GENERAL VIROLOGY

Viruses

• Viruses are the smallest infectious agents.

• They are obligatory intracellular parasites
because they have no metabolic activity.
•

Viruses Can Infect All Organisms In Nature

1. Bacteriophages: are bacterial viruses.

2. Animal viruses: infect vertebrates, including man.

 Differences between Viruses & Bacteria

Viruses are very small in size, ranging form 20-300 nm.

So:

• They can only be seen under the electron

microscope (except poxviruses).

• They can pass through bacterial filters.

• They need ultracentrifugation for

sedimentation.
 Differences between Viruses & Bacteria

• Viruses contain only one type of nucleic acid (DNA or

RNA), never both.

• They are not susceptible to antibacterial agents.

• They are obligatory intracellular parasites, i.e. can only

replicate inside living cells.

• They can not be cultivated in the laboratory on artificial

culture media.
 Viral Cultivation

Embryonated egg

Cell culture (tissue culture)

Laboratory animals (intact animals) 8

 structure & composition of viruses

• The complete virus particle (virion) is composed of a

nucleic acid core (DNA or RNA) surrounded by a protein
coat (capsid).

• The nucleic acid & the protein coat are called nucleocapsid.

• Some viruses have additional lipoprotein layer called

envelope, other viruses are non-enveloped (naked).
STRUCTURE OF VIRUSES
 Viral Capsid

• It is formed of subunits called capsomeres.

• Viral capsid has the following functions:

• It protects the nucleic acid.

• It mediates attachment to host cell (in non-

enveloped viruses).
• It is the antigenic part of the virus.

• It is responsible for the viral morphology (or

symmetry).
 Viral Symmetry
Icosahedral
symmetry Helical
symmetry
1. Icosahedral symmetry: Icosahedral or isomeric cubic viruses
resemble a crystal with 20 triangul facets
& 12 corners. This include all DNA viruse except
poxviruses (brick-shaped) & some RNA viruses.

2. Helical symmetry: The viral nucleic acid is closely

associated with the protein capsid forming a coil- shaped
helical nucleocapsid. This includes many of RNA viruses, e.g.
rabies virus.
3. Complex symmetry: e.g. the brick-shaped poxviruses &
bacteriophages.
Complex Symmetry
 Viral Nucleic Acid (Genome)
1

• It is responsible for virulence, i.e.

• it is the infectious part of the virus.
• Also, it carries the genetic information of the virus.

• Only one type of nucleic acid is present in the virus,

either DNA or RNA.
 Viral Nucleic Acid (Genome)
2

• Most DNA viruses are double-stranded (ds) while most

RNA viruses are single- stranded (ss).

• The viral ssRNA may be positive-sense strand (+sense)

or negative-sense strand (-sense).
 Viral Envelope 1

• It is formed of lipoproteins & is composed of lipids (derived

from the host cell membrane during release by budding) and
proteins (virus- specific).

• Enveloped viruses are less stable than naked viruses as they

are sensitive to heat, drying, detergents & lipid solvents,
(e.g. ether). Therefore, they are transmitted mostly via
blood & body fluids.
 Viral Envelope 2

• It has glycoprotein spikes (of viral origin) which are the

organ of attachment of the enveloped virus to host cell
receptors.

• Therefore, dissolving the envelope inhibits attachment &

the virus loses its infectivity.
 classification of viruses

A- Classification by symptomatology:

• It is the old classification based on diseases they produce,

i.e. tropism, e.g. neurotropic viruses, enteroviruses, ...
etc.

B- The Hierarchical Classification (into families, subfamilies,

genera, species, types, subtypes & strains) based on:

1. Type of nucleic acid (DNA or RNA).

2. Virus size.
3. Virus capsid symmetry.
4. Presence or absence of envelope.
5. Virus replication strategy.

C- The Baltimore Classification: based on virus genome

replication strategy in order to generate positive
strand mRNA:

dsDNA, (+)ssDNA, dsDNA-RT, (+)ssRNA-RT,

(+)ssRNA, (-)ssRNA, dsRNA
 VIRUS
REPLICATION 8

• Viruses are inert particles without metabolic activities.

• They depend on living host cells for providing the
virus components under the information given by the
virus genome.

• With the exception of the poxviruses, all DNA viruses

replicate in the nucleus of the host cell.

• With the exception of the orthomyxoviruses &

retroviruses, all RNA viruses replicate in the cytoplasm
of the host cell.
 stages of virus replication 1

1. Attachment (adsorption):
Adsorption of the virus occurs
to specific receptor sites on
the surface of the susceptible
host cell (thus determining
host range & viral tropism).
2. Penetration (Internalization):
3. This occurs either by:

Endocytosis in case of non-enveloped viruses

Or

Fusion of viral envelope with host cell

membrane in case of enveloped viruses

4. Uncoating: The nucleic acid is released from the capsid
by lysosomal enzymes & is available for replication.

5. Eclipse: This is the time from uncoating until assembly

of mature viruses. During this phase, no infectious
viruses can be detected in the host cell.

6. Synthesis of viral components: Specific messenger

RNAs are transcribed from the viral nucleic acid, & are
translated by the host cell ribosomes to form viral
components according to the type of viral nucleic acid as
follows:
 DNA-Viruses mRNA

(by the host’s transcriptase; DdRp enzyme from the

negative-sense strand in the host’s cell nucleus).
 RNA-Viruses

-transcribed
dsRNA the negative sense strand is
by viral RNA polymerase (RdRp) into mRNA.

-mRNA.
Positive strand (+ssRNA) acts directly as

- Negative strand (-ssRNA) positive RNA

strand (mRNA) by viral RdRp.
•Retroviruses which contain +ssRNA, by the action of the
reverse transcriptase enzymes, will produce complementary
ssDNA (cDNA) ds DNA.

• This is either integrated in host cell genome (causing

transformation) or transcribed by host’s DdRp to mRNA.
7. Assembly (morphogenesis):
8.
The nucleic acids are enclosed within the protein coats to
form mature viruses (virions).

This occurs either in the nucleus of host cell, e.g. herpes

viruses or in the cytoplasm, e.g. polioviruses.

9. Release: New viruses are released either by:

a- Lysis of host cell & release of new viruses in case
of non-enveloped viruses.

b- Budding through the cell membrane in case of

enveloped viruses.
 pathogenesis of viral diseases 1

I. Entry of viruses:
• Viruses enter the body either by inhalation, ingestion,
contact (urogenital system) & through skin (injections,
blood transfusion, insect animal bites).

• Viruses usually replicate in the primary site of entry.

Some viruses produce disease at the portal of entry
(local viral infections), others have to spread to
distant organs (either via the blood i.e., viraemia, or
by other means, e.g. along nerves) & produce systemic
(deep) viral infections.
Differences between Local & Systemic Viral Infections

Local Systemic (Deep)

Infections Infections
Specific disease common cold Measles
example (rhinovirus)
Site of pathology Portal of entry At distant sites

Incubation period Relatively Relatively long

short
Viraemia Absent Usually present

Duration of immunity Usually short Usually life-long

Igs involved Secretory IgA IgM & IgG

 II. Fate of Viral Infections
1
1. Inapparent or subclinical or abortive viral infections: Viral
infection without overt signs & symptoms.

2. Apparent infections (disease): This may be local or

systemic with the appearance of clinical signs & symptoms.

3. Persistent (chronic) viral infections : the virus is

continuously detected with mild or no clinical symptoms,
e.g. chronic hepatitis B.
 II. Fate of viral infections
4. Latent2 viral infections: The virus persistsin a
dormant form & may flare up intermittently to produce
disease, e.g. herpes viruses.

5. Slow infections: Infections with long incubation periods

(months or years). They are caused by two types of
infectious agents:
- Conventional viruses, e.g. a variant of measles virus which
causes subacute sclerosing panencephalitis (SSPE).
- Unconventional agents (prions).
 Lab Diagnosis of Viral
Infections
I. Direct methods:

a. Direct detection (of viruses and/or their antigens

and/or their nucleic acid)

b. Isolation of viruses (on tissue culture or

embryonated eggs or living animals)

II. Indirect methods:

a. Serological diagnosis
b. Skin tests
 treatment of viral infections

• Viruses can not be treated with antibiotics because they

lack the structural targets on which antibiotics can act.

• Viruses are obligate intracellular parasites

antiviral drugs must selectively inhibit viral replication
without causing damage to the host cells (TOXICITY!!!).

• The number of antiviral drugs is limited compared to

antibacterial drugs (COST!!!).
 1-Fusion Inhibitors
(to block virus entry)
• Fuzeon: for HIV

2-Inhibit Uncoating

• Amantadine: for influenza A virus

• Rimantadine: (a less toxic derivative of

amantadine): for influenza A virus.
3- neuroaminidase Inhibitors
(to interfere with the release of
virus from infected cells)

• Oseltamivir (Tamiflu): for influenza A & B

viruses.
• Zanamivir: for influenza A & B viruses.
4. Inhibit Viral DNA Polymerase
(Nucleoside analogues)

• Acyclovir (Zovirax):
- Topical acyclovir used for primary genital herpes,
herpetic corneal ulcer & herpetic skin lesions (effective
against HSV-I, II & VZ virus).

- Parenteral acyclovir (effective in treatment of HBV

infection).
• Ganciclovir: effective against CMV.
• Vidarabine (Adinine arabinoside, Ara-A): used for
herpes viruses, vaccinia & HBV.

• Iododeoxyuridine (IDU): used only topically in the

treatment of herpetic keratoconjunctivitis.
 V. Inhibit viral mRNA Synthesis

• Ribavirin (Virazole):

• Aerosol: used for:

• Pneumonitis caused by RSV in infants
• Influenza B infection

• Parenteral: used for the treatment of HCV in

addition to IFN.
 VI. Inhibit RT
(i.e. inhibit early stages of viral replication)

• Azidothymidine (Zidovudine, AZT), Lamivudine (3 TC) &

Stavudine (d4T): used in treatment of AIDS.

• Zalcitabine (dideoxycytosine, dde): used in treatment of

AIDS & HBV.

VII. Protease Inhibitors

(i.e., inhibit late stages of HIV replication by inhibiting cleavage
of polypeptide)

• Indinavir
• Ritonavir .Sanquinavir
 VIII. Inhibition of Viral Protein
Synthesis

• Methisazone: for poxviruses (small pox)

• Interferons: for chronic HBV, HCV & HPV

 Hepatitis Viruses

Viruses infecting the liver as a primary target:

HAV: Picornaviridae (non-enveloped, positive-sense ssRNA)
HBV: Hepadnaviridae (enveloped, partially dsDNA)
HCV: Flaviviridae (enveloped, +ssRNA)
HDV: Deltaviridae (defective, ssRNA)
HEV: Caliciviridae (non-enveloped, +ssRNA)

Viruses infecting the liver as a secondary target:

yellow fever virus, Epstein-Barr virus (EBV) and cytomegalovirus
(CMV).
 hepatitis a virus (hav)

• HAV is one of the Picornaviridae family.

• HAV is a non-enveloped ssRNA virus.

• There is only one serotype.

• HAV causes hepatitis A (previously called infectious

hepatitis).

• The disease occurs in sporadic or epidemic forms.

 Pathogenesis & Clinical Picture

• Reservoir: humans (mostly affects children & young

adults).

• Transmission: Faeco-oral route (rarely by blood).

• Incubation period: 2-6 weeks.

• C.P.: Fever, GIT symptoms (anorexia, nausea, vomiting),

jaundice, dark urine.

• Mostly subclinical, but if symptomatic, usually mild

symptoms, self-limited, no chronicity. Long-lasting
immunity.
 Laboratory Diagnosis

• Marked elevation of liver enzymes & bilirubin.

• Detection of anti-HAV IgM (by ELISA or RIA) during

the acute phase.

• Detection of anti-HAV IgG during convalescence.

• Detection of HAV particles in stools or blood by

E/M or RT-PCR.
 Prevention & Control

• General: Proper hand washing, chlorination or boiling of

drinking water,
proper sewage disposal.
• Specific:
• Active:
• Inactivated vaccine (Havrix): 2 doses I.M. at 0 & 6
months. Given to high-risk people above 2 years in
endemic countries.
• A combination vaccine (Twinrix): immunizes against
HAV & HBV), given at 0, 1, 6 months,
recommended for 16 years of age or older.

• Passive: HAV-Ig for post-exposure prophylaxis to prevent

the
disease in immunodeficient persons.
 hepatitis e virus
(hev)
• Itis a Calicivirus (non-enveloped, +ssRNA), characterized by
faeco-oral transmission and a short incubation period of
about 6 weeks.

• Diseaseis of self-limited nature (either sporadic or in the

form of epidemics), affecting mainly young adults.

• Thereis a risk of fulminant hepatitis and high mortality

due to DIC, especially in pregnant females (up to 25%).
 hepatitis e virus
(hev)
Diagnosis

• Detection of anti-hepatitis E virus IgM by ELISA.

• RT-PCR is used to detect viral RNA in stools.

 hepatitis b virus (hbv)

• HBV is an enveloped partially dsDNA virus of

Hepadnaviridae family that causes serum hepatitis.

• The intact virion, known as the Dane particle, is spherical

with
42 nm diameter, and is composed of:

• Envelope (Outer shell): containing HBsAg which is

released into the blood (There are two other forms of
such particles, 22 nm spherical and 22 X 200 nm
tubular particles which are non-infectious because there
is no viral DNA in these particles).
• Nucleocapsid: contains 2 additional Ags:
• HBcAg: which is confined to the liver cells
• HBeAg: which is secreted from infected cells into
the blood

Structure of HBV

22 nm

42 nm
22 X 200nm
Electron Micrograph of Serum containing HBV
 Modes of HBV Transmission
Blood & percutaneous transmission (Transmission via blood
transfusion is rare nowadays due to routine screening).

Sexual contact (heterosexual or homosexual).

Perinatally (mother to fetus):

most commonly by contact of maternal blood to the infant's
mucosa at the time of delivery.

Transplacental transmission accounts for a minority of cases.

 Risk Factors for Hepatitis B
• Sexual partner of a hepatitis patient or carrier
• Parenteral drug addicts
• Infants of infected mothers
• Household contacts with a hepatitis patient
• Patients receiving transfusion of blood or blood
products e.g., haemophiliacs
• Haemodialysis patients
•
• Occupational exposure to blood & infectious body fluids
(health care workers)
• Individuals undergoing tattooing
HBV is a hepatotropic virus that replicates in the liver
and causes hepatic dysfunction (immune- mediated by
Tc cells).

Extra-hepatic manifestations (in 10-20%) may occur

(rash, urticaria and polyarthralgia, vasculitis and
glomerulonephritis can result from immune complex
deposition in the skin, joints & glomeruli).
Incubation period: 6 weeks - 6 months

Onset of the disease: gradual

Clinical manifestations: depend on the age at infection, level

of HBV replication & host's immune status:
• Perinatally infected infants: generally no signs or
symptoms with normal levels of liver enzymes but more
liable to chronicity (app. 90%) and HCC.

• Older children & adults: symptomatic in 33-50% of

infections.
• Constitutional symptoms such as malaise & anorexia may
precede jaundice by 1-2 weeks.

• Clinical symptoms & signs: include nausea, vomiting,

abdominal pain and jaundice. Skin rashes, joint pains and
arthritis may occur. The liver is enlarged and tender.

• Clinical Outcomes of Acute HBV Infection

• Full spontaneous recovery: within 4-6 months (due

effective cell-mediated & humoral immune responses).

• Fulminant hepatitis: occurs in 1-2% of patients with acute

disease. Acute hepatic failure occurs in approximately 0.1-
 0.5% due to:
• massive immune-mediated lysis of infected hepatocytes.
• A more virulent HBV strain.
• Co-infection with another hepatitis virus (HCV or HDV).

• Chronic infection:
• in 5-10% (due to limited cell-mediated & humoral
immune responses) in the form of chronic hepatitis or
chronic carriers.
Complications
Chronic infection (in 5-10%) can lead to long
term complications:
1. Chronic active hepatitis & liver cirrhosis
liver cell failure & death.
2. Hepatocellular carcinoma (HCC).
 Chronic Chronic carriers
active
hepatitis
HBsAg Persistence For ˃ 6 months For ˃ 6 months
Liver enzymes Elevated Normal
Viral load high Low or undetectable
HBeAg May be present Usually absent
Liver biopsy Chronic hepatitis No significant
hepatitis
Outcome May end in cirrhosis May remain
&
apparently healthy
HCC
or progress to
chronic active
hepatitis
 Laboratory Diagnosis
Hepatitis B virus Markers 1
(HBV Antigens & Antibodies)

1. HBsAg: can be detected in the blood during the

incubation period and active disease.

It usually declines within a period of 12 weeks.

Its persistence for more than 6 months indicates a

chronic carrier state.

2. Anti-HBs: appears late, with the disappearance of HBsAg

and denotes immunity.
3.HBcAg: is present only in the liver cells and can not be
detected in blood.
4.Anti-HBc: of 2 Ig classes, IgM and IgG:
• IgM anti-HBc is detectable at the time of clinical onset
and declines within 6 months, thus it is a valuable
diagnostic test for recent HBV infection when other
markers are negative.
• (There is a period designated the window phase during
which HBsAg has disappeared while anti-HBs is not yet
detectable.
• During this phase, IgM anti-HBc is always positive and
diagnostic).
• IgG anti-HBc persists indefinitely as a marker of past
infection.
 A. Hepatitis B virus Markers 3
5. HBeAg: It can be detected in the serum in the late
incubation period and during the acute illness.
Its presence is associated with high infectivity of the
patient.
Its disappearance is a good prognostic sign.

6. Anti-HBe: Its detection is a strong evidence of

recovery & low infectivity).

N.B.: Persistent HBeAg & absence of HBeAb is an

indication for treatment, as such a patient is developing
chronic active hepatitis.
A. Viral DNA: can be detected by PCR. It is indicative of
viral replication and is important in the diagnosis of
chronic infection.

B. Liver function tests, e.g. serum alanine

aminotransferase (ALT) and bilirubin are markedly
elevated.
 Interpretation of hepatitis B markers
Tests Results Interpretation

HBsAg Positive
HBcIgM Positive Acute HBV infection
HBsAb Negative
HBsAg Negative
HBcIgM Positive Window phase of acute HBV infection
HBsAb Negative
HBsAg Positive
HBcIgG Positive Chronic HBV infection
HBcIgM Negative
HBsAb Negative
HBsAg Negative
HBcIgG Positive Immunity following natural HBV infection
HBsAb Positive

HBsAg Negative
Immunity following HBV vaccination
HBcAb Negative
HBsAb Positive

Treatment
No specific treatment is available for acute illness.

Antiviral drugs are approved only for the treatment of

chronic hepatitis B (e.g., IFN-alpha & lamivudine).
 Prevention & Control

1. General Measures

• Screening of blood before transfusion.

• Implementation of infection control practices

(standard precautions) such as:
• hand hygiene
• use of PPE, disposable syringes, tattoo needles …
etc.
• avoid recapping of the used needles
 2. Specific Prophylaxis

A. Recombinant vaccines:
by using HBsAg produced in yeast.

Given in 3 I.M. doses:

at 0, 1, 6 months (for adults,
deltoid).
At 2, 4, 6 months (for infants,
thigh).
 Passive Immunization

B. Hepatitis B immunoglobulin (HBIG) + vaccination

given as post-exposure prophylaxis to:
• Neonates born to HBsAg positive mothers.

• Unvaccinated or incompletely vaccinated persons

(e.g. HCW after needle-prick injury).

N.B., Non-responders are given only 2 doses of HBIG, one

month apart.
 hepatitis delta virus (hdv)

• It is a unique defective enveloped ssRNA

containing an internal core protein (delta antigen).

• HDV can only replicate in patients with HBV infecti

(either a co-infection or a super-infection).

• As HDV is dependent on HBV it follows a similar

epidemiology. It can be controlled through control of
hepatitis B infection.

• Diagnosis: By detection of anti-HDV antibodies or delta

antigen or RT-PCR for viral RNA.
hepatitis c virus (hcv)
HCV is one of the Flaviviridae family.

HCV is an enveloped ssRNA virus.

There are 6 genotypes (the most common in Egypt &

the middle East is genotype 4).
 HCV Transmission

• Mainly parenterally through exposure to contamin blood

(IV drug addicts, haemodialysis, needle-p injury,
shaving razors, ear piercing,…..). Transmission blood
transfusion is rare nowadays due to routine
screening.

• Less efficiently transmitted (unlike HBV & HIV) by mucosal

exposures to blood or body fluids (e.g., perinatal transmission
from infected mother or sexual intercourse with an infected
partner).

• Up to 40% of cases show no identifiable source or route of

transmission.
 HCV Pathogenesis

• Viral replication occurs in the hepatocytes.

• Destruction of liver cells may result from the host’s

immune response (Tc cells).
clinical Manifestations
• Mostly subclinical

• Acute hepatitis in 20% of cases (I.P.: 4-6 months): clinical

manifestations are milder than HBV.

• Spontaneous resolution may follow acute infection.

• Complications: chronic hepatitis (app. 80%) which may end in
liver cirrhosis or HCC.

• Extra-hepatic manifestations of chronic HCV infection: Mostly

affect the skin and mucous membranes; such as lichen planus
(LP), psoriasis, and vasculitis.
 Laboratory
• Detection of Diagnosis
anti-HCV antibodiesby ELISA, or the more
specific RIBA test (recombinant immunoblotting assay).
Seroconversion may take up to 6 months.

• RT-PCR for detection of viral RNA in blood. This is

useful in:
• Diagnosis of early cases before seroconversion.
• Serologically confirmed cases to demonstrate active viral
replication and, thus, the need for therapy.
• Follow up the response to treatment.
• Genotyping of HCV (which is the strongest predictor of
response to therapy by ribavirin & IFN).
 Interpretation of tests used in the diagnosis of HCV infection:
Anti- HCV Interpretation
HCV RNA
Negative Negative Susceptible

Positive Negative Resolved HCV infection

Negative Positive Early acute HCV infection or chronic HCV

infection in immunocompromised person
Positive Positive Acute or chronic HCV infection
 Infection Prevention & Control
• No specific vaccine or Ig is available for immunoprophylaxis.

• Avoid exposure to blood-borne viruses by preventing

exposure to blood or body fluids by practicing standard
precautions.

• In case of exposure:
• wash promptly the injured site with soap & water or
• wash with saline in case of blood splash to the eyes
vigorously.

• Post-exposure follow-up is recommended by screening for

HCV RNA for up to 6 months.
 Treatment
• A combination of alpha-interferon & ribavirin has been
used.

• The response to treatment depends upon the virus

genotype:

• Genotypes2 or 3 have higher response to therapy

than that of genotype 1.

• Genotype 4 subtype a (which is the commonest in

Egypt) has poor response to therapy.
 Treatment
• Sofosbuvir (Sovaldi): is a nucleoside analogue inhibitor. It is
more effective with shorter treatment duration & with less
side effects.

• It is used with:
• Ribavirin for the treatment of genotypes 2 & 3.

• Interferon for the treatment of genotypes 1 & 4.

retroviruses
 Family Retroviridae
• The name is derived from the fact that these viruses
contain a reverse (retro) transcriptase, i.e., RNA-
dependent DNA polymerase (RdDp).

Important members of Retroviridae family

• Lentiviruses: (Human immunodeficiency viruses; HIV- 1 &
HIV-2): cytocidal "slow" viruses; characterized by long
incubation period, chronic disease with prolonged clinical
latency & persistent viral replication & affection of CNS.
• Deltaretroviruses: (Human T-cell lymphotropic viruses;
HTLV-1 & HTLV-2): oncoviruses that can transform cells
in vitro & in vivo but do not possess a specific oncogene.
They can cause T-cell leukemia.
 Human Immunodeficiency Viruses

• Since the initial description of HIV-1 in 1983 &

HIV-2 in 1986, these two viruses are the primary
cause of AIDS.

• HIV-1 is the major cause of AIDS worldwide while

AIDS caused by HIV-2 is much less severe, slower in
progression and limited mostly to West Africa.

• Both viruses replicate in CD4+ T helper cells.

Structure of HIV (100 nm)
 The Envelope
• Composed of lipid membrane in which is embedded a
complex glycoprotein (gp160).

• gp160 is cleaved by host enzymes into 2 virus-specific

glycoproteins; gp120 & gp41:
• gp120 is a surface (SU) protruding protein cap
held to transmembrane gp41 responsible for viral
binding to host cell receptors.

• gp41 is transmembrane (TM) protein stem embedded

in the envelope mediates the fusion of the viral
envelope with the host cell membrane.
 HIV Genome 1

• Genome of two identical copies of a positive sense

ssRNA, each of which has a copy of the virus nine genes:

• Three essential genes: gag, pol & env

• Six regulatory (accessory) genes

 HIV Genome 2

env gene:
• encodes gp160 that is cleaved into gp120 & gp41.
• Rapid mutation occurs antigenic variants

pol gene: encodes RT, integrase & protease enzymes gag

gene: encodes the core proteins (e.g. p24)

 Pathogenesis of HIV Infection 1

HIV Transmission

1. Sexual (hetero- or homosexual) transmission

2. Parenteral transmission (e.g. blood transfusion, sharing

syringes or accidental needle prick injury)

3. Vertical Transmission: during pregnancy (25%),

childbirth or through breast-feeding
 Pathogenesis of HIV Infection 2
Cells that are infected by HIV

• CD4+ T helper lymphocytes: CD4 antigen is the

receptor for HIV.

• Monocytes/macrophages

• Oligodendrocytes, astrocytes, neurones & glial cells

• Follicular dendritic cells (FDCs): in lymph nodes

Except for CD4 T cells, the other cells serve as a reservoir for
further infection of T cells.
 Mechanisms of Th Cell Depletion

• Direct killing of infected cells by the replicating virus.

• Killing of infected CD4 Th cells by CD8 Tc cells.

Increased susceptibility to infections & malignancies

 HIV Replication

• Attachment
• Penetration
• Uncoating
• Reverse transcription
• Integration
• Proviral transcription
• Translation
• Cleavage
• Assembly
• Release
HIV Replication
 Clinical Background
A. Acute HIV Infection
(Acute Retroviral Syndrome, Early Stage)

• During this phase, the blood contains many viral

particles that spread throughout the body (particularly
the lymphoid organs).

• After an incubation period of 2-4 weeks, up to 70% of

HIV-infected individuals present as a transient illness
(acute retroviral syndrome), characterized by acute flu-
like or infectious mononucleosis-like illness.
 A. Acute HIV Infection
• Symptoms: fever, malaise, arthralgia, myalgia,
maculopapular rash, pharyngitis, oral ulcers,
lymphadenopathy, weight loss & aseptic meningitis (D.D.
from similar conditions).
• The symptomatic phase of acute HIV infection lasts
between 7-10 days (as CD8+ T cells & antibodies
dramatically reduce HIV levels).
• The induced immune response succeeds in controlling but
not eliminating the virus.
 B.Clinical Latency
(Middle Stage)
• Acute HIV infection is followed by an extended period of
clinical latency (despite continuous replication of the virus in
the lymphoid organs not true latency).

• This period may extend up to 10 years depending on:

• virus type,
• immune response,
• use of antiretroviral therapy.
 B. Causes of Clinical Latency
(i.e., immune response evasion)

• The rapid virus mutation.

• Integration of the virus in the chromosome of

infected cells.

• Down regulation of MHC I expression on infected cells

prevent recognition by Tc cells.

• Loss of Th cell responses.

 C. Immunodeficiency Stage
(Late Stage)

• The average AIDS incubation period is 8 - 10 years.

• However, some HIV-infected people have progressed to AIDS

within the first two to three years following infection.
 C. AIDS
• A healthy, uninfected person usually has 800 - 1,200 CD4+
T cells/mm3 of blood.

• During HIV infection, the number of these cells progressively

declines in the blood.

• When CD4+ T cell count falls below 200/mm3, the infected

person becomes particularly vulnerable to the opportunistic
infections (main cause of death) & cancers characteristic of
AIDS (Kaposi's sarcoma, lymphomas), in addition to weight
loss, diarrhea & neurologic manifestations.
 Opportunistic Infections
• Fungal:
• Pneumocystis jiroveci (pneumonia)
• Cryptococcus neoformans (meningitis)
• Candida albicans (oral thrush)

• Bacterial:
• Mycobacterium avium-intracellulare
• Mycobacterium tuberculosis

• Viral:
• CMV (retinitis, colitis, pneumonitis & hepatitis)
• HSV
• VZV
Diagnosis of HIV Infection
 TEST Purpose

A. Serological tests
ELISA Initial Screening
Western Blot Analysis Confirmation Test
B. Other supplementary tests

p24 antigen Early Marker of Infection

(detection of a recent
infection)

1. Detection of virus in blood

Virion RNA or proviral DNA
(detection of a recent
infection)
2. Confirm treatment efficacy
Isolation and culture of virus Only available in research labs
1. Diagnosis of AIDS
2. Confirm treatment efficacy
CD4 count

A. Serology
(HIV Antibody Screening Tests)
• HIV-specific antibodies are detectable 3-4 weeks after
infection (i.e., seroconversion).

• Newborns of infected mothers have passively acquired

maternal IgG & no commercial tests for HIV-specific IgM
are available.
 Western Blot

• Western blot is:

• More specific than EIA (as it
detects specific Abs against
certain viral Ags, e.g., gp41 &
P24).

• Confirmatory test (as some

conditions may give a false reactive
EIA, e.g. SLE, lyme disease,
syphilis).
 B. Supplementary Tests
• Molecular methods: to detect viral nucleic acid
• PCR for the detection of HIV proviral DNA in
infected cells (qualitative test)
• or RT- PCR to determine the viral load in plas
(quantitative test).

• P24 antigen: it is used for routine screening in blood &

plasma centres to detect HIV during the “window period”
as it is an early marker of infection & its presence
indicates viral replication.

• Virus isolation on cell cultures: only in research labs.

• CD4 count: <200 cells/mm3 & CD4/CD8 ratio <1
(normally 2:1) are diagnostic of AIDS.
 Treatment
• No treatment is available that cures AIDS, despite the
use of many highly active antiretroviral drugs (HAART)
that suppress HIV replication, preventing the
destruction of the immune system.

• In addition, new problems related to drug toxicity & the

occurrence of resistant mutants are emerging.
 Co-receptor Blockers

• These drugs interfere with binding of HIV to the

chemokine receptors on susceptible cells, e.g., maraviroc.
 Fusion Inhibitors

• These drugs bind to gp41, preventing binding or fusion of

HIV envelope to lymphocytes, e.g., enfuvirtide (Fuzeon).
 RT Inhibitors
(prevent the synthesis of proviral DNA)

• Nucleoside analogues RT inhibitors: e.g., AZT, DDC,

DDI & lamivudine.
• Non-nucleoside RT inhibitors (NNRTIs):
e.g., Nevirapine
 Integrase Inhibitors

• These drugs prevent integration of proviral DNA

into the host’s genome.
e.g., raltegravir.
Protease Inhibitors
(prevent the cleavage of proviral polyproteins)
• They are the most potent inhibitors of HIV
replication to date.
e.g. Ritonavir & Indivavir
 HAART
(Highly Active Anti-Retroviral Therapy)

• HAART is a combination of 2 RT inhibitors & a

protease inhibitor.

• Advantages of combination regimen:

• Less possibility of emergence of resistant mutants.
• Less toxic doses to be administered.
 Monitoring anti-HIV Therapy

1. Viral load measurement (quantitative PCR).

2. CD4 count: done every 3-6 months during periods of

clinical stability and more frequently if symptomatic
disease occurs.
Prevention & Control
• No vaccine for human use is available.

• Ongoing trials on monkeys, using a vaccine containing

gp120 are hampered by the appearance of gp120 genetic
variants.
 Avoid Exposure to the Virus
• In the community: by health education &
awareness regarding transmission & avoidance.

• In the healthcare setting: by applying infection control

practices (Standard Precautions):
• Proper handling & disposal of sharps.
• Screening of blood before donation.
• Proper disinfection of surfaces contaminated by blood or
body fluid spills (e.g., by Na hypochlorite).
 Prevention &
• Post-exposure Control
chemoprophylaxis :
• immediately started within 2 hours &
continued for 4 weeks.
• consists of 2 or 3 antiretroviral drugs.
• Prevent vertical transmission:

• Pregnant women: screening for HIV.

• Infected women:
• Treatment during pregnancy
• C.S. delivery rather than vaginal delivery
• Treatment of neonates .No breast feeding
 herpesviruses

Family Herpesviridae (Herpesviruses)

• Members of this family often cause life-long latent

recurring infections which progress slowly.
 HERPESVIRUSES

• DNA viruses, having a lipid

envelope.

• Spikes of viral glycoproteins

project from the envelope.
 Types of Herpesviruses

• Herpes simplex virus (HSV-1, HSV-2)

• Varicella-Zoster virus (VZV)
• Epstein-Barr virus (EBV)
• Cytomegalovirus (CMV)
• Human herpesvirus 6 (HHV6)
• Human herpesvirus 7 (HHV7)
• Human herpesvirus 8 (HHV8)
 HSV-1 & HSV-2

Similar in morphology & structure, but can be distinguished

by the following:

• Location of the lesion:

• HSV-1 above the waist
• HSV-2 below the waist.
 Pathogenesis & Clinical
PicturePrimary HSV Infections
(Exposure to the virus for the first time)

• Probably transmitted by direct contact.

• Involves the mucous membrane of the mouth, lips, skin of

face, nose, eyes and genital tract.

• Clinically, appears as vesicles on an erythematous base,

vesicles rupture and its contents dry forming crusts which
finally heal (within 7-10 days) without scarring.
 Pathogenesis & Clinical
Picture Latent Infections
• Replication occurs at the site of the entry of the virus in
the epithelium.

• Virus particles are transported along the axons to the

sensory (dorsal root) ganglion to establish a latent
infection.

• HSV-1 latency is in the trigeminal ganglion while in HSV-2

latency is in the sacral ganglia.

• Latency remains for the life-time of the host.

 Pathogenesis & Clinical
Picture
Reactivation & Recurrence

• Reactivation of the latent virus:

• may be restricted to asymptomatic shedding.
• or may produce clinically obvious disease (at any site
innervated by the affected neurons).

• Provoked by various stimuli: fever, UV exposure, sunlight,

trauma, stress, immuno-suppression and in case of HSV-2
by sexual intercourse.

• The presence of specific antibody reduces the severity - but

not the recurrence- of infection (cell-to-cell spread).
 Clinical Types of HSV
I- Infection
HSV-1 Diseases

• Acute gingivostomatitis (commonest).

• Recurrent herpes labialis (fever blisters or cold sores):
reactivation of the 1ry gingivostomatitis.
•
• Encephalitis (most serious).
•
• Keratoconjunctivitis: It may lead to corneal ulcers, scarring &
blindness.
•
• Herpetic whitlow (felon) is a pustular lesion of the distal
phalynx of a finger or hand (e.g. dentists).
•
• Disseminated infections: e.g. pneumonia as in AIDS patients.
Herpes Labialis
Herpetic Whitlow
 Clinical Types of HSV Infection

II- HSV-2 diseases

• Herpes genitalis
• (classic presentation) extensive bilateral painful vesicular
lesions in the genital area, accompanied by fever, dysuria &
inguinal lymphadenopathy.

• Neonatal herpes
acquired during birth, is the most serious consequence of
genital herpes.

• Aseptic meningitis.
 Laboratory Diagnosis of HSV Infections

• Isolation of the virus on tissue culture.

• Direct detection of HSV in vesicle fluid by electron

microscopy.

• Detection of viral DNA by PCR.

• Detection of viral antigen by direct immunofluorescence or

ELISA.

• Serological diagnosis to detect IgM antibodies

that indicates recent infection or reactivation.
 Treatment

• Idoxuridine (IDU) topically is used in the treatment of

eye and skin infections.

• Acyclovir & vidarabine: inhibit viral DNA synthesis.

Acyclovir (Zuvirax) is available for topical, oral and I.V.
use.

• Foscarnet:
• inhibit HSV DNA polymerase.
• Used in treating acyclovir-resistant HSV infections.
 Prevention

• Immunocompromised (e.g., transplant recipients) are given

acyclovir to prevent viral reactivation.

• Caesarean section: recommended for mothers with

active genital HSV infection to avoid neonatal infection.

• Recombinant vaccines under trial.

 varicella-zoster virus (vzv)

• Infection with VZV presents in two clinical forms:

• The primary infection; varicella (chickenpox) is a
generalized eruption.

• The reactivation infection; zoster (shingles) is a localized

form.

N.B.: There is only one antigenic type of VZV.

• Chickenpox (varicella): epithelial cell infection resulting in an
exanthem of macules, papules, pustules, vesicles & shallow
ulcers.

• Shingles (zoster): peripheral nerve cell infection with an

eruption in the overlying epidermis.
 Pathogenesis & Clinical Features
1 1. Varicella (Chickenpox)

• The virus enters by airborne route.

• Incubation period: 2 weeks.

• The typical rash of varicella appears first on the trunk then

spread to the face & limbs.

• The skin rash is initially macular & rapidly evolves through

papules to clear vesicles.

• The vesicles changes to pustules which dry to form scabs

which heal without scar formation.
 Pathogenesis & Clinical Features
2 1. Varicella (Chickenpox)

• The patient is usually a child 4-10 years old.

• The disease usually runs a benign course.

• Some cases are complicated by secondary skin infection,

pneumonia or cerebellar ataxia.

• Pregnant women infected in the first half of pregnancy may

pass infection to the foetus which at birth may show
foetal varicella syndrome with high mortality rate.
Varicella
(Chickenpox)
Varicella
(Chickenpox)
Varicella
(Chickenpox)
 Pathogenesis & Clinical Features 3

2. Zoster (Shingles)
• It results from reactivation of latent varicella infection in the
neurons.
• The virus reaches the ganglion from the periphery by
travelling along nerve axons or by blood during viraemic stage
of varicella infection during childhood.

• The disease usually occurs in older

people.
• It manifests as painful vesicular eruption, unilateral & confined
to one dermatome, usually thoracic or lumbar.

• The condition may follow trauma to the spinal cord or may

complicate lymphomas, leukaemia or immunosuppression.
Zoster (Shingles)
 Treatment

• Acyclovir (IV) is effective in the treatment of

varicella & zoster.

• It is not used for all cases, but indicated in the

following conditions:
• Immunocompromised patients.
• Ophthalmic zoster (to avoid corneal scarring).
• Varicella complicated by pneumonia.
• Neonatal infection.
 Prevention & Control

• Acyclovir & interferon: for immune deficient children.

• VZ immune globulin (VZIG): for contacts.

• Varicella vaccine (Varivax): LAV, one S.C. dose, for

children 1-12 years of age.

• Zoster vaccine (Zostavax): one S.C. dose, for individuals

above 60 years of age.
 epstein-barr virus (ebv) hhv- 4

• Widespread & mostly asymptomatic.

• The virus is excreted & transmitted via the saliva &

multiply in the oropharyngeal mucosa.

• EBV receptors are also present on B-

lymphocytes.
 EBV Diseases

• Infectious mononucleosis (glandular fever).

• Others:
• Nasopharyngeal carcinoma.
• Burkitt’s lymphoma.
• Oral hairy leukoplakia (in AIDS patients).
• Hodgkin’s disease.
• T-cell lymphoma.
 Infectious Mononucleosis (Glandular Fever)

Pathogenesis & Clinical Features

• Incubation period: 30-50 days.
• Fever, sore throat, skin rash & cervical lymphadenopathy
which becomes generalized with or without
hepatosplenomegaly.
•
• The virus attacks B cells resulting in the appearance of
antibodies.
• This is followed by a marked T cell response which is
detected as large number of atypical lymphocytes in the
peripheral blood.
Laboratory
Diagnosis
1. Blood picture: A high total leucocytic count (up to
25,000/cmm) with predominance of monocytes &
atypical lymphocytes.

2. Detection of heterophil antibodies.

3. Definitive diagnosis requires the demonstrate

4. Detection of EBV nucleic acids in patient’s saliva or

throat washing using DNA probes or PCR.
A subunit vaccine based on major viral
glycoprotein is under trial.
 cytomegalovirus (cmv) hhv- 5

• The name “cytomegalovirus“ was chosen on account of

the swollen state of virus-infected cells.

• The virus is widespread.

• Primary infections occur in 40-60% of individuals &

the virus persists in the host for life (latent infection).

• Reactivation is common.
 Transmission of CMV

• Transplacental (congenital).

• Other methods:
• Close contact
• Sexual intercourse
• Breast feeding
• Blood transfusion
• Organ transplantation
 Clinical Features
Most infections are asymptomatic:
• Congenital Infection: It may cause still birth or abortion. In
5% of infected babies, congenital abnormalities occur
“cytomegalic inclusion disease”: growth retardation,
microcephaly, hepatosplenomegaly, thrombocytopenia &
blindness.

• Mononucleosis syndrome: similar to that caused by EBV.

However, pharyngitis & lymphadenopathy are unusual &
heterophil antibodies are not found.

• Infection in immunocompromised patients: may manifest as

pneumonitis, encephalitis, hepatitis, retinitis … etc.
 Laboratory Diagnosis

• Isolation of the virus from throat washings or urine on

tissue culture.

• Detection of viral DNA by PCR or hybridization assay.

• Detection of viral antigens in urine or saliva.

• Serodiagnosis: Detection of CMV IgM or rising titre of

IgG by EIA or latex agglutination assay.
 Treatment

• Ganciclovir used for CMV infections in

immunosuppressed patients.

Prevention & Control

• Screening blood donors & organ donors and exclusion

of seropositive ones.

• Vaccines are under trial.

 Human Herpes Virus 6 (HHV6)

• HHV6 is the cause of a common disease of infancy called

Exanthem subitum (roseola infantum or sixth disease).

• It is characterized by high fever & skin rash) & possibly

multiple sclerosis.

Roseola Infantum
 Human Herpes Virus 7 (HHV7)

• HHV7 is associated with:

• persistent salivary glands infection

&
• may cause fatal encephalitis.
 Human herpes virus 8 (Kaposi’s
Sarcoma-Related Herpesvirus)

This virus was identified in 1994

from tissue of Kaposi’s sarcoma
in patients with AIDS.
adenoviruses
 adenoviruses

• Adenoviruses are a frequent cause of acute upper

respiratory tract infections, in addition to other infections.

• They were isolated from adenoidal tissue of children, hence

the name adenovirus.

• Human adenoviruses are divided into 6 groups (A - F)

comprising 51 serotypes.
 Characteristic Features

• Widespread in nature.

• Inclusion bodies: The viruses replicate in the cell nucleus

forming inclusion bodies. These form the basis of latent
infection.

• Latent infection can occur in lymphoid tissues.

• Reactivation is caused by immunosuppression, e.g. in AIDS

patients.
 Oncogenic Potential

• Some strains induce tumours in newborn rodents and cell

transformation of tissue culture cells.

• Adenovirus oncogenesis has never been observed in

humans.
 Vector

• The adenovirus genome is easily manipulated in vitro.

• Therefore, it can be used as a vector to carry and

express foreign genes for therapeutic purposes (gene
therapy) or for vaccination.
 Morphology
•
• Virions are icosahedral, non-enveloped, 70-90 nm in
diameter with dsDNA genome.

• Adenoviruses are the only viruses with fibres protruding from

the capsid, serving as the organ of attachment, a strong
haemagglutinin & toxic to human cells.
 Adenovirus Infections in Humans
1
• Adenovirus illnesses occur most commonly among school-aged
children.
• Approximately 50% of the infections are asymptomatic,
self-limiting and induce long- lasting type-specific immunity.

• Transmission occurs by respiratory droplets, faecal-oral route

& contact (hand-to-eye or sexual).

• Incubation period is 5 to 8 days.

 Adenovirus Infections in Humans
2

A- Respiratory Diseases
• Acute febrile pharyngitis.
• Pharyngo-conjunctival fever.

• Acute respiratory disease (pharyngitis, fever, cough and

malaise) occurring in epidemic form especially among military
recruits.

• Pneumonia represents 10% of pneumonias in childhood.

• Pertussis syndrome caused by group C.
 Adenovirus Infections in Humans
3
B- Eye Infections

• Swimming pool conjunctivitis (pink eye)

• Follicular conjunctivitis resembling chlamydial

conjunctivitis
• Epidemic keratoconjunctivitis:
• the most serious
• highly infectious
• may leave opacities in the cornea
• Acute haemorrhagic conjunctivitis
 Adenovirus Infections in Humans
4

C- GIT Diseases

• Infantile gastroenteritis
• Infantile intussusception

D- CNS Infections

• Meningitis & encephalitis

 Adenovirus Infections in Humans
5 E- Genitourinary infections

• Acute haemorrhagic cystitis in children.

• Venereal diseases:
• Orchitis
• Cervicitis
• Urethritis

• Ulcers on external genitalia (similar to herpetic

lesions).
 Adenovirus Infections in Humans
6 F- Other diseases

• Hepatitis in children with liver transplants.

• Infections in the immunocompromised including AIDS

patients (pneumonia & disseminated disease).

• Nosocomial infections: Adenoviruses cause 10% of

pneumonia cases in hospitalized children.
 Laboratory Diagnosis

• Ideally by isolation of the virus from clinical

specimens.

Or

• By serology (a fourfold or greater rise of antibody titer is a

good evidence of infection).
 Treatment

• Antiviral agents have generally been ineffective against

adenovirus infections.

• Intravenous ribavirin is a potential treatment.

 Prevention

• Chlorination of swimming pools, drinking water,

wastewater.

• High hygiene standards in ophthalmology practice.

• Measures to prevent nosocomial transmission.

• Vaccination:
• No vaccine for general use is currently available.

• Adenovirus vaccine has been given to the military

recruits in the USA since 2006.
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