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1. How do we classify viruses according to Baltimore classification?

They are grouped into seven distinct classes based on modes of replication and genome type.
Class 1: Double stranded DNA
Class 2: Single stranded DNA
Class 3: Double stranded RNA
Class 4: Single stranded RNA (+ve sense)
Class 5: Single stranded RNA (-ve sense)
Class 6: Single stranded RNA (+ve sense) replicating through DNA intermediate
Class 7: Double stranded DNA replicating through single stranded RNA intermediate

2. What is cytopathic effects (CPE)

Virus infection of cells is complex and results in many changes to the host cell, known
collectively as cytopathic effect or cpe".

Cytopathic effect or cytopathogenic effect (abbreviated CPE) refers to damage to host cells
during virus invasion..

Structural changes in a host cell resulting from viral infection. CPE occurs when the infecting
virus causes lysis (dissolution) of the host cell or when the cell dies without lysis because of
its inability to reproduce.

3. How does virus cause CPE in cell line.
CPE is usually a secondary result of changes in the host metabolism caused by viral
Viruses may halt or alter host cell DNA synthesis, transcription, and/or protein synthesis
Altered shape

4. Why is CPE important in diagnostic?

Cytopathic effect is an important tool for virologists concerned with isolating and identifying
viruses from infected animals or humans.

5. What are the different types of CPE?

Total destruction (ENTEROVIRUS)
- Cells shrink rapidly, become pyknotic.
Subtotal destruction (TOGAVIRUS)
- Some cells dead/detached
Focal degeneration (HERPESVIRUS)
- Localised foci of infection
- Enlarged, rounded, refractile cells
- Strangling of cytoplasm
Swelling and clumping (ADENOVIRUS)
- Cells greatly enlarge and clump together in grape-
Foamy degeneration (RETROVIRUS)
- Numerous cytoplasmic vacuoles
- Plasma membranes of 4 or more cells fuse
- Enlarged cell with 4 or more nuclei
Inclusion bodies
- Areas of altered cell staining
- Single or multiple-depends on virus
- Round/irregular
- Intranuclear/intracytoplasmic
- Eosinophilic/basophilic
- Indicate areas of viral protein synthesis or nucleic acid synthesis or virion assembly

6. Explain the meaning of viral pathogenesis

Study of how biological viruses cause diseases in their targeted hosts at a cellular or molecular
level. It also refers to the process of which an infection actually leads to a diseased state with
generally the same mechanisms involved throughout different viral strains.

7. Describe briefly the pathogenesis of the following viruses:
a) Hepatitis virus

There are two major types of Hepatitis which are Hepatitis A and Hepatitis B and each
pathway of pathogenesis is unique. For Hepatitis A, the liver cells, especially hepatocytes
would be directly infected with the Hepatitis A virus and induce a direct cytopathic effect.
The virus that is now in the hepatocyte would encode its own genome and cause viral
replication to happen, and then finally induce apoptosis. For Hepatitis B, the hepatocytes
would be infected with the Hepatitis B virus and what would follow is the infected cells
would undergo a immune lysis effect. At the same time, once viral replication is complete,
the surface of the infected cell would exhibit HBsAg which is the surface antigen of the
Hepatitis B virus. Once it exhibits the surface antigen, it will begin to attack the immune
system and finally also cause apoptosis amongst cells.
b) HIV virus

The pathogenesis of HIV viruses begins with the viral genome with its reverse transcriptase
entering the host cell before a copy of the DNA is synthesized by the reverse transcriptase
and subsequently the RNA is degraded to synthesize a second strand of DNA. The following
step involves the DNA circularizing to form a circular DNA by itself or forming a circular DNA
with the host cell DNA. If it forms a circular DNA on its own, it is an unintegrated provirus,
and vice versa if it forms a circular DNA with the host DNA. With the previous step
completed, the host cell is now activated, and proceeds in transcribing the viral genome to
produce messenger RNAs and viral genome RNAs. And as any other cell functions, the viral
RNAs will be translated and yielding viral enzymes which include proteases and even
structural proteins. The structural proteins especially membrane proteins are then
transported to the host cell membrane to undergo the final assembly procedure with the
viral genomes and budding finally takes place and proceeds to infect other host cells.

c) Dengue virus
The pathogenesis begins as soon as the virus has been injected into the body of the host,
humans especially by the mosquitoes. The dengue virus uses a secretory pathway which
helps in the maturity of the virus through the changing levels of acidity. It will move through
the cellular compartments such as the endoplasmic reticulum and Golgi apparatus. As the
dengue virus matures, it is capable of fusing with the cell membranes to ensure their
maturation and so that they would avoid infecting their own host cell. As soon as it matures,
it can begin to infect cells by changing the conformation of its outer protein shell. As the
virus matures, it is shown to have 2 linked protein layers which are the precursor membrane
protein and also the envelope protein. The precursor membrane protein serves to prevent
the immature virus to bind with membranes of other cells, and as soon as it matures, the
link between both protein layers is severed by enzyme furin which finally reveals the
envelope protein site which will finally make the protein to be able to infect other cells and
membranes. At this stage, the dengue virus will be able to easily infect other cells, inject in
their DNA, and in the end, generate many more copies of the dengue virus to be spread all
over the body and cause Dengue fever and other symptoms.
8. What is transformed cell?

Transformed cells are simply cells that have been transformed due to the viral infection and
induced to form tumors with an alteration of the host DNA by the viral DNA which
consequently affects the growth and morphology of the cell or possibly even chromosomal

There are 6 most prominent changes when observing a transformed cell, cell proliferation,
changes in the cell molecular level, changes in the metabolic of the cell, changes in the
intracellular components, tumorigenicity and the production of viral products.

9. Describe the different characteristics of transformed cell.
(refer notes of transformed cell)
10. What are the groups of viruses associated with cancer and give an example of a virus from each

There are 2 major groups of tumor viruses which are DNA tumor viruses and RNA tumor
Examples from DNA tumor viruses include papilloma viruses, polyoma viruses, adenoviruses,
herpes viruses, Epstein-Barr virus, and Hepatitis B virus.
An example of RNA tumor virus include retroviruses (including oncovirinae and lentiviruses)
especially Human T cell lymphotropic virus -1 and 2 which causes cancer in human.

11. Explain the meaning of antigenic shift and antigenic drift in relation to an influenza virus
pandemic outbreak.

Antigenic Shift

The other type of change is called antigenic shift. Antigenic shift is an abrupt, major change in
the influenza A viruses, resulting in new hemagglutinin and/or new hemagglutinin and
neuraminidase proteins in influenza viruses that infect humans. Shift results in a new influenza A
subtype or a virus with a hemagglutinin or a hemagglutinin and neuraminidase combination that
has emerged from an animal population that is so different from the same subtype in humans
that most people do not have immunity to the new (e.g. novel) virus.

Antigenic Drift

Antigenic drift is a mechanism for variation in viruses that involves the accumulation of
mutations within the genes that code for antibody-binding sites. This results in a new strain of
virus particles which cannot be inhibited as effectively by the antibodies that were originally
targeted against previous strains, making it easier for the virus to spread throughout a partially
immune population. Antigenic drift occurs in both influenza A and influenza B viruses.

12. Describe the mechanism antibodies and other non-specific molecules in process of destroying
pathogen. (10 marks)

The mechanism of antibodies in destroying pathogens usually involves B cells and is either T cell-
independent, or T-cell dependent. Antibodies are also known as the effector molecules of the
humoral immunity and there are several types of mechanisms on how antibodies especially
destroy pathogens. They include opsonization, neutralization, agglutination, precipitation,
complement fixation and even bacterial tagging. (CHOOSE 5 out of 6). These methods serve to
increase the efficiency of phagocytosis. In opsonization, the antigen will be covered by
antibodies and subsequently, the antibodies will bind to the Fc receptors of the phagocytes to
be ingested and destroyed by the phagocytes. Secondly, neutralization which is to prevent
adherence of bacteria, virus or exotoxin to the cell by having the antibodies to block the pili,
virus attachment site or the exotoxin binding site of the pathogen, hence disabling them to
infect the cells, and then be ingested by phagocytes. Thirdly, agglutination simply attaches the
antibody to multiple cells hence making a clump of the bacterium and rendering them immobile
and easy targets for phagocytes. Next is via precipitation whereby the antibodies will form an
aggregate with the antigen molecules and if it is complementary, it will result in the rupturing of
the cells and viruses, hence destroying the pathogens. Complement fixation however works on
the basis that the antibodies would bind to the antigens on the pathogens as their
complementary parts and cause a lysis effect on the pathogenic organism, thus destroying it.
And finally, through bacterial tagging is where the antibodies act as markers on the
pathogenic compound and alerts the phagocytes to come and attack and then destroy the
pathogen. Other forms of pathogen destroying molecules include antitoxins that serve to
neutralize the bacterial exotoxins.

13. Describe relationship between development of immune response cell and immunodeficiency
disease. (5 marks)

Immunodeficiency diseases are categorized into primary and secondary immunodeficiency
diseases, whereby the primary immunodeficiency is caused from a genetic or developmental
defect of the immune system whereby the condition might be present at birth or even stay
hidden until a stage of life where it will manifest itself. Secondary immunodeficiency disease or
acquired immunodeficiency disease is due to the loss of immune functions caused by exposure
to various agents. In these cases, the development of immune response is often difficult as they
would be deficient in ether B cells or even T cells. Hence usually, the best way to overcome tis
problem and develop an immune response for those with immunodeficiency diseases is either
through replacement of the missing protein, missing cell type or even the missing or defective
gene that is causing the immunodeficiency disease in the first place.
14. What is 4 potentially producing type of vaccine through molecular technique? (10 marks)

1. Inactivated proteins are one of the forms of producing vaccine through molecular
technique. They can be divided into 2 major groups that are subunit vaccine and also
synthetic vaccines. Subunit vaccines utilize bacteria or yeast to mass produce large
quantities of viral or bacterial protein which contain only a part of the microorganism and
are a safer option as it would not lead to side effects, but are less effective as it only induces
humoral immunity. Synthetic vaccines on the other hand, utilize almost the same concept as
subunit vaccine but it starts with the determination of the epitope of the virus particle
which counters protective antibodies and subsequently sequences it and synthesizes the
gene to produce protiens as in subunit vaccine.
2. DNA vaccine is simply a DNA sequence that can also be used directly as a vaccine as the
sequence is obtained from the viral genes that code for an essential protein that is vital for
viral growth or replication. By injecting the said DNA sequence into the host, the protein is
produced and the immune system is able to directly produce and immunity towards the
protein, hence, immunity towards the organism is produced.
3. Live deleted vaccines function by deleting the genes that code for the virulence of the virus
or simply proteins that contribute towards development of immune response in humans. By
this way, the virus strain is less virulent and lacks the ability to cause diseases, hence
producing safe and stable vaccines.
4. Live recombinant vaccines are established by the construction of a recombinant with the
myxomatosis virus and also the protein vp60 of the Hemorrhagic Disease of the Rabbit. This
method is quite effective as it is able to be used against more than one type of disease.
5. Anti-idiotype vaccine are simply based on the idea of using antibodies to trigger the same
response as an antigen would usually do to obtain an immune response. And this method is
used specially for cancer patients as it targets lymphomas primarily.
6. Plant-made pharmaceuticals are simply by the insertion of the viral or bacterial genes into
the plant chromosomes to give rise to transgenic plants and animals, and then, when these
plants or animals are consumed, the immune response would be triggered in the humans to
counter it.