low molecular weight.
Despite its small size the infectious RNA replicates autonomously in susceptible
cells i.e no helper virus is required.
The infectious RNA consists of one molecular species only.

Host Range
The plants susceptible to viroids are potato, citrus, cucumber and
chrysanthemum, hops, stunt, tomato banchy top etc.
 The host range of PSTV is the members of Solanaceae and Compositae family.
Symptoms vary according to cultivars, strain and age of infection.
Stem and petiole are more acute for infection than the other parts.
 Diseased tubers get elongated i.e with pointed ends having numerous eyes and
heavy brows.
The viroids are contangious and spread mainly through mechanical injury/
contact but also through pollen and true seeds from the infected plants.
The control measures for diseases are the use of disease free seeds, early
roguing (to remove disease plant) and avoiding cutting of potato tubers

Viroid Genome
Viroid are low molecular weight (1.1-1.3 x 105 Da) nucleic acid.
Viroids are the only pathogen that do not code for any protein.
 They differ from viruses in lacking protein coat.
The PSTV has been found to be present in nucleus of the infected cells but not
the other subcellular organelles of potato.
About 200-10,000 copies of PSTV are found in each cell.
Viroid genomes are just a small fragment of RNA molecule which are
commonly circularized and remain as naked RNA strand consisting of about 250-
370 nucleotides.
The genes lack the initiation codon (AUG) for protein synthesis.
Mostly the nucleotides are paired resulting in dsRNA molecule due to the
presence of intra molecular complementary regions. Hence it appears as rods.

The dsRNA has closed folded, three dimentional structure. The closed single
stranded circle has extensive intrastrand base pairing and interspersed
unpaired loops.
Viroids have five domains as P, TL, CCR, V and TR domain.
 Most changes in pathogenicity of viroids seem to arise from variation in the
pathogenicity domain (P) and left terminal domain ( TL).
The other domains are the central conserved region (CCR), variable domains
(V), and rigid terminal domain (TR).
The folded structure probably protects it from the attack by cellular enzymes.
RNA does not code for any protein just like introns.

Origin of Viroid
There are some speculations regarding the origin of viroids.
According to watson et al. (1987) viroids are supposed to be the primitive
viruses and must have originated from cellular RNAs. In most of the healthy
plants RNA template is used for RNA synthesis. Viroids would have originated
from this RNA as they did not induce the biosynthetic machinery of their host
from their own replication.
Except tRNAS and 5S RNA, several low molecular weight RNAs have been found
to be associated with several virus infections such as tobacco leaves infected by
TMV, E.coli infected by QB phage and oncogene RNA viruses etc. Therefore, it is
supposed that viroids would have been originated from virus induced low
molecular weight RNAs which later on adapted as autonomously replicating
infectious entities.
With the discovery of split genes and RNA splicing in eukaryotes it has been
suggested that viroids might have originated through circularization of spliced out
introns.

Replication of Viroids
There is no convincing evidence for the replication of viroid genome.
It is likely that nucleic acid codes for an enzyme replicase which is essential for its
replications.
There are two families of viroids.
1. Avsunviroidae
2. Pospiviroidae
The members of Avsunviroids replicate in chloroplasts whereas Pospiviroids replicate
inside the nucleus and nucleolus.
Three enzymes are required for replication of viroids.
1. RNA polymerase
2. RNase
3. RNA ligase
RNA polymerase II is involved in synthesis of mRNA from DNA but this enzyme use viroid’s
RNA as template and catalyzes the synthesis of new RNA by rolling circle mechanism.
Probably Avsunviroids replicate via a symmetric rolling circle mechanism. Members of the
Avsunviroid lack a CCR and possess a ribozyme activity. Hence, they possess catalytic
properties to carryout self-cleavage and ligation of genomes from larger replication
intermediates.

Symmetric rolling circle mechanism
•The infectious circular (+) RNA strand of a viroid serves as a template to make a large
linear multimeric negative strand by using RNA polymerase II.
•In Avsunviroid replication, the long sense RNA is self cleaved by ribozyme activity. A
negative circle is formed upon circularization of RNA.
•A second rolling circle event makes a long linear positive strand, which is again
cleaved by the activity of ribozyme. Then the short viroid RNA is ligated to form the
circular structure.
Symmetric and asymmetric rolling circle mechanism of replication in viroids

Asymmetric rolling circle mechanism
Pospiviroids use an asymmetric mechanism. Thereafter, Pospiviroids synthesize
(+) sense RNA from this long linear molecule via asymmetric replication pathway.
The (+) RNA strand is cleaved into a unit viroid lengths by RNase activity of the
host. Then this molecule is ligated to form a circular viroid.
There are two possibilities for genome replications:
1. RNA dependent replication
2. DNA dependent Replication
1. RNA dependent replication
In this replication it appears that RNA directed RNA polymerase are present to a
limited extent in the normal cell of plant which may synthesize the RNA molecules
directed by the RNA.

2. DNA dependent Replication
 In this replication viroids are transcribed from a cellular DNA of the host cell,
complementary to viroid RNA.
 In the infected cell new DNA may be produced with the infecting viroid RNA
which serves as template.
 This makes the assumption for the presence of reverse transcriptase i.e RNA
directed DNA polymerase. From this the viroid RNA are synthesized.
Viroid RNA
Infection
Reverse transcriptase
DNA Viroid RNA
Branch and Robertson (1984) have analyzed the viroid specific nucleic acids on
tomato plants infected by PSTV.
They conclude that:
(i) Viroids replicate by direct RNA to RNA copying
(ii) The host cells possibly contain the machinery needed for replication of
viroid RNA

Cyanophages
Cyanophages are the viruses that attack on cyanobacteria i.e members of the
blue-green algae. These viruses are commonly called as blue green algal viruses
or Cyanophages.
 Cyanophages use cyanobacteria for its replication and multiplication.
First time Cynophages were isolated by Safferman and Morris (1963) from
waste stabilization pond of Indiana University that attacked and destroyed Green
Genera.: Lyngbya, Plectonema and Phormidium. Therefore they named the virus
by using the first letter of three genera as LPP.
A large number of other cynophages are SM-1, AS-1, N-1, C-1, AR-1. A-1, etc.
Several serological strains of LPP were isolated and named as LPP-1, LPP-2,
LPP-3, LPP-4 and LPP-5.
Cyanophage is classified in a bacteriophage family that is Myoviridae,
Podoviridae and siphoviridae.

Morphology of Cyanophages
The LPP-1 group of Cyanophages resemble T3 and T7 bacteriophages as they
possess icosahedral head and short tail.
N-1 cyanophages resemble T2 and T4 phage because their head is icosahedral but
the tail is long .
G-III and D-1 groups do not show any relationship with T-phages.
The tail of cyanophages may be contractile or non-contractile. In some groups of
cyanophages tail is absent.

Growth Cycle of Cyanophages
The replication of genetic material of cyanophages has been reviewed by Padan
and Shilo (1973) Sherman and Brown ( 1978) .
Like bacteriophages, cyanophages too follow the same one step growth curve.
The growth cycle of cyanophages resembles with that of T4 phages however the
latent and rise period is different.
Multiplication of LPP-1 is carried out in the following manner.
1. Adsorption
2. Injection
3. Reduce Protein synthesis
4. Multiplication
5. Assembly
6. Release

1. Adsorption- Virus is attached or absorbed on the surface of host cell.
2. Injection- Genome of phage is injected in the host cell and protein coat is
left outside the cell. DNA injection mechanism is still unknown.
3. Reduce Protein synthesis- As soon as genome enters the rate of protein
synthesis of host cell is reduces and blocked.
4. Multiplication- The cyanophages starts to multiply.
5. Assembly- The viral nucleic acid and protein coat starts to assemble and
form a procapsid.
6. Release- After assembly, the cyanophage gets release from the host cell by
lysis of cell.

After insertion of genome three types of proteins are formed:
1. Earliest Proteins: These proteins are formed immediately after genome enters.
2. Early Proteins: These proteins are formed after 2 hours of entry of genome till
lysis of the cell.
3. Late Proteins: They are formed after 4 hours of infection until the host lysis.
Further degradation of host cell genome takes place after 3 hours of infection.
The degraded DNA material of host cell is used for synthesis of the viral
genome.
The latent period of LPP-1 and N-1 is 7 hours.
The plaque forming units that is PFU may also vary from virus to virus.
Burst size: It is a number of phages release after multiplication and replication of
Viruses from the host cell.
LPP-1: 350 PFU
AS-1: 50 PFU
N-1: 100 PFU

Mycoviruses
Mycoviruses are associated with fungi and also called as mycophages.
Most of the mycoviruses are latent but some mycoviruses induce symptoms.
In 1962, Hollings first time noticed some viruses that infected the cultivated
mushrooms, Agaricus bisporus causing die back disease which caused the loss of
crop and the degeneration of mycelium in the compost.
So far 5000 fungal species are known to contain mycoviruses.
Most of the species of Penicillium and Aspergillus have been found to be
infected with viruses.
The existence of mycoviruses appears to be intracellular.
The dsRNA segments are separately enclosed into identical capsids. This
feature of mycoviruses differentiates them from plant and animal dsRNA viruses
in which the genetic material segments are, usually, all enclosed in a single
virion.

Types of Mycoviruses
So far very few mycoviruses have been fully characterized and most are only the
virus like particles (VLPs).
 Some of the mycoviruses are isometric particles (105-110 nm diameter) –
capsid is roughly spherical polyhedron.
 The mycoviruses have a heterogenous properties with a diameter ranging from
25-50 nm and particle weight from 6-13x 106 dalton.
Most of the mycoviruses have single capsid protein but different molecular
weight from 25 to 130 x 103 dalton. Some of the viruses have more than one
capsids.
Mycoviruses are classified into following groups:
(i) ds RNA mycoviruses
(ii) (+) ssRNA mycoviruses
(iii) (+) ssRNA mycoviruses with RT
(iv) (+) ssDNA mycoviruses

ICTV classified Mycoviruses into two groups as per their taxonomy:
(1) Penicillium chrysogenum virus group
(2) P. stoloniferum virus group
Mycoviruses have been categorised into four type as per their particle
morphology for their taxonomy affinity:
(i) Rod-shaped particles
(ii) Filament particles
(iii) Isometric particles
(iv) Bacilliform particles
Host range
Mycoviruses are found in all four phyla of the true fungi:
(i) Chytridiomycota
(ii) Zygomycota
(iii) Ascomycota
(iv) Basidiomycota

Replication of Mycoviruses
Buck (1979, 1980) has reviewed the replication of mycoviruses inside the fungal
cell. He has reported some host enzymes capable of transcribing the ssRNA and
dsRNA in laboratory conditions and probably dsRNA in vivo.
Some dsRNA mycoviruses code RNA polymerases necessary for effective in vivo
transcription and replication of dsRNA.
Mycoviruses are found in fungal spores and it is believed that they are
transmitted through the spores. The presence of viral-RNA in the fungal cells does
not appear to affect any cellular properties such as antibiotic production.
In undivided genome of virus of Saccharomyces cervisiae, two types of RNA
polymerase activity has been detected: ds→ssRNA (transcriptase) and ss→dsRNA.
In AfV-S virus the transcriptase activity has been noted and possibly replication
occurs through semiconservative strand displacement.
PsV-S shows replicase activity in vitro giving rise to dsRNA progeny molecules
that remain encapsulated. This type of semiconservative replication and strand
displacement also found in adenovirus DNA.

Examples of Mycoviruses
(i) Mycoviruses of Mushrooms
At least six viruses and VLP have been reported from the cultivated mushrooms
A. bisporus.
The mycoviruses occur in a mixture of cells and are extremely hard to separate.
It has been reported that the presence of viruses in sporophores of mushrooms
resulted in reduction in crop yield, and decreased in mycelial growth on malt agar
of cultures taken from the sporophores.
In recent years, there has been many reports of normal yields and mycelial
growth from virus infected mushroom crops with the suggestions that the
mycoviruses are not pathogenic.
The possible reasons for the conflicting reports are:
(a) The presence of morphologically indistinguishable viruses of differing virion size
in a single fungal cell.

(b) Existence of variants within one specific virus that contains additional dsRNA
segments associated with pathogenicity. The number and size of dsRNA segments
vary in different mushroom viruses.
(c) The development of tolerance against infection in present-day genotypes than
the former races of mushroom. This would have been through the suppression of
virus replication and through the production of a mycotoxin (patulin) in several
species of Penicillium and Aspergillus.
(ii) Mycoviruses in Plant Pathogenic Fungi:
Due to the presence of mycoviruses in pathogenic fungi, the virulence of
pathogens gradually declines to result in even death of fungi.
Fungus isolates of cereals (caused by Gaeumannomyces graminis) containing
only one kind of VLPs were mostly more pathogenic than virus-free isolates.
 The isolates with both kinds of virus particles tended to be less pathogenic than
either of the other two classes.

In addition, a highly pathogenic isolate of G. graminis from wheat roots gradually
lost the virulence over a period of 17 months in culture.
In virulent isolates no viruses could be detected. After a few months, 35 nm
virions and later on 26 nm virions were observed in increasing quantities resulting
in gradual loss in pathogenicity of the fungus.
In Helminthosporium victoriae, the cause of Victoria blight of oat, two
serologically unrelated mycoviruses designated as 190S and 145S from their
sedimentation value occurred in hypo-virulent cultures.
Hypo-virulence could be transferred to normal culture by hyphal anastomosis.
From more than 40 plant pathogenic fungi, mycoviruses have been reported but no
consistent correlation with hypo-virulence could be established.

Prions
 An infectious agent different from both viruses and viroids, can cause disease
in animals and humans. This agent is called prions i.e proteinaceous infectious
particles causes TSE (Transmissible Spongiform Disease) which attacks the central
nervous system (the brain).
Discovered by Stanley B. Prusiner, which are the class of infectious self
reproducing pathogens mainly composed of proteins. He won the Nobel Prize in
Physiology or Medicine in 1997 for his work proposing an explanation for the
cause of bovine spongiform encephalopathy (mad cow disease) and its human
equivalent, Creutzfeldt-Jacob disease.
Prusiner coined the term prion which means proteinaceous and infectious and
lack nucleic acid.

The Mystery of Kuru
In the 1950s, a district medical officer working in the highlands of New Guinea
observed a fatal disease among the people of the Fore tribe. The Fore people called
this sickness kuru, which means "trembling in fear." After initially becoming unable
to walk, victims of kuru lost the ability to swallow or chew. Drastic weight loss
would inevitably lead to death. Today we know that kuru is one of several diseases
in humans and animals caused by prion proteins.
Basic Structure Normal prions contain about 200-250 amino acids twisted into
three telephone chord-like coils known as helices, with tails of more amino acids.
The mutated, and infectious, form is built from the same amino acids but take a
different shape.
Prions are 100 times smaller than the smallest known virus.
Differences From Bacteria & Viruses
Prions do not contain nucleic acid; they don’t have DNA or RNA. They are
extremely resistant to heat and chemicals.
Prions are very difficult to decompose biologically; they survive in soil for many
years.

Cause of Prion disease
The main cause of prion disease is cannibalism i.e eating of one human by
another human.
There are two types of cannibalism:
(1) Endocannibalism: (Eating humans from the same community)
(2) Exocannibalism: (eating humans from other communities)
Cannibalism may be:
(i) Sanctioned by a cultural norms
(ii) Necessity in extreme situations of famine
(iii) Insanity

It is found in geographically isolated tribes in the Fore highlands of New
Guinea.
 The tribal ground up the brain into a pale grey soup, heated it and ate it.
Therefore ingestion of brain tissue of dead relatives for religious reasons was
likely the route of transmission.
Nature of Prions (PrPC and PrPSc)
Prion proteins are in the forms of fibre which also occur as fold rods. The
normal form of endogenous prion protein found in a variety of tissues is
referred to as PrPC (C refers to cellular or common Prp), whereas the misfolded
form of PrPC is called PrPSc which is responsible for the formation of amyloid
plaques that results in neurodegeneration.
PrPSc is an infectious form of (Sc refers to ‘ Scrapie’ a prion disease occuring in
sheep).

Prions are proteins that are unique in their ability to reproduce on their own and
become infectious. They can occur in two forms called PrP-sen and PrP-res.
Both PrP-sen and PrP-res are made up of the exact same string of amino acids.
However, the two forms have different shapes.
PrP-sen is produced by normal healthy cells. The sen stands for “sensitive”
because this version of the protein is sensitive to being broken down. PrP-sen is
present mainly in neurons in the brain, but is also found in other cell types.
Scientists don’t know the exact function of PrP-sen, but there is evidence that it
may be involved in communication between neurons, cell death, and controlling
sleep patterns.
The second type of prion protein, known as PrP-res, is the disease-causing form.
Organisms with it develop spongiform disease. “res” stands for “resistant” because
this version of PrP is resistant to being broken down.

Unlike other infectious agents, prions do not contain genetic material.
However, once they infect an individual, prions can replicate. How is this
possible? Scientists are still working out the details, but evidence supports the
idea that when PrP-sen comes into contact with PrP-res it is converted to PrP-
res. The result is a chain reaction that multiplies copy after copy of the
infectious prion. Because of their abnormal shape, PrP-res proteins tend to stick
to each other. Over time, the PrP-res molecules stack up to form long chains
called “amyloid fibers”.
Can a protein be infectious
The resistance form of PrPC is PrPSc which is a protease. There is no chemical
difference between two forms of protein except the confirmational difference
between PrPC and PrPSc .
The PrPC is mainly alpha helical and do not contain beta-sheet.
This altered structure is extremely stable and accumulates in the infected
tissue causing cell death and tissue damage resulting in death of animals.

Spread of Prion
Use of the by-products of one animal to feed another is a major factor in the spread of
the prion diseases. Government regulations can prevent this but a large number of
companies that manufacture the animal feed are not complying with regulations.
There are several hypotheses for the spread of this disease.
(a) Some workers are of the opinion that disease is transmitted by the prp alone. The
infectious pathogen is Prp which has been chemically modified. When abnormal prp
enters the normal brain cells, possibly it binds with normal prp and induces the
enzymes that modify its structure into the abnormal confirmation. The newly formed
abnormal prp in turn attacks the other normal prp molecules. But the other
researchers feel that this hypothesis is not adequate.
(b) According to the opinion of the other group the genetic informations cannot be
transmitted by the protein between the hosts. Proteins are now known to carry the
genetic information by the protein between the hosts. Proteins are now known to
carry the genetic information, therefore, possibly the infectious agent is a virio, a tiny
scrapie-specific nucleic acid coated with Prp protein. The nucleic acid may not be
transmitted but interacts host cells to cause disease. Many strains of scrapie agent
have been isolated from the infected cells.
(c) Other believe that prion diseases are caused by unknown viruses with usual
properties.

Prion Diseases
Human Prion Disease
•Creutzfeldt-Jakob Disease (CJD)
•Variant Creutzfeldt-Jakob Disease (vCJD)
•Gerstmann-Straussler-Scheinker Syndrome
•Fatal Familial Insomnia
•Kuru
Animal Prion Disease
•Bovine Spongiform Encephalopathy (BSE)
•Chronic Wasting Disease (CWD)
•Scrapie
•Transmissible mink encephalopathy
•Feline spongiform encephalopathy
•Ungulate spongiform encephalopathy

Creutzfeldt-Jakob disease
Classic CJD is a human prion disease. It is a neurodegenerative disorder with
characteristic clinical and diagnostic features. This disease is rapidly progressive
and always fatal. Infection with this disease leads to death usually within 1 year
of onset of illness.
Variant Creutzfeldt-Jakob disease
Variant Creutzfeldt-Jakob disease (vCJD) is a prion disease that was first described
in 1996 in the United Kingdom. There is now strong scientific evidence that the
agent responsible for the outbreak of prion disease in cows, bovine spongiform
encephalopathy (BSE or ‘mad cow’ disease), is the same agent responsible for the
outbreak of vCJD in humans.
Bovine spongiform encephalopathy
BSE (bovine spongiform encephalopathy) is a progressive neurological disorder of
cattle that results from infection by an unusual transmissible agent called a prion.
The nature of the transmissible agent is not well understood. Currently, the most
accepted theory is that the agent is a modified form of a normal protein known
as prion protein. For reasons that are not yet understood, the normal prion
protein changes into a pathogenic (harmful) form that then damages the central
nervous system of cattle.

Chronic wasting disease
Chronic wasting disease (CWD) is a prion disease that affects deer, elk, reindeer,
sika deer and moose. It has been found in some areas of North America,
including Canada and the United States, Norway and South Korea. It may take
over a year before an infected animal develops symptoms, which can include
drastic weight loss (wasting), stumbling, listlessness and other neurologic
symptoms. CWD can affect animals of all ages and some infected animals may die
without ever developing the disease. CWD is fatal to animals and there are no
treatments or vaccines.

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