1. The document discusses the structure and replication cycle of viruses. 2. Viruses consist of genetic material (DNA or RNA) surrounded by a protein coat called a capsid, and some have an outer lipid envelope. 3. Viral replication involves the virus entering the host cell, expressing its genes to produce viral proteins and genetic material, assembling new virus particles, and exiting to infect new host cells.

1. 1
ASSISTANT PROFESSORASSISTANT PROFESSOR
UNIVERSITY COLLEGE OF PHARMACY,UNIVERSITY COLLEGE OF PHARMACY,
UNIVERSITY OF THE PUNJABUNIVERSITY OF THE PUNJAB
BY

3.  A virus is a small infectious agent or obligatory
intracellular parasite that can replicate only inside the
living cells of an organism. Viruses can infect all types
of organisms, from animals and plants to bacteria.
 Virus particles consist of two or three parts: the
genetic material made from either DNA or RNA, long
molecules that carry genetic information; a protein
coat that protects these genes; and in some cases an
envelope of lipids that surrounds the protein coat
when they are outside a cell.

4.  A completely assembled and infectious virus outside
its host cell is known as a virion. Virions lack the
chemical machinery for generating energy and
synthesizing large molecules. Therefore they must rely
upon the structures and chemical components of their
host cells for infections and replication.
 The shapes of viruses range from simple helical and
icosahedral forms to more complex structures. The
average virus is about one one-hundredth the size of
the average bacterium. Most viruses are too small to
be seen directly with an optical microscope.

5.  Since Dmitri Ivanovsky's 1892 discovered that the agent
which caused tobacco mosaic disease was filterable. He
obtained bacteria free filterate from ground up infected
plants and placed on the healthy leaves of tobacco. He
found that filterate produced the disease in healthy plant.
After that the presence of similar filter passing ,
ultramicroscopic agents was seen in the victims of many
disease including foot and mouth disease ( herpes and
voricella infections) and yellow fever as well. In 1935
stanley then purified these filterable agent by crystallization
and found that causative agent have only nucleic acid and
protein intheir structure. Hence the agents are simply
described as “virus”

7.  Viruses are the smallest agents able to cause disease in
living things. They range in size of from the large 250 nm of
poxvirus to the 20nm of paravovirus. At the upper end of
spectrum, the virus approximate the size of the smallest
bacteria such as the chlamydiae and mycoplasmas, at the
lower end they have the same diameter as ribosomes.
 Some filoviruses have a total length of up to 1400 nm;
their diameters are only about 80 nm. Most viruses cannot
be seen with an optical microscope so scanning and
transmission electron microscopes are used to visualise
virions. Negative staining technique is more appropriate
technique for it.

8. Helical
 These viruses are composed of a single type of capsomers
stacked around a central axis to form a helical structure, which
may have a central cavity, or hollow tube. This arrangement
results in rod-shaped or filamentous virions: These can be short
and highly rigid, or long and very flexible. The genetic material, in
general, single-stranded RNA, but ssDNA in some cases, is
bound into the protein helix by interactions between the
negatively charged nucleic acid and positive charges on the
protein. Overall, the length of a helical capsid is related to the
length of the nucleic acid contained within it and the diameter is
dependent on the size and arrangement of capsomers. The well-
studied tobacco mosaic virus is an example of a helical virus.

9. Structure of tobacco mosaic virus: RNA coiled in a helix of
repeating protein sub-units

10. Icosahedral
 Most animal viruses are icosahedral or near-
spherical with icosahedral symmetry. A regular
icosahedron is the optimum way of forming a
closed shell from identical sub-units. The
icosahedron is polyhedron with 20 triangular faces
and 12 corners. The minimum number of identical
capsomers required is twelve, each composed of
five identical sub-units.

11. Electron micrograph of icosahedral adenovirus

12. Envelope
 Some species of virus envelop themselves in a
modified form of one of the cell membranes such as
an outer lipid bilayer known as a viral envelope and is
similar to the host cell membrane, except that it
includes viral specified components. It is acquired
during the replication in the host cell and is unique to
each type of the virus. The influenza virus and HIV
use this strategy. Most enveloped viruses are
dependent on the envelope for their infectivity.

14. Complex
 These viruses possess a capsid that is neither purely
helical nor purely icosahedral, and that may possess
extra structures such as protein tails or a complex
outer wall. Some bacteriophages, such as
Enterobacteria phage T4, have a complex structure
consisting of an icosahedral head bound to a helical
tail, which may have a hexagonal base plate with
protruding protein tail fibres. This tail structure acts like
a molecular syringe, attaching to the bacterial host
and then injecting the viral genome into the cell.

16.  The poxviruses are large, complex viruses that
have an unusual morphology. These are brick
shaped with microscopic filaments occuring in a
swirling pattern at the periphery of the virus.

18.  Genomic diversity among viruses
Nucleic acid
 DNA
 RNA
 Both DNA and RNA (at different stages in the life
cycle)
Shape
 Linear
 Circular
 Segmented

19. Strandedness
 Single-stranded
 Double-stranded
 Double-stranded with regions of single-
strandedness
Sense
 Positive sense (+)
 Negative sense (−)

20.  A virus has either DNA or RNA genes and is called a DNA
virus or a RNA virus, respectively. The vast majority of
viruses have RNA genomes. Plant viruses tend to have
single-stranded RNA genomes and bacteriophages tend to
have double-stranded DNA genomes. Usually the nucleic
acid is unbroken but in some instances (as in influenza
viruses) it exists in separate segments. Segmented
genomes confer evolutionary advantages; different strains
of a virus with a segmented genome can shuffle and
combine genes and produce progeny viruses or (offspring)
that have unique characteristics. This is called
reassortment or viral sex.
 Viral genomes are circular, as in the polyomaviruses, or
linear, as in the adenoviruses.

21.  ssDNA, linear Parvovirus
 dsDNA, linear Poxvirus
 ssDNA, circular Phage X174
 dsDNA, circular Baculoviruses
 ssRNA, linear Tobacco Mosaic Virus
 dsRNA, linear Reovirus
 ssRNA, circular Hepatitis D virus
 Note: there are no viruses known with circular
dsRNA genomes

22.  RNA virus follow a slightlt different pattern. The RNA
can be act as m RNA molecule and immediately
supplying the code for protein synthesis such virus is
said to have sense and called positive stranded
RNA virus or sense virus (e.g polio virus). In the
other RNA viruses however the RNAis used as a
template to synthesize a complementary strand of
RNA. The original strand is said to have antisense
and virus is said to be antisense virus or negative
strand RNA virus( e.g Measles virus). Usually the
RNA polymerase enzyme is present in the virus to
synthesize the complementary strand .

23.  The capsid protects the genome. It also gives the
shape of the virus and responsible for the helical,
icosahedral or complex symmetry. Generally the
capsid is subdivided into protein sub units called
capsomeres (the organization of capsomere yeilds
the viral symmetry). The number of capsomeres is
the characteristics for the particular virus. For
example 162 capsomeres are making up the
capsid in herpes virus and 252 in adenovirus.

24.  The capsid provides a protective covering
for the genome because the construction of
amino acids resists temperature, pH and
other environment fluctuations. Also the
capsid contains some enzymes to assist cell
penetration during replication. The capsid
can stimulate an immune response during
disease period. The capsid plus genome is
called nucleocapsid or genocapsid.

25.  Many viruses are surrounding by a flexible membrane
known as envelope. The envelope is composed of lipids
and proteins and is similar to the host cell membrane,
except that it includes viral specified components. It is
acquired during the replication in the host cell and is
unique to each type of the virus. In some viruses including
influenza and measles viruses, the envelope contains
functional projections known as spikes. The spikes often
contain enzymes to assist viral attachment to the host
cells. Indeed enveloped virus lose their infectivity when the
envelope is destroyed. Also when the envelope is present
the symmetry of the capsid may not be apparent since the
envelop is generally a loose fitting structure.

27.  Viruses are by far the most abundant biological entities on
Earth and they outnumber all the others put together. They
infect all types of cellular life including animals, plants,
bacteria and fungi. However, different types of viruses can
infect only a limited range of hosts and many are species-
specific. Some, such as smallpox virus for example, can
infect only one species – in this case humans are said to
have a narrow host range. Other viruses, such as rabies
virus, can infect different species of mammals and are said
to have a broad range. The viruses that infect plants are
harmless to animals, and most viruses that infect other
animals are harmless to humans.

28.  The host range of some bacteriophages is limited
to a single strain of bacteria and they can be used
to trace the source of outbreaks of infections by a
method called phage typing. HIV virus can only
cause AIDS in human being but it is harmless in
monkeys. Even within host range , many viruses
only infect certain cell types or tissues within
multicellular animal or plants. This limitation is
called tissue tropism. e.g HIV infect T helper cells.

30.  Viral populations do not grow through cell division,
because they are acellular. Instead, they use the
machinery and metabolism of a host cell to
produce multiple copies of themselves, and they
assemble in the cell.
 The best known replication process that has been
carried out by bacteriophages of the T-even group
including T2, T4 and T 6 has been studied. These
are large group of complex DNA virions with a
characteristics head and tail but without envelop.
We shall use phage replication in E.coli as a model
for this virus. The following events will take place:

31.  The first phase in the replication of the
bacteriophage is contact with the host cell. There
is no long distance chemical attraction between
two, so the collision is a chance event. For the
attachment to occur, sites on the phage`s tail fiber
must match with a complementary receptor site on
the cell wall of the bacterium. The actual
attachment consists of a weak chemical union
between virion and bacterium receptor site.

32.  In the next stage the tail of the phage releases the
enzyme lysozyme to dissolve a portion of the
bacterial cell wall. Then the tail sheath contracts,
and the tail core drives through the cell wall. As
the tip of the core reaches the cell membrane
below, the DNA passes through the tail core and
on through the cell membrane into the bacterial
cytoplasm. for most bacteriophages the capsid
remain outside.

33.  Inside the host cell, phage genes code for the disruption
of the host chromosome. The phage DNA then uses the
bacterial nucleotides and cell enzymes to synthesize
multiple copies of itself. m RNA molecules transcribed
from phage DNA appear in the cytoplasm, and the
biosynthesis of phage enzymes and capsid proteins
begins. Because viral capsids are the repeating units of
capsomeres, a relatively simple genetic code can be
used over and over. For a number of minutes called the
eclipse period no new viral capsids are present.

34.  In this phase the replicated bacteriophages DNA
and capsid are assembled into complete virions.
The enzymes encoded by virions genes guide the
assembling in step by step fashion. In one area,
phage head and tail are assembled from protein
sub units. In other the heads are packaged with
DNA and in a third the tails are attached to the
head.

35.  The final phase of viral replication is the release phase.
For bacteriophages, this also called the lysis stage. For
some phages, the important enzyme in the process is
lysozyme, encoded by the bacteriophage genes late in
the sequence of events. The enzyme degrades the
bacterial cell wall and the newly release bacteriophages
are set free to infect other bacteria. The time that passes
from phage attachment to the release of new viruses is
commonly referred to as burst time. For bacteriophages
the burst time averages from 20 to 40 minutes. And as a
result 50 to 200 new phages will emerge from the host
cell.

36. Fig. 19-5-5
Phage assembly
Head Tail Tail fibers
Assembly
Release
Synthesis of viral
genomes and
proteins
Entry of phage
DNA and
degradation of
host DNA
Attachment1
2
4
5
3

37.  The lysogenic cycle replicates the phage
genome without destroying the host
 The viral DNA molecule is incorporated into the
host cell’s chromosome and is called a
prophage.
 Every time the host divides, it copies the phage
DNA and passes the copies to daughter cells
 Viruses that can be lysogenic or lytic are called
temperate phages.
Animation: Phage Lambda Lysogenic and Lytic CyclesAnimation: Phage Lambda Lysogenic and Lytic Cycles

38. Fig. 19-6
Phage
DNA
Phage
The phage injects its DNA.
Bacterial
chromosome
Phage DNA
circularizes.
Daughter cell
with prophage
Occasionally, a prophage
exits the bacterial
chromosome,
initiating a lytic cycle.
Cell divisions
produce
population of
bacteria infected
with the prophage.
The cell lyses, releasing phages.
Lytic cycle
Lytic cycle
is induced
or
Lysogenic cycle
is entered
Lysogenic cycle
Prophage
The bacterium reproduces,
copying the prophage and
transmitting it to daughter cells.
Phage DNA integrates into
the bacterial chromosome,
becoming a prophage.
New phage DNA and proteins
are synthesized and
assembled into phages.

40.  It is a specific binding between viral capsid proteins and
specific receptors on the host cellular membrane. This
specificity determines the host range of a virus. For
example, HIV infects a limited range of human
leucocytes. This is because its surface protein, gp120 on
CD4 receptor cells. This mechanism has evolved to
favors those viruses that infect only cells in which they
are capable of replication. Attachment to the receptor
can induce the viral envelope protein to undergo
changes that results in the fusion of viral and cellular
membranes with the help of spikes.

41.  Virions enter the host cell through receptor-
mediated endocytosis or membrane fusion. This is
often called viral entry. In some case the viral
envelope fuses with the plasma membrane and
release the nucleocapsid into the cytoplasm and
in other case the whole enveloped virion enter the
cell.

42.  It is a process in which the viral capsid is
removed: This may be by degradation by viral
enzymes or host enzymes or by simple
dissociation; the end-result is the releasing of the
viral genomic nucleic acid.

43.  Now this process diverges once again because
some viruses contain DNA and some contains
RNA. The DNA of DNA viruses supplies the
genetic codes for enzymes that can synthesize
viral parts. RNA virus follows a slightly different
pattern. The RNA can be act as m RNA molecule
and immediately supplying the code for protein
synthesis such virus is said to have sense and
called positive stranded RNA virus or
sense virus (e.g polio virus).

44.  In the other RNA viruses however the RNA is
used as a template to synthesize a
complementary strand of RNA. The original strand
is said to have antisense and virus is said to be
antisense virus or negative strand RNA
virus( e.g Measles virus). Usually the RNA
polymerase enzyme is present in the virus to
synthesize the complementary strand.

45.  Other RNA virus called retro virus has a
particularly interesting method of replication. Retro
virus carry their own enzyme called reverse
transcriptase. The enzyme use the viral RNA as a
template to synthesize single –stranded DNA ( the
term reverse transcription). Once formed the DNA
serves as a template to form a complementry
DNA strand. The viral RNA Is then destroyed, and
the two DNA strands twist around each other to
form a double helix.

46.  The DNA now migrates to a cell nucleus and
integrates into one of the host cell`s
chromosomes, where it is known as provirus
from this position the DNA encoded the new
retroviruses. Whenever the host divides, the viral
genome is also replicated. The viral genome is
mostly silent within the host; however, at some
point, the provirus may give rise to active virus,
which may release from the host cells. Enveloped
viruses (e.g., HIV) typically are released from the
host cell by budding. During this process the virus
acquires its envelope, which is a modified piece of
the host's plasma or other, internal membrane.

47. Entry byEntry by
direct fusiondirect fusion

48. Fig. 19-7
Capsid
RNA
Envelope (with
glycoproteins)
Capsid and viral genome
enter the cell
HOST CELL
Viral genome (RNA)
Template
mRNA
ER
Glyco-
proteins
Capsid
proteins Copy of
genome (RNA)
New virus

49. Fig. 19-8a
Glycoprotein
Reverse
transcriptase HIV
RNA (two
identical
strands)
Capsid
Viral envelope
HOST CELL
Reverse
transcriptase
Viral RNA
RNA-DNA
hybrid
DNA
NUCLEUS
Provirus
Chromosomal
DNA
RNA genome
for the
next viral
generation
mRNA
New virus

50. Fig. 19-8b
HIV
Membrane of
white blood cell
HIV entering a cell
0.25 µm
New HIV leaving a cell

51. SUNARYATI
ATTACHMENT
PENETRATION HOST
FUNCTIONS
ASSEMBLY
(MATURATION)
Transcription
REPLICATION
RELEASE
UNCOATING
Translation
MULTIPLICATION
Click after each step to view process

53. SUNARYATI
 Virus
injected into
appropriate
region
 Method
widely used
for
production
of vaccines

54. SUNARYATI

55. SUNARYATI

56. SUNARYATI
 Cytopathic effect - normal monolayer
structure is disrupted by viral
infection
 Cell lines developed from embryonic
tissue
 Continuous cell lines (immortal) - HeLa
 Maintenance of cell culture lines is
technically difficult; must be kept free
of microbial contamination.