This document provides an overview of viruses, including their definition, properties, structure, life cycle stages, pathogenesis, and methods of detection and treatment. Key points include: - Viruses are the smallest infectious agents that can only replicate inside host cells. They have either DNA or RNA genomes contained within a protein capsid. Some have an outer envelope. - The viral life cycle involves adsorption to a host cell, penetration, uncoating, replication of the viral genome, assembly of new viral particles, and release. - Viruses can cause disease through direct cell damage, immune response effects, and ability to evade clearance. Persistent infections occur when viruses avoid immune response or infect privileged sites.

1. BY:
Amr Shalaby

2. Definition:
Viruses are the smallest known infectious
agents, they can infect man, animals, plants,
insects & even bacteria ( Bacteriophage ) .
NB: The word ( Virus ) is a latin word
meaning ( Poison )

3. Properties:
1- Their size is very small (20-300nm) so they
only can be seen by EM except ( poxvirus ).
2- They are obligate intracellular parasites
,which can replicate only inside the host cells
as they lack the required machinery for
replication.
3- They can’t be grown on artificial culture
media , but only on living cells.
4- Their genome is either DNA or RNA ( but
never both )

4. Structure:
The virion ( the complete infectious virus
particle ) is constructed of two components ..
1- The nucleic acid core .
2- The capsid ( a protein coat protect the
genome ).
3- Other components : enzymes &
matrix protein ( may be present )
NB: They are together called the nucleocapsid
NB: Some viruses are enclosed in an
envelope.

5. 1-viral nucleic acid genome:
- Either DNA or RNA.
- Single or Double stranded.
- Linear or Non-linear.
- Segmented or Non segmented.
- All virus genomes are haploid ( 1 copy )
except : Retrovirus which are 2 copies of
linear RNA ( diploid )

6. 2- Viral Capsid :
- protein coat of the virus
- makes most of the virion mass
- composition small protein subunits called
capsomers ,this arrangement determines the
virus symmetry
functions of capsid :
1) Protection of genome from destruction
2) Attachment to specific receptors on cells
3) Antigenic : induce Ab & activate Tc
4) Arrangement of the capsomers

7. Viral Envelope:
Structure :
surrounded by lipid or lipoprotein envelope
& covered by glycoprotein spike like
projections
Source :
partially or totally derived from host cell
membrane during release of virus by Budding
Importance :
1- Sensitive to heat , detergent & ether
2- Loss of envelope causing loss of infectivity

8. Envelope proteins :
A- matrix protein : link nucleocapsid to
envelope
B- spike glycoprotein attached to cell receptors
C- antigenic structure
D- determine type specificity of the virus
Viral enzymes:
Carry enzyms important for their replication.

9. Atypical virus like agents :
A- Defective viruses : viruses can't replicate
without a helper providing the missing
function
B- Pseudovirions : contain host cell DNA
instead of viral during viral replication parts of
host DNA incorporated in the viral capsid
infectious but not replicative
C- Viroids : infectious agents composed only of
Single Stranded circular RNA with some
double stranded regions causing plant
diseases
D- Prions : infectious particles composed of
solely of proteins i.e. no nucleic acid & cause
slow diseases e.g mad cow disease

10. Definition : It is the intracellular phase of
virus life cycle that starts by the contact of a
virion depending completely on the cell's
metabolic function .
Stages :
1-Adsorption 2-Penetration
3-Uncoating 4-Transcription
5-Translation 6-Synthesis of nucleic acid
7-Assembley of new virions
8-Release of new virions

11. 1-Adsorption of virus to host cell:
Binding between receptor binding site (on
viral surface) & specific receptor on host cell .
The exact fitting between them is the basis of
viral tropism ( the specificity of the virus to a
particular host tissue ) .

12. 2-Penetration:
-Enveloped viruses: by fusing to plasma
membrane
-Non enveloped: by endocytosis: by
endocytosis (then liberation inside cell)

13. 3-Uncoating:
- proteolytic enzymes of the host attack virus
destructing its capsid (liberation of genome)
NB: Uncoating mark the beginning of eclipse
phase ( virus cannot be detected but genome is detected by
molecular test )

14. 5-Transcription:
-1- In double strand DNA viruses :
-mRNA is transcribed from the negative strand of
DNA by host cell DNA dependent RNA polymerase .
2- In ssRNA viruses of +ve sense:
ssRNA itself act as mRNA for translation into protein .
3- In ssRNA viruses of –ve sense:
transcribed by RNA dependent RNA polymerase into
complementary mRNA

15. 6-Translation :
Viruses use the cellular ribosomes to translate
their viral mRNA into:
-non structural ptns (early ptns): replication
enzymes
-structural ptns (late ptns): coat ,core, cote
ptns

16. 7-Genome synthesis:
By using single strand as template .
8-Assembly:
Assembly of genome & coats to form mature
viruses e.g herpes virus
9-Release:
- Non enveloped: lysis of cells
-Enveloped: budding (taking part from cell
membrane) with no cell lysis

17. Defenetion:
It's the process by which a viral infection
leads to disease .
NB: Infection Vs disease
ŸInfection : entry of the virus into the body produces
no symptoms or transient symptoms due to local infection
.
ŸDisease : virus at target organ produces signs and
symptoms associated with disease .
NB: The majority of viral infections are
subclinical

18. Outcome of viral infection :
Acute infection:
Recovery , death , progression to chronic
Chronic infection:
- Silent subclinical infection for life .
- Long silent period before disease .
- Reactivation to cause acute disease .
- Chronic disease with relapses and exacerbations .
- Cancers .

19. Factors in viral pathogenesis :
1- Cellular pathogenesis :
cells can respond to viral infections in 3 ways :
ŸNo apparent change ,Death ,Transformation .
2- Viral entry :
Skin, Conjunctiva and other mucous membranes,
Respiratory tract, GIT and Genitourinary tract .
3- Cell tropism :
viral affinity to specific tissue determined by :
Ÿcell receptors for virus
Ÿcell transcription factors that recognize viral
promoters and enhancer sequences .
Ÿability of the cell to support virus replication .

20. 4- Course of viral infection :
Primary replication :
The virus replicates after gaining initial entry into the host .
This determines whether the infection will be localized at the
site of entry r spread to become a systemic infection .
Systemic spread :
Apart from direct cell-to cell contact, the virus may spread
via the blood or lymphatic causing viraemia or through the
nerves to reach the target organ .
Secondary replication :
Takes place at susceptible organs/tissues following systemic
spread .

21. 5- Cell damage :
- Viruses may replicate throughout the body
without any symptoms if they don't cause
significant cell damage or death .
- Retroviruses don't generally cause cell
death, being released from the cell by budding
rather than cell lysis, and cause persistent
infections .
- Picornaviruses cause lysis and death of the
cell in which they replicate .

22. 6-Immune response :
It has the greatest impact in the outcome of
infection . Cellular immunity plays the major
role in clearing the viral infection whereas
humoral immunity protects againre reinfection
.
7- Viral clearance or persistence :
The majority are cleared but some viruses may
cause persistent infections .

23. Mechanism of viral persistence
1- Antigenic variation
2- Immune tolerance, causing a reduced
response to an antigen, may be due to genetic
factors or prenatal infection .
3-Infection of immuneprivileged sites within
the body e.g HSV in sensory ganglia in the
CNS .
4-Direct infection of the cells of the immune
system itself e.g Retrovirus (HIV) often
resulting in immunosuppression .

24. 1-Direct detection in clinical
specimens:
1- light microscopy : can be used for large viruses e.g.
Poxviruses in skin lesions and for inclusions bodies e.g. Negri
bodies of Rabies viruse in nerve cells .
2- Electron microscopy : used to demonstrate large
number of virus particles in vesicular fluid or tissue extract
treated with special stains.

25. 3- Immuoelectron microscopy (IEM) : by adddition
of specific antisera to clinical samples leading to aggregation of
virus particles which can be see easier than separate virus . e.g.
Hepatites A virus ad rotavirus detectio in stools.
4- Immunofluorescence microscopy : fluorescein
labeled specific antisera are added to smears from lesions and
visualized by fluorescense microscope.e.g. diagnosis of rabies in
brain smears.
5- Solid-phase immunoassays : Radioimmunoassay
(RIA) and Enzyme linked immunosorbent assay (ELISA) are
used to detect virl antigens in clinical specimens.e.g. detection of
p24 antigen of HIV in blood .

26. 6- Nucleic acid hybridization : labeled DNA probes
are used to detect virus nucleic acid by hybridization with
its
complementary part in the sample.
7- Polymerase chain reaction : by amplification of a
short sequence of the target nucleic acid which maybe of a small
amount in the sample to facilitate its detection .

27. 2- Isolation of viruses :
A- cell cultures :
These are pieces of animal or human tissue to which
trypsin is added to separate the cells .Cells are grown with
a growth medium containing serum , on glass or plastic
tubes , bottles or plates with a flat side . A monolayerof
cells is formed on the flat side into which the viruses is
inoculated there are 3 types of cell cultures :
1. primary cell lines : prepared from organ fragments
2. Human diplod cell lines : which are fibroblasts from
human embryo tissue , the grow rapidly.
3. Continuous (heteroploid) cell lines : from tumor
cell , they can divide identically.

28. Detection of viruses in cell cultures:
1.Cytopathic effects (CPE) : change :
a.Cell death & detachment from the glass surface (poliovirus)
b.Rounding & cluster formation (adenovirus)
c.Syncytium or multinucleated giant cell formation
(measles)
d.Transformation (tumor viruses)

29. 2. Plaque formation : virally infected areas in cell
cultures that can be seen by naked eye as unstained areas
when stained with crystal violet .
3.Inclusion bodies : structures seen by LM :
-Intranuclear (Herpesvirus)
-Inracytoplasmic (pox & rabies virus *Negri bodies*)
4.Haemagglutination : cell culturebfluid + RBCs >>
clumping of RBCs on areas infected with virus.

30. 5.Interference : growth of some viruses can be detected
by their interference with growth of CPE producing viruses .
6. Flouresence ab staining : florescein labeled ab +
infected cells >> fluorescence by fluorescent microscope.
7.Neutralization tests : viruses with CPE + ab + cells >>
NO more CPE .
8.Serology for ag : ELISA & complement fixation .
9. Decrease acid production : in dying cells & detected
by color change using a PH indicator .

31. B- Embryonated eggs :
Viruses can be grown in the amniotic or allantoic cavity on
the choriallantoic membrane or in the embryo itself .
The virus is detected by lesions (pocks) on the chorioallantoic
membrane or by the hemagglutination in the fluid from
cavities
C- Laboratory animals :
Inoculation of the virus into laboratory animals was
mainly used in the past before using tissue culture .
However it still used to study viral pathogensis
.oncogensis and immune response against viruses .white
suckling mice are the most widely used for virus
inoculation

32. 4- Serelogical methods to detect
anti viral antibodies :
By detecting arising antibody titer throught
obtaining two samples
The first one in the acute phase and the second after
10-14 days .
A four-fold rise in antibody titer indicates infection
Detection of IgM antibodies in a single serum
sample indicates infection . Also the presence of IgM
to any virus in a serum of newborn indicates
infection in utero , the used test include
neutralization ,ElIsa, RIA,IF,complement fixation
or haemagglutination inhibition

33. 4- Skin test:
Are used to detect cell mediated immunity against
some viral infections e.g. mumps

34. 1- chemotheraputic antiviral .
2- Cytokines therapy .
3- Antiviral immunoglobulins .

35. 1- chemotheraputic antiviral :
Chemotherapy aims at the use of a chemical
that inhibit virus replication steps .
1 . Nucleoside analogues :
a-azidothymidine :
-Synthetic thymidine analogue.
- Inhibit replication of HIV by inhibiting viral reverse
transcriptase and block proviral DNA synthesis .
- Dideoxyinosine (DDI) : same action , less toxic
b-Deoxythiacytidine and stavudine :
-used if resistance to treatment with AZT or DDI develop .
c-Acyclovir :
-Guanisine analogue inhibting Herpes simplex virus .
-Inhibits virus specific DNA polymerase .

36. 2 . Nucleotide analogues :
They differ from the nucleoside analogs in having
an attached phosphate group . their ability to persist in
cells for long periods of time increases their potency e.g.
cidofovir
3 . Non nucleoside reverse transcriptase
inhibitors :
They act by binding directly to reverse
transcriptase and disrupt the enzyme catalytic site e.g.
nevirapine.
4 . Protrease inhibitors :
Such drugs inhibit the viral protease that is
required at the late stage of replication cycle . e.g.
saquinavir used for treatment of HIV infection

37. 5 . Fusion inhibitors :
Fuzeon is a large peptide that blocks the
virus and cellular membrane fusion step involved in
entry of HIV-1 into cells.
6. Other types of antiviral agents :
- Ribavirin : Synthetic nucleotide effective against
many DNA & RNA viruses .
-Amantadine & rimantadine : Synthetic amines
inhibiting uncoating of influenza A but not B virus .
-Zanamivir : Inhibits the release of influenza virus
from infected cells .
-Foscarnet : A viral polymerase inhibitor of herpes
viruses . It also inhibits the reverse transcriptase of
HIV
-Methisazone : Is of historical interest as an
inhibitor of poxviruses .

38. Combination chemotherapy:
These are strategies to use more than one drug
for therapy of viruses especially those that
undergo mutation inside the body , Examples:
1-HAART(highly active antiretroviral therapy)
used to treat HIV with nucleoside analogue AZT ,a
nonnucleoside nalogue Lamivudine ,and protease
ihibitor eg, Saqwinavir,Ritonavir.
2-Pegylated interferon alpha , ribavirinand
protease inhibitor to treat HCV
3- Pegylated inter feron alpha with
Lamivudin to treat HBV

39. 2-Cytokines Therapy:
Examples:
1-Antiviral cytokines
Type 1 interferon :inhibits viral replication
.therapeutic targets are HBV,HCV,herpes
zoster,papilloma,HIV.
side effects of therapy are fever,malaise,fatigue,muscle
pain and depression
Type 2 interferon :up regulates expression of class2
MHC,enhance activity of CTL and macrophageand
inhibit viral replication . Therapeutic targets are viral
encephalitis ,slow viruses,prions. side effects are
rare.include kidney,liver, heart,and bone marrow toxicit

40. 2-Regulators of lymphocyte functions
Interleukin-2 (IL-2) induces proliferation of B ,T cells
and CTL and stimulates NK cells.
Therapeutic targets is local treatment of viral skin
and mucous membranes lesions .
Side effects of therapy are : depression,
ascites,renal failure, hepatic failure and mental
changes

41. 3- Antiviral immunoglobulins :
These are used for passive immunization and immunotherapy .The
injection of human hyperimmune globulin provides an immediate
partial or complete
protection last for 2-4 weeks Examples :
1- Vaccine induced anti HBs human immuneoglobulin (HBIG)
- Co-administered with r-HBs vaccine to newborns of mothers with
active HBV- infection .
- Persons with needle stick injuries with first dose of accelerated
vaccination with r-HBs
2- Vaccine induced human anti rabies immunoglobulin (HRIG) :to
provide rapid protection after exposure to rabies virus until vaccine
immunity develops by active vaccination .injected IM around the bite
site .

42. Source
Basics in medical microbiology and
immunology
part IV VIROLOGY
By
Staff members of medical microbiology and
immunology department
Faculty of medicine ,Zagazig university
Thank you
ASh