1. بسم الله الرحمن الرحيم 1 1 1

2. Basic Virology: Introduction
Viruses are not cells
They are not capable of independent replication
They synthesize neither their own energy nor their own proteins
They are too small to be seen in light microscope.

3. Basic Virology: Introduction
Comparison of Viruses and Cells
Property
Viruses
Cells
Type of nucleic acid
DNA or RNA but not both
DNA and RNA
Proteins
Few
Many
Lipoprotein membrane
Envelopeviruses present in some
Cell membrane present in all cells
Ribosomes
Absent
Present
Mitochondria
Present in eukaryotic cells
Enzymes
None or few
Multiplication by binary fission or mitosis No
Yes

4. Virus Size & Structure
Viruses range in size from (~20 nm to ~300 nm) .
Most viruses appear as spheres or rods in the electron microscope.

5. Virus Size & Structure Capsid
All viruses have protein coat called capsid that covers genome.
Capsid is composed of repeating subunits called capsomers virus symmetric appearance used for classification.
Some viruses, capsid is covered with lipoprotein envelope.

6. Virus Size & Structure Nucleocapsid
It composed of nucleic acid genome & capsid proteins.

7. Virus Size & Structure Nucleocapsid Viral nucleocapsids have :
-Spherical (icosahedral) symmetry (enveloped or naked)
-Helical symmetry (enveloped).

8. Viral Nucleic Acids Viruses contain either DNA or RNA, but not both.
These DNA & RNA genomes can be either single- stranded or double-stranded.
Some RNA viruses (e.g. influenza virus & rotavirus), have segmented genome.
All viruses have one copy of their genome (except retroviruses, which have two copies).

9. Viral surface proteins
Viral Proteins
Viral surface proteins
It mediate attachment to host cell receptors (determines host & organ specificity of virus).
Surface proteins are targets of antibody which "neutralizes" (inhibits) viral replication.
Some viruses produce antigenic variants of their surface proteins evade host defenses.
Internal proteins :
They are DNA or RNA polymerases.

10. Viral Proteins Matrix protein
It mediates interaction between viral nucleocapsid proteins & envelope proteins.
Antibody against one antigenic variant (serotype) will not neutralize different serotype.
Some viruses have one serotype; others have multiple serotypes.

11. Viral Envelope
Envelope consists of membrane that contains lipid derived from host cell & proteins encoded by virus.
Envelope is acquired as virus exits from cell in process called budding.

12. Viral Envelope Enveloped viruses : -Easily inactivated
-transmitted by direct contact via blood & body fluids.
Naked viruses
Survive longer in environment
Transmitted by indirect means e.g. fecal-oral route

13. Viral Growth Curve
One virion infects cell & hundreds of progeny virions are produced within hours.
This is remarkable amplification & explains rapid spread of virus from cell to cell.
The eclipse period
It is time when no virus particles are detected within infected cell & occurs soon after cell is infected.

14. Viral Replication The steps in viral replication are as follows:
Attachment
Penetration and uncoating.
Transcription & Translation
Assembly
Release

15. Viral Replication 1-Attachment
Virus particles can only infect cells possessing surface “receptors” specific to particular virus species.
Virus attached to cell with:
Capsid (Naked viruses)
Envelope proteins
(enveloped viruses)

16. Viral Replication 2-Penetration
Viruses penetrate into cell by means of pinocytosis (viropexis).
In enveloped viruses, envelope fuse with cell membrane, releasing virus into cytoplasm.
Adsorption of such an enveloped virus to two cells at the same time may result in cell fusion

17. Viral Replication 3- Uncoating
It involves release of nucleic acid from capsid
It is activated by cellular enzymes & contribution from cell membranes (except smallpox virus)

18. 4- Replication of nucleic acid
Viral Replication
4- Replication of nucleic acid
DNA viruses
All DNA viruses genome is double-stranded (except parvoviruses, single-stranded)
They use host cell RNA polymerase to synthesize viral mRNA.
All DNA viruses replicate in nucleus (except poxviruses in cytoplasm).

19. 4- Replication of nucleic acid
Viral Replication
4- Replication of nucleic acid
RNA viruses
Genome of all RNA viruses is single-stranded (Except reoviruses, e.g., rotavirus double-stranded).
All RNA viruses replicate in cytoplasm, except retroviruses, influenza virus, & hepatitis D virus, which require intranuclear step in their replication.

20. Viral Replication Viral proteins:
Early proteins are typically enzymes used in synthesis of viral components, whereas late proteins are typically structural proteins of progeny viruses.
poliovirus & retroviruses, translate their mRNA into precursor polyproteins, which must be cleaved by proteases to produce functional proteins.

21. Viral Replication Assembly and release:
All enveloped viruses acquire their envelope by budding through the external cell membrane as they exit the cell,
herpesviruses, acquire their envelope by budding through nuclear membrane.

22. Viral Replication

23. Viral Replication Lysogeny
It is the process by which viral DNA becomes integrated into host cell DNA, replication stops, and no progeny virus is made.
Later, if DNA is damaged by, for example, UV light, viral DNA is excised from the host cell DNA and progeny viruses are made.
The integrated viral DNA is called a prophage.

24. Viral Replication Lysogeny
Bacterial cells carrying a prophage can acquire new traits, such as the ability to produce exotoxins such as diphtheria toxin.
Transduction is the process by which viruses carry genes from one cell to another.
Lysogenic conversion is the term used to indicate that the cell has acquired a new trait as a result of the integrated prophage.

25. Viral Replication

26. Genetics
Mutations in the viral genome can produce antigenic variants and drug-resistant variants.
Mutations can also produce attenuated (weakened) variants that cannot cause disease but retain their antigenicity and are useful in vaccines.
Temperature-sensitive mutants can replicate at a low (permissive) temperature but not at a high (restrictive) temperature.
Temperature-sensitive mutants of influenza virus are used in vaccines against this disease.

27. Genetics
Reassortment (exchange) of segments of the genome RNA of influenza virus is important in the pathogenesis of the worldwide epidemics caused by this virus.
Complementation occurs when one virus produces a protein that can be used by another virus.
A medically important example is hepatitis D virus that uses the surface antigen of hepatitis B virus as its outer coat protein.

28. Genetics
Phenotypic mixing occurs when two different viruses infect the same cell and progeny viruses contain proteins of both parental viruses.
This can endow the progeny viruses with the ability to infect cells of species that ordinarily parental virus could not.

29. Pathogenesis The Infected Patient
Viral infection in the person typically has four stages:
- incubation period,
-prodromal period
- specific-illness period,
- recovery period.
The main portals of entry are the respiratory, gastrointestinal, and genital tracts, but through the skin, across the placenta, and via blood are important as well.

30. Pathogenesis The Infected Patient
Transmission from mother to offspring is called vertical transmission; all other modes of transmission, e.g., fecal–oral, respiratory aerosol, and insect bite, are horizontal transmission.
Transmission can be from human to human or from animal to human.
Most serious viral infection are systemic, i.e., the virus travels from the portal of entry via the blood to various organs.
some are localized to portal of entry as common cold & involves only upper respiratory tract.

31. Pathogenesis Pathogenesis
The symptoms of viral diseases are usually caused by death of the infected cells and a consequent loss of function.
For example, poliovirus kills neurons, resulting in paralysis.

32. Pathogenesis Immunopathogenesis
It is the process by which the symptoms of viral diseases are caused by the immune system rather than by the killing of cells directly by the virus.
One type of immunopathogenesis is the killing of virus-infected cell by the attack of cytotoxic T cells that recognize viral antigens on the cell surface

33. Pathogenesis
Damage to the liver caused by hepatitis viruses occurs by this mechanism.
Another is the formation of virus–antibody complexes that are deposited in tissues.
Arthritis associated with parvovirus B19 or rubella virus infection occurs by this mechanism.

34. Pathogenesis
Viruses can evade host defenses by producing multiple antigens, thereby avoiding inactivation by antibodies.
and by reducing the synthesis of class I MHC proteins, Thereby decreasing the ability of a cell to present viral antigens and blunting the ability of cytotoxic T cells to kill the virus-infected cells.
Viruses produce receptors for immune mediators, as IL-1 and TNF, thereby preventing the ability of these mediators to activate antiviral processes

35. Persistent Viral Infections
Carrier state refers to people who produce virus for long periods of time and can serve as a source of infection for others.
The carrier state that is associated with hepatitis C virus infection is a medically important example.
Latent infections are those infections that are not producing virus at the present time but can be reactivated at a subsequent time.
The latent infections that are associated with herpes simplex virus infection are a important example.

36. Persistent Viral Infections
Slow virus infections refer to those diseases with a long incubation period, often measured in years.
Some, such as progressive multifocal leukoencephalopathy, are caused by viruses, whereas others, such as Creutzfeldt-Jakob disease, are caused by prions.
The brain is often the main site of these diseases.

37. Host Defenses
Host defenses against viruses fall into two major categories:
(1) Nonspecific, of which the most important are interferons and natural killer cells
(2) Specific, including both humoral and cell-mediated immunity.
Interferons are an early, first-line defense, whereas humoral immunity and cell-mediated immunity are effective only later because it takes several days to induce the humoral and cell-mediated arms of the immune response

38. Nonspecific Defenses Interferons
Interferons inhibit virus replication by blocking production of viral proteins, by degrading viral mRNA.
They induce the synthesis of a ribonuclease that specifically cleaves viral mRNA but not cell mRNA.
Double-stranded RNA viruses are the most potent inducers of interferons.
Many viruses induce interferons, and many viruses are inhibited by interferons, i.e., neither the induction of interferons nor its action is specific.

39. Nonspecific Defenses Interferons
Interferons act by binding to a receptor on the cell surface that signals the cell to synthesize the ribonuclease and the other antiviral proteins.
Interferons do not enter the cell and have no effect on extracellular viruses.
Alpha & beta interferons have a stronger antiviral action than gamma interferon.
Gamma interferon activates macrophages.

40. Nonspecific Defenses
Natural killer (NK) cells are lymphocytes that destroy cells infected by many different viruses, i.e., they are nonspecific.
NK cells do not have an antigen receptor on their surface.
NK cells recognize and destroy cells that do not display class I MHC proteins on the surface.
They kill cells by secreting perforins and granzymes.

41. Nonspecific Defenses
Phagocytosis by macrophages and the clearance of mucus by the cilia of the respiratory tract are also important defenses.

42. Nonspecific Defenses
Increased corticosteroid levels suppress various host defenses and predispose to severe viral infections as disseminated herpesvirus infections.
Malnutrition predisposes to severe measles infections in developing countries.
The very young and the very old have more severe viral infections.

43. Specific Defenses
Active immunity to viral infection is mediated by both antibodies and cytotoxic T cells.
It can be elicited either by exposure to the virus or by immunization with a viral vaccine.
Passive immunity consists of antibodies preformed in another person or animal.
The duration of active immunity is much longer than (years) that of passive immunity (weeks to a few months).

44. Specific Defenses
Passive immunity is effective immediately, whereas it takes active immunity 7 to 10 days in the primary response (or 3–5 days in the secondary response) to stimulate detectable amounts of antibody.
Herd immunity is the protection of an individual that results from immunity in many other members of the population (the herd) that interrupts transmission of the virus to the individual.
Herd immunity can be achieved either by immunization or by natural infection of a sufficiently high percentage of the population.

45. Laboratory Diagnosis Identification in Cell Culture
The presence of a virus in a patient's specimen can be detected by seeing a "cytopathic effect" (CPE) in cell culture.
CPE is not specific, i.e., many viruses cause it.
A specific identification of the virus usually involves an antibody-based test as fluorescent antibody, complement fixation, or ELISA.

46. Laboratory Diagnosis Microscopic Identification Inclusion bodies
They are formed by aggregates of many virus particles, can be seen in either the nucleus or cytoplasm of infected cells.
They are not specific.
Two important examples are the nuclear inclusions formed by certain herpesviruses and the cytoplasmic inclusions formed by rabies virus (Negri bodies).

47. Laboratory Diagnosis Multinucleated giant cells
They are formed by several viruses, notably certain herpesviruses, respiratory syncytial virus & measles virus.
Fluorescent antibody staining of cells obtained from the patient or of cells infected in culture can provide a rapid, specific diagnosis.
Electron microscopy is not often used in clinical diagnosis but is useful in the diagnosis of certain viruses, as Ebola virus, that have a characteristic appearance and are dangerous to grow in culture.

48. Laboratory Diagnosis Serologic Procedures
The presence of IgM can be used to diagnose current infection.
The presence of IgG cannot be used to diagnose current infection because the antibody may be due to an infection in the past.
acute and convalescent serum sample should be analyzed.
An antibody titer that is fourfold or greater in the convalescent serum sample compared to the acute sample can be used to make a diagnosis.

49. Laboratory Diagnosis Detection of Viral Antigens & Nucleic Acids
The presence of viral proteins, such as p24 of HIV and hepatitis B surface antigen, is commonly used in diagnosis.
The presence of viral DNA or RNA is increasingly becoming the "gold standard" in viral diagnosis.
Labeled probes are highly specific and rapidly.
Small amounts of viral nucleic acids can be amplified using reverse transcriptase to produce amounts detectable by the probes e.g."viral load" assay of HIV RNA.