Viruses infect host cells and use the host's cellular machinery to replicate themselves. This involves the virus attaching and entering the host cell, releasing its genome, producing new viral components, assembling new virus particles, and causing the host cell to burst and release the new virus particles to infect other cells. Viruses can spread systemically throughout the host's body or remain localized to sites of infection. The replication cycle allows viruses to efficiently propagate and spread infection.

1. VIRAL PATHOGENESIS

2. Introduction
A virus is a set of genes, composed of either DNA or RNA, packaged in a protein
containing coat.
The resulting particle is called a virion.
Viruses that infect humans are considered along with the general class of animal
viruses
Viruses that infect bacteria are referred to as bacteriophages, or phages.
Virus reproduction requires that a virus particle infect a cell and program the
cellular machinery to synthesize the constituents required for the assembly of new
virions.
Thus, a virus is considered an intracellular parasite. The infected host cell may
produce hundreds to hundreds of thousands of new virions and usually dies.
Tissue damage as a result of cell death accounts for the pathology of many viral
diseases in humans. In some cases, the infected cells survive, resulting in persistent
virus production and a chronic infection that can remain asymptomatic, produce a
chronic disease state, or lead to relapse of an infection.
In some circumstances, a virus fails to reproduce itself and instead enters a latent
state (called lysogeny in the case of bacteriophages), from which there is the
potential for reactivation at a later time.

3. • Vertebrates have had to coexist with viruses for a long time because
they have evolved the special non-specific interferon system, which
operates in conjunction with the highly specific immune system to
combat virus infections.
The biological and genetic bases for these phenomena are :
• Different viruses can have very different genetic structures, and this
diversity is reflected in their replicative strategies.
• Because of their small size, viruses have achieved a very high degree
of genetic economy.
• Viruses depend to a great extent on host cell functions and,
therefore, are difficult to combat medically. They do exhibit unique
steps in their replicative cycles that are potential targets for antiviral
therapy.

4. Virus size
• Viruses are approximately 100- to 1000-fold smaller than the cells
they infect.
• The smallest viruses (parvoviruses)are approximately 20 nm in
diameter, whereas the largest animal viruses (poxviruses) have a
diameter of approximately 300 nm and overlap the size of the
smallest bacterial cells (Chlamydia and Mycoplasma).
• Therefore, viruses generally pass through filters designed to trap
bacteria.

5. Virus design
• The basic design of all viruses places the nucleic acid genome on the inside
of a protein shell called a capsid.
• Some animal viruses are further packaged into a lipid membrane, or
envelope, which is usually acquired from the cytoplasmic membrane of the
infected cell during egress from the cell.
• Viruses that are not enveloped have a defined external capsid and are
referred to as naked capsid viruses.
• The genomes of enveloped viruses form a protein complex and a structure
called a nucleocapsid, which is often surrounded by a matrix protein that
serves as a bridge between the nucleocapsid and the inside of the viral
membrane.
• Protein or glycoprotein structures called spikes, which often protrude from
the surface of virus particles, are involved in the initial contact with cells.

7. Functions of the capsid/ viral envelope
• Protect the nucleic acid genome from damage during the extracellular passage of
the virus from one cell to another
• Aid in the process of entry into the cell
• Package enzymes essential for the early steps of the infection process.
• In general, the nucleic acid genome of a virus is hundreds of times longer than
the longest dimension of the complete virion. It follows that the viral genome
must be extensively condensed during the process of virion assembly.
• For naked capsid viruses, this condensation is achieved by the association of the
nucleic acid with basic proteins to form what is called the core of the virus.
• The core proteins are usually encoded by the virus, but in the case of some DNA-
containing animal viruses, the basic proteins are histones scavenged from the
host cell.
• For enveloped viruses, the formation of the nucleocapsid serves to condense the
nucleic acid genome.

8. Viriods and Prions
• Two classes of infectious agents exist that are structurally simpler than viruses.
• Viroids are infectious circular RNA molecules that lack protein shells. They are
responsible for a variety of plant diseases.
• Viroids are plant pathogens that consist only of a circular, independently replicating RNA
molecule.
• The single-stranded RNA circle collapses on itself to form a rodlike structure.
• The only known mammalian pathogen that resembles plant viroids is the deltavirus
(hepatitis D), which requires hepatitis B virus proteins to package its RNA into virus
particles.
• Co-infection with hepatitis B and D can produce more severe disease than can infection
with hepatitis B alone.
• Prions are mutated forms of a normal protein found on the surface of certain animal
cells. Prions, which apparently lack any genes and are composed only of protein.
• The mutated protein, known as a prion, has been implicated in some neurological
diseases such as Creutzfeldt-Jakob disease and Bovine Spongiform Encephalopathy.
There is some evidence that prions resemble viruses in their ability to cause infection.
Prions, however, lack the nucleic acid found in viruses.

9. • Individual viruses, or virus particles, also called virions, contain
genetic material, or genomes, in one of several forms.
• Unlike cellular organisms, in which the genes always are made up of
DNA, viral genes may consist of either DNA or RNA.
• Like cell DNA, almost all viral DNA is double-stranded, and it can have
either a circular or a linear arrangement.
Almost all viral RNA is single-stranded; it is usually linear, and it may
be either segmented (with different genes on different RNA
molecules) or non-segmented (with all genes on a single piece of
RNA).

10. A. Tobacco mosaic virus.
B. Bacteriophage X174.
C. Bacteriophage T4.

11. GENOME STRUCTURE
• Genomes can be made of RNA or DNA and be either double stranded or
single stranded.
• For viruses with single-stranded genomes, the nucleic acid can be either of
the same polarity or of a different polarity from that of the viral mRNA
produced during infection.
• In the case of adeno-associated viruses, the particles are a mixture of
about half containing (+)DNA; the other half contain (-)DNA.
• The arenaviruses and bunyaviruses are unusual in having an RNA genome,
part of which has the same polarity as the mRNA and part of which is
complementary to the corresponding mRNA.
• Both linear and circular genomes are known.
• Whereas the genomes of most viruses are composed of a single nucleic
acid molecule, in some cases several pieces of nucleic acid constitute the
complete genome. Such viruses are said to have segmented genomes.
• One virus class (retroviruses) carries two identical copies of its genome and
is therefore diploid.

12. CAPSID STRUCTURE
• Subunit Structure of Capsids
• The capsids or nucleocapsids of all viruses are composed of many copies of
one or at most several different kinds of protein subunits.
• All viruses code for their own capsid proteins, and even if the entire coding
capacity of the genome were to be used to specify a single giant capsid
protein, the protein would not be large enough to enclose the nucleic acid
genome.
• Thus, multiple protein copies are needed, and, in fact, the simplest
spherical virus contains 60 identical protein subunits.
• Viruses are such highly symmetric structures that it is not uncommon to
visualize naked capsid viruses in the electron microscope as a crystalline
array.
• The presence of many identical protein subunits in viral capsids or the
existence of many identical spikes in the membrane of enveloped viruses
has important implications for adsorption, hemagglutination, and
recognition of viruses by neutralizing antibodies

16. Viral multiplication
• A virus multiplication cycle is typically divided into the following discrete phases:
• (1) adsorption to the host cell,
• (2) penetration or entry,
• (3) uncoating to release the genome,
• (4) virion component production,
• (5) assembly, and
• (6) release from the cell.
• This series of events is called the productive or lytic response.
• Some viruses can also enter into a very different kind of relationship with the
host cell in which no new virus is produced, the cell survives and divides, and the
viral genetic material persists indefinitely in a latent state. This outcome of an
infection is referred to as the non-productive response.
• The non-productive response is called lysogeny in the case of bacteriophages and
under some circumstances may be associated with oncogenic transformation by
animal viruses.

17. • The outcome of an infection depends on the particular virus host combination
and on other factors such as:
• the extracellular environment,
• multiplicity of infection, and
• physiology and developmental state of the cell.
• Those viruses that can enter only into a productive relationship are called lytic or
virulent viruses.
• Viruses that can establish either a productive or a non-productive relationship
with their host cells are referred to as temperate viruses.
• Some temperate viruses can be reactivated or induced to leave the latent state
and enter into the productive response.
• Whether induction occurs depends on the particular virus -host combination, the
physiology of the cell, and the presence of extracellular stimuli.

18. GROWTH AND ASSAY OF VIRUSES
• Viruses are generally propagated in the laboratory by mixing the virus and
susceptible cells together and incubating the infected cells until lysis occurs.
• After lysis, the cells and cell debris are removed by a brief centrifugation and the
resulting supernatant is called a lysate.
• The growth of animal viruses requires that the host cells be cultivated in the
laboratory.
• To prepare cells for growth in vitro, a tissue is removed from an animal and the
cells are disaggregated using the proteolytic enzyme trypsin.
• The cell suspension is seeded into a plastic petri dish in a medium containing a
complex mixture of amino acids, vitamins, minerals, and sugars.
• In addition to these nutritional factors, the growth of animal cells requires
components present in animal serum. This method of growing cells is referred to
as tissue culture, and the initial cell population is called a primary culture.

19. • The cells attach to the bottom of the plastic dish and remain attached
as they divide and eventually cover the surface of the dish.
• When the culture becomes crowded, the cells generally cease
dividing and enter a resting state. Propagation can be continued by
removing the cells from the primary culture plate using trypsin and
reseeding a new plate.
• When a virus is propagated in tissue culture cells, the cellular changes
induced by the virus, which usually culminate in cell death, are often
characteristic of a particular virus and are referred to as the
cytopathic effect of the virus.

20. Plaque assay
• Viruses are quantitated by a method called the plaque assay.
• Briefly, viruses are mixed with cells on a petri plate such that each
infectious particle gives rise to a zone of lysed or dead cells called a
plaque.
• From the number of plaques on the plate, the titer of infectious
particles in the lysate is calculated. Virus titers are expressed as the
number of plaque-forming units per milliliter (pfu/mL).

21. Plaque assays
A. Bacteriophage B. Adenovirus.

22. Process of viral infectivity
• ADSORPTION
• The first step in every viral infection is the attachment or adsorption of the infecting particle to
the surface of the cell.
• Adsorption involves virion attachment proteins and cell surface receptor proteins
• A prerequisite for this interaction is a collision between the virion and the cell.
• Viruses do not have any capacity for locomotion, and so the collision event is simply a random
process determined by diffusion.
• Therefore, like any bimolecular reaction, the rate of adsorption is determined by the
concentrations of both the virions and the cells.
• Only a small fraction of the collisions between a virus and its host cell lead to a successful
infection, because adsorption is a highly specific reaction that involves protein molecules on the
surface of the virion called virion attachment proteins and certain molecules on the surface of
the cell called receptors.
• Typically there are 10 receptors on the cell surface. Receptors for some bacteriophages are found
on pili, although the majority adsorb to receptors found on the bacterial cell wall. Receptors for
animal viruses are usually glycoproteins located in the plasma membrane of the cell.

24. Tropism
• A particular kind of virus is capable of infecting only a limited spectrum of
cell types called its host range. Thus, although a few viruses can infect cells
from different species, most viruses are limited to a single species.
• For example, dogs do not contract measles, and humans do not contract
distemper.
• In many cases, animal viruses infect only a particular subset of the cells
found in their host organism. Clearly this kind of tissue tropism is an
important determinant of viral pathogenesis.
• In most cases studied, the specific host range of a virus and its associated
tissue tropism are determined at the level of the binding between the cell
receptors and virion attachment proteins.
• Thus, these two protein components must possess complementary
surfaces that fit together in much the same way as a substrate fits into the
active site of an enzyme.

25. ENTRY AND UNCOATING
• Paramyxoviruses (eg, measles), some retroviruses (eg, HIV-1), and
herpesviruses enter by a process called direct fusion.
• The envelopes of these viruses contain protein spikes that promote
fusion of the viral membrane with the plasma membrane of the cell,
releasing the nucleocapsid directly into the cytoplasm. Because the
viral envelope becomes incorporated into the plasma membrane of
the infected cell and still possesses
• its fusion proteins, infected cells have a tendency to fuse with other
uninfected cells.
• Cell fusion is a hallmark of infections by paramyxoviruses and HIV-1
and can be important in the pathology of diseases such as measles
and acquired immunodeficiency syndrome (AIDS).

26. Direct fusion

27. Viropexis
• In viropexis, the adsorbed virions become surrounded by the plasma
membrane in a reaction that is probably facilitated by the multiplicity of
virion attachment proteins on the surface of the particle.
• Pinching off of the cellular membrane by fusion encloses the virion in a
cytoplasmic vesicle termed the endosomal vesicle.
• The nucleocapsid is now surrounded by two membranes, the original viral
envelope and the newly acquired endosomal membrane.
• The surface receptors are subsequently recycled back to the plasma
membrane, and the endosomal vesicle is acidified by a normal cellular
process.
• The low pH of the endosome leads to a conformational change in a viral
spike protein, which results in the fusion of the two membranes and
release of the nucleocapsid into the cytoplasm.
• In some cases, the contents of the endosomal vesicle may be transferred to
a lysosome prior to the fusion step that releases the nucleocapsid.

28. Viropexis

29. Replication
• Some viruses replicate at the site of entry, cause disease at the same site
(e.g., respiratory and gastrointestinal infections), and do not spread
throughout the body.
• Others spread to sites distant from the point of entry and replicate at these
sites.
• For example, the poliovirus enters through the gastrointestinal tract but
produces disease in the central nervous system.
• Once inside the cell, the virus replicates itself through a series of events.
Viral genes direct the production of proteins by the host cellular machinery.
• The first viral proteins synthesized by some viruses are the enzymes
required to copy the viral genome.
• Using a combination of viral and cellular components, the viral genome can
be replicated thousands of times.
• Late in the replication cycle for many viruses, proteins that make up the
capsid are synthesized. These proteins package the viral genetic material to
make newly formed nucleocapsids.

30. Assembly and Release from host cells.
• The process of enclosing the viral genome in a protein capsid is called
assembly.
• Replication of viral particles increases within the host cell until the cell
membrane can no longer contain all that is within its boundaries. The
cell expands beyond a size that the cell membrane can maintain its
integrity and result in lysis- this process is called host cell lysis. The
virions are then free to infect other susceptible cells.
• Another method is called budding/ blebbing. The newly formed
nucleocapsid pushes against the host cell membrane until the
membrane evaginates and pinches off behind the virus.
• The released virus is coated with host cell membrane, now called viral
envelope.
• Budding is a slower process than host cell lysis.

31. Viral release by budding

32. Viral shedding
• The last step in the infectious process is shedding of the virus back
into the environment.
• This is important to maintain a source of viruses in a population of
hosts. Shedding often occurs from the same body surface used for
entry.
• During this period, an infected host is infectious (contagious) and can
spread the virus.

33. Virus-Host interactions
• The interaction between a virus and its host cell can result in a variety
of effects.
• Viruses can be either cytopathic/ non cytopathic.
• Cytopathic viruses are those that kill the host cell. Cytopathic viruses
can trigger apoptosis (programmed cell death) which culminates in
the death of the host cell, often before viral replication can occur.
• Non- cytopathic viruses do not immediately produce cell death and
result in latent/ persistent infections. As a result, they are subdivided
into productive and non-productive.
• Non-cytopathic viruses that produce persistent infection with the
release of only a few new viral particles at a time are said to be
productive.
• Non-cytopathic viruses that do not actively make virus at detectable
levels for a period of time are considered non-productive.

34. Tropism
• Viral affinity for specific body tissues (tropism) is
determined by
– Cell receptors for virus.
– Cell transcription factors that recognize viral promoters
and enhancer sequences.
– Ability of the cell to support virus replication.
– Physical barriers.
– Local temperature, pH, and oxygen tension enzymes
and non-specific factors in body secretions.
– Digestive enzymes and bile in the gastrointestinal tract
that may inactivate some viruses.

35. • The ability of a virus to cause disease in an
infected host
• A virulent strain causes significant disease
• An avirulent or attenuated strain causes no or reduced disease
• Virulence depends on
– Dose
– Virus strain (genetics)
– Inoculation route - portal of entry
– Host factors - eg. Age SV in adult neurons goes persistent but is lytic
in young

36. Influenza virus
• Influenza viruses are members of the orthomyxovirus group, which
are enveloped, pleomorphic, single-stranded RNA viruses.
• They are classified into three major serotypes, A, B, and C, based on
different ribonucleoprotein antigens.
• Influenza A viruses are the Influenza B viruses are more antigenically
stable; are only known to naturally infect humans; and usually occur
in more localized outbreaks.
• Influenza C viruses appear to be relatively minor causes of disease,
affecting humans and pigs.
• Influenza A and B viruses each consist of a nucleocapsid containing
eight segments of negative-sense, single-stranded RNA of virus-
specified protein (M1).

37. • Type A, the most dangerous, infects a wide variety of mammals and
birds. It causes the most cases of the disease in humans and is the
type most likely to become epidemic.
• Type B infects humans and birds, producing a milder disease that can
also cause epidemics.
• Type C apparently infects only humans. It typically produces either a
very mild illness indistinguishable from a common cold or no
symptoms at all. Type C does not cause epidemics.

38. • Two virus-specified glycoprotein, which is enveloped in a glycolipid
membrane derived from the host cell plasma membrane.
• The inner side of the envelope contains a layer proteins,
hemagglutinin(HA) and neuraminidase (NA), are embedded in the outer
surface of the envelope and appear as spikes over the surface of the virion.
• The hemagglutinin and neuraminidase function in viral attachment and
virulence.
• Hemagglutinin is so named because of its ability to agglutinate red blood
cells from certain species (eg, chickens, guinea pigs) in vitro.
• Hemagglutinin enables the virus to bind to and invade cells, and
neuraminidase allows the virus to move among cells. But these proteins
also act as antigens—that is, they are recognized as foreign matter by the
human or other host organism, and this recognition triggers an immune
response in the host.

40. Influenza virus

41. • Influenza, also known as flu, contagious infection primarily of the
respiratory tract. Influenza is sometimes referred to as grippe.
Influenza is caused by a virus transmitted from one person to another
in droplets coughed or sneezed into the air.
• It is characterized by coldlike symptoms plus chills, fever, headaches,
muscle aches, and fatigue.
• Most people recover completely in about a week. But some people
are vulnerable to complications such as bronchitis and pneumonia.
This group includes children with asthma, people with heart or lung
disease, and the elderly.

42. • In addition to humans, influenza occurs in pigs, horses, and several
other mammals as well as in certain wild and domesticated birds. At
least some influenza viruses can jump from one species to another.
• There are 16 HA and 9NA antigenic forms known, they can recombine
to produce various HA/NA subtypes of influenza. All subtype
combinations infect birds.
• Because influenza is highly contagious and spreads easily, it usually
appears as epidemics—that is, outbreaks involving many people. If an
outbreak spreads around the world- it is called a pandemic.

43. • Influenza type A and B viruses continually change. Some changes
involve a series of genetic mutations that, over a period of time,
cause a gradual evolution of the virus called antigenic drift, this
process accounts for most of the changes in influenza viruses that
occur from one year to the next.
• Other changes, less common but more injurious, involve abrupt
changes in the hemagglutinin or neuraminidase. This type of change
is called antigenic shift and results in a new subtype of the virus.
• Type A viruses undergo both kinds of transformations; influenza type
B viruses apparently change only by the process of antigenic drift.

44. • Once a person has been infected by a specific strain of influenza, he
or she has built up immunity to that strain in the form of antibodies.
• The person’s immune system then can recognize the strain’s
hemagglutinin or neuraminidase and attack them if they reappear.
The antibodies offer some protection against antigenic drifts, but not
against antigenic shifts.
• Thus, because the viruses continually change, they can cause
repeated waves of infection, even among people previously infected.
• Antigenic shift means that once a human strain and an animal strain
recombine to create a new strain. This strain has the ability to infect
humans but has antigens on its surface that are unfamiliar to the
human immune system.

45. Transmission
• Influenza viruses pass from person to person mainly in droplets
expelled during sneezes and coughs.
• When a person breathes in virus-laden droplets, the hemagglutinin
on the surface of the virus binds to enzymes in the mucous
membranes that line the respiratory tract.
• Enzymes, known as proteases, cut the hemagglutinin in two, which
enables the virus to gain entry into cells and begin to multiply.
• These proteases are common in the respiratory and digestive tracts
but not elsewhere, which is why the flu causes primarily a respiratory
illness with occasional gastrointestinal symptoms.
• Low humidity favours transmission of influenza virus.

46. • The virus is acquired by inhalation or ingestion of virus-contaminated
respiratory secretions.
• During an incubation period of 1 – 2 days, the virus adheres to the
epithelium of the respiratory system.
• The virus attached to the epithelial cell by its hemagglutinin spike
protein, causing part of the cell’s plasma membrane to bulge inward,
seal off, and form a vesicle.
• This encloses the virus in an endosome.
• After contact with the endosomal membrane, fusion occurs and the
RNA nucleocapsid is released in to the cytoplasmic matrix.

47. Symptoms and Diagnosis
• Influenza is an acute disease with a rapid onset and pronounced
symptoms.
• After the influenza virus invades a person’s body, an incubation
period of one to two days passes before symptoms appear.
• Classic symptoms include sore throat, dry cough, stuffed or runny
nose, chills, fever with temperatures as high as 39ºC (103ºF), aching
muscles and joints, headache, loss of appetite, occasional nausea and
vomiting, and fatigue.
• For most people flu symptoms begin to subside after two to three
days and disappear in seven to ten days.
• However, coughing and fatigue may persist for two or more weeks.

48. • These symptoms arise from the death of respiratory epithelial cells,
probably due to attack by activated T cells.
• These symptoms are more debilitating than symptoms from common
cold.
• Recovery usually occurs in 3 -7 days, during which cold-like
symptoms appear as the fever subsides.

49. • Death from influenza itself is rare. But influenza can aggravate
underlying medical conditions, such as heart or lung disease.
• Invading influenza viruses produce inflammation in the lining of the
respiratory tract, damage that increases the risk that secondary
infections will develop.
• Common complications include bronchitis, sinusitis, and bacterial
pneumonia, occurring most frequently in older people, people on
chemotherapy, and people with acquired immunodeficiency
syndrome (AIDS) or other diseases that compromise the immune
system. If properly treated, these complications seldom are fatal.
• For the diagnosis of influenza in a patient, the virus must be isolated
from the person’s nasal or cough secretions or blood and identified
under a microscope.

50. Treatment
No drugs can cure influenza, but certain antiviral medicines can relieve
flu symptoms.
Available by prescription, these drugs provide modest relief, but only if
taken on the first or second day of symptoms.
The drugs amantadine (sold under the brand name Symmetrel) and
rimantadine (Flumadine), both in pill form, work against hemagglutinin
and are effective in treating type A influenza.
Two other drugs inhibit neuraminidase and are effective against both
type A and type B strains: oseltamivir (Tamiflu) is in pill form and
zanamivir (Relenza) is an inhalant.

51. • A flu vaccine consists of greatly weakened or killed flu viruses, or
fragments of dead viruses.
• Antigens in the vaccine stimulate a person’s immune system to
produce antibodies against the viruses.
• If the flu viruses invade a vaccinated person at a later time, the
sensitized immune system recognizes the antigens and quickly
responds to help destroy the viruses.
• Flu viruses constantly change so different virus strains must be
incorporated in vaccines from one year to the next.