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Virology
7105326
Two-Credit Hour Course
(Summer Semester 2015-2016)
Part 14
The Family Retroviridae
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The Family Retroviridae
Viruses that belong to the family Retroviridae are known as retroviruses. A special feature that
characterizes retroviruses is that they have an enzyme that is known as reverse transcriptase. Retroviruses
utilize this enzyme to convert their RNA genome into DNA, in a step that occurs immediately after the
uncoating process.
The conversion of the RNA genome into DNA is a process that can be described as the reversion of the
regular transcription process (during the regular transcription process, an RNA molecule (such as mRNA)
is made by an RNA polymerase that utilizes a DNA template. This RNA polymerase is known DNA
dependent RNA-polymerase).
In retroviruses, this process in reversed and this is by the conversion of their viral RNA genome to viral
DNA genome (provirus), a process that is mediated by an enzyme that utilizes a RNA template to
generate a DNA molecule. The enzyme is known as the retroviral reverse transcriptase. (Thus, these
viruses were given the name retroviruses or the name Retroviridae) (The underlined part of their name
represents the reversion process, in other words, which is described above) (Retro in Latin means,
backward)
Classification of Retroviruses:
The family Retroviridae is classified into 7 subfamilies (7 genera) as shown in the image below.
Note: Lenti means slow (in terms of the disease progression)
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Clinically, the most important retroviruses that cause diseases in humans are:
Two of them are known to cause disease in humans, which are:
Human Immunodeficiency Virus (HIV-1 and HIV-2), which belong to the subfamily
Lentivirinae
Human T cell Lymphotrophic virus (Human T cell Leukemia virus) (HTLV-1 and HTLV-2),
which belong the subfamily, Deltaretrovirinae
The Structure of the HIV Virus:
The HIV genome:
 Single-stranded (ss) RNA of positive polarity that is tightly associated with the HIV protein, p7.
 The 5’ end of the HIV genome is associated with a human tRNA that is bound to its 5’ end by
hydrogen bonds. This tRNA functions as a primer for the HIV reverse transcriptase enzyme
Note: The HIV virus has two 2 copies of its genome, which are NOT complementary to each other, thus it
can be described as diploid genome.
Organization of the HIV genome: the HIV RNA genome has three main genes, which are:
1- The gag gene that codes p24 (capsid protein) , p17 (matrix protein) , and p7 proteins
(genome-associated protein)
2- The pol gene that codes for the HIV enzymes, reverse transcriptase, protease and integrase (and for an
additional enzyme, which is the HIV ribonuclease)
3- The env gene that codes for envelope proteins gp41 and gp120
Note: the genome has other genes that encode for regulatory and accessory proteins. These genes are
found between the pol and env genes.
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The HIV Capsid:
It is made of the HIV protein, p24
It has a conical morphology/symmetry
HIV enzymes:
Three main enzymes are usually found within the capsid of the HIV virus, these are:
1- The HIV Reverse transcriptase
2- The HIV Integrase and
3- The HIV Protease
The HIV Matrix protein (p17):
The HIV enveloped is connected to the HIV capsid by a matrix protein that is known as p17
The HIV Envelope Proteins
HIV virus has envelope glycoproteins that have knob-like projections.
There are two types of HIV envelope proteins, known as:
 gp120: it mediates binding to the main receptor on the host cell, which is the CD4, which can be
found on helper T cells and Macrophages.
 gp4: it binds to HIV co-receptor on the surface of the host cell to mediate fusion between the viral
envelope and the host cell membrane, a process that leads for the internalization of the
nucleocapsid into the cytosol of the host cell.
Notes:
120 and 41 represent their molecular weight in Kilo Dalton, respectively
The envelope potions of the HIV have a globular or a knob-like appearance rather than a spike-like
appearance
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What are CD4 and CCR5 and (CXCR4)? (In other words, what are the normal functions of CD4
and CCR5 (CXCR4)?
 CD4 is the co-receptor of the T cell receptor of helper T cells (CD4+T cells).
 CCR5 (and CXCR4), are both chemokine receptors.
 The envelope protein gp120, binds to CD4 (which is considered the main receptor of the HIV
virus on the surface its host cells
The envelope protein gp41 binds to one of the chemokine receptors (CCR5 or CXCR4)
(accordingly, these chemokine receptors are considered the HIV virus co-receptors)
Binding of gp41 to one of the chemokine receptors, mediate the fusion process between the HIV
envelope and the host cell membrane, in process that leads for the internalization of the HIV
nucleocapsid into the cytoplasm of the host cell).
HIV Replication:
After internalization and the uncoating steps, the HIV reverse transcriptase mediates the reverse
transcription process (takes place in the cytoplasm):
 The HIV reverse transcriptase first synthesizes a DNA-RNA hybrid molecule
 The HIV reverse transcriptase has also an RNase activity, which mediates the
degradation of the parental RNA molecule of the DNA-RNA hybrid molecule
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 Then, the enzyme mediates the synthesis of a complementary DNA strand to result in
the generation of a linear dsDNA of the HIV genome (provirus).
With the aid of the p17 protein, the HIV provirus is then transported to the nucleus of the host
cell.
Within the nucleus of the host cell, the HIV integrase mediates the integration of the HIV DNA
provirus with host cell genome. The integrated provirus thus becomes a stable part of the cell
genome.
Transcription and translation of integrated viral DNA (provirus) sequences:
 Long terminal repeats (LTR) at either end of the provirus contain promoter and enhancer
sequences that control transcription and expression of the viral genes.
 Initially, the provirus is transcribed into a full-length RNA by the host cell RNA polymerase II,
which is then exported into the cytoplasm of the host cell.
In the cytoplasm of the host cell:
 Some of the full-length RNA will serve as the genome of the of progeny viruses
 Some of the full-length RNA is translated to produce the virion proteins including viral reverse
transcriptase and integrase that will be incorporated into the virion.
 Other copies of this full-length RNA are spliced, creating new translatable sequences that are
used for the production of regulatory proteins.
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History of Human Immunodeficiency Virus (HIV):
In 1981, Acquired immune deficiency syndrome (AIDS) was first reported in some young homosexual
males that exhibited the following symptoms.
 Severe pneumonia caused by Pneumocystis jiroveci, which usually does not cause infection in
healthy individuals
 Kaposi sarcoma (ordinarily an extremely rare form of cancer)
 Sudden weight loss
 Swollen lymph nodes
 General suppression of immune function
Late on, similar cases were reported in non-homosexual and non- drug users patients, who had
received blood or blood products by transfusion.
By 1984, AIDS was recognized as an infectious disease caused by a virus, and eventually HIV was
isolated from AIDS patients.
Worldwide, new infections are almost equally distributed between men and women, with heterosexual
activity accounting for the majority of cases.
Although combinations of drugs recently used to slow the progression of AIDS in developed countries;
95 % of HIV-infected people live in developing countries because of logistic and financial reasons
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Transmission of HIV among humans:
1. Sexual contact
2. Transfusions (blood, plasma, clotting factors, or cellular fractions of blood)
3. Contaminated needles
4. Perinatal transmission
An HIV-infected woman has a 15-40% chance of transmitting the infection to her newborn, either:
a) Transplacentally
b) During passage of the baby through the birth canal
c) Via breast-feeding.
Perinatally infection with HIV-1 is responsible for approximately 20% of all AIDS cases in developing
countries because of the high rates of HIV-1 infection in women of childbearing age.
Pathogenesis and clinical significance:
The most important pathology of HIV disease results from the immunodeficient state (AIDS) that leads to
opportunistic diseases that are rare in the absence of HIV infection.
 In about 50% of HIV-infected individuals, the progression from HIV infection to AIDS occurs in an
average of 10 years.
 Once an HIV-infected individual develops AIDS, and, if untreated, it is uniformly fatal within about 2
years of diagnosis.
Note: there is a significant fraction (about 10%) of HIV-infected individuals who have not developed AIDS
after 20 years.
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How quickly does a person infected with HIV develop AIDS?
 The length of time can vary widely between individuals. If left untreated,, the majority of people
infected with HIV will develop signs of HIV-related illness within 5–10 years, although this can
be shorter.
 The time between acquiring HIV and an AIDS diagnosis is usually between 10–15 years, but
sometimes longer.
 Antiretroviral therapy (ART) can slow the disease progression by preventing the virus
replicating and therefore decreasing the amount of virus in an infected person’s blood (known as
the ‘viral load’).
HIV Pathogenesis
Initial infection:
 At the portal of entry (infection site), initially, the HIV virus infects macrophages.
 Then, the virus disseminates via the blood to localize in the lymphoid tissue, where it infects
CD4+ lymphocytes.
Acute phase viremia:
 Several weeks after the initial infection with HIV, 30 -70% of individuals experience an acute
disease syndrome similar to infectious mononucleosis.
 During this period, there is a high level of virus replication occurring in CD4+ cells with large
amounts of virus and capsid protein (CA antigen/p24) are present in the blood stream.
 The circulating anti-HIV antibodies appear in 1 to 10 weeks after the initial infection
(Seroconversion)
 A constant level of virus and virus-infected cells is maintained by a combination of replacement
of the killed CD4+ cells with cells newly produced in lymphoid organs.
 Lymph nodes become infected; they later serve as the sites of virus persistence during the
asymptomatic period.
Latent period:
 The acute phase viremia is eventually reduced significantly with the appearance of a HIV-specific
cytotoxic T-lymphocyte response and anti-HIV antibodies.
 The latent phase (period) starts just after the cessations of the acute phase.
 The latent period is a clinically symptomatic and may last up to 10 years.
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During the latent period:
 The majority (90%) of HIV pro-virus infected cells are transcriptionally, silent.
 There are transient peaks of viremia that are often correlated with stimulation of the immune
system (activation of infected CD4 T cells).
 As long as the immune response is sufficiently effective to maintain a relatively stable, low level
of virus production, the infection remains relatively clinically asymptomatic.
 The immune system remains functional as long as the level CD4+ cells is within the normal range
The length of this latent asymptomatic period varies, however, may last up to 10 years.
By the end of the latent period (pre-AIDS stage), HIV-infected individuals may experience multiple,
nonspecific conditions, such as:
1- Persistent, generalized lymphadenopathy
2-Diarrhea
3- Chronic fevers
4- Night sweats, and weight loss.
5- During this period, the more common opportunistic infections such as herpes zoster and candidiasis may occur
repeatedly.
6- The CD4+ cell count is declined, but still higher than 200 cell/µl of blood.
Progression to AIDS:
A number of virologic and immunologic changes occur that affect the rate of this progression
 T-cell precursors in the lymphoid organs are infected and killed, so the capacity to generate new
CD4+ cells is gradually lost.
 Co-infection with a number of the herpesviruses, such as human Herpesvirus type 6.
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 Appearance of HIV mutants with altered antigenic specificity which are NOT recognized by the
existing humoral antibody or cytotoxic T lymphocytes.
 The eventual result is an increasingly rapid decline in CD4+ count, accompanied by loss of
immune capacity.
Once the CD4+ T cell count reaches below 200/µl, there will b e an obvious increase in the
frequency of serious diseases and opportunistic infections.
In this case, the patient is said to have AIDS (AIDS-defining illnesses).
Note: cells other than CD4+ lymphocytes can be infected such as monocyte-macrophage lineage that
are not killed as rapidly as CD4+ T cells and can transport the virus into other organs.
Opportunistic infections:
Multiple re-current opportunistic infections with fungi, bacteria, protozoa and viruses occur as the CD4+
cell count declines below 200 cell/ µl
Notes:
 About 30% of AIDS patients die from tuberculosis.
 The most characteristic neoplasm present in AIDS patients is Kaposi sarcoma (KS) and
lymphomas that are associated with HHV-8 infection.
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Laboratory identification:
 Detection of anti-HIV antibodies
 Detection of HIV proteins
 Detection of HIV nucleic acid
Note: there is still a 25-day window between the time that virus is first present in the blood and antibody
can be detected.
Treatment
Highly Active Anti-retroviral Therapy (HAART):
Virtually every step in the HIV replication cycle is a potential target for an antiviral drug, but only those
directed against reverse transcriptase, viral protease, and viral fusion have been used successfully.
A combination of three different drugs administered together can reduce the plasma viral load to
undetectable levels.
Why HIV treatment is not totally successful?
Note: Due to lower availability of anti-retroviral drugs in developing countries and lack of a vaccine,
education concerning methods for preventing transmission of HIV is currently the primary means of
preventing spread of the virus.
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Human T-Cell Lymphotrophic Viruses, HTLVand HTLV-2
HTLV-1:
Transmission:
Sexual contact, blood transfusion, transplacentally and breast feeding
Following infection of CD4+ T cells with HTLV, the RNA genome of the virus is converted into DNA
(provirus) (by the reverse transcriptase enzyme), which then integrates with the host cell genome in a
process that is mediated by the integrase enzyme.
The majority of infected individuals are asymptomatic carriers. In some cases, HTLV-1 infection can be
associated with the development of malignancy such as Adult T cell Leukemia and HAM:
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Adult T cell Leukemia (ATL):
About 1% of infected individuals may develop Adult T-cell leukemia (ATL) during their life-time (20-30
years after infection).
In those individuals, HTLV induce malignant host cell transformation, a process that includes both
immortalization and proliferation of the infected T cells.
Transformation mechanism:

HTLV-1 has two special genes (in addition to the standard retroviral genes gag, pol, and env)
called tax and rex.

In infected T-cells the Tax protein induces NF-B, which stimulates the production of
interleukin-2 (IL-2) and the IL-2 receptor.

The increase in levels of IL-2 and its receptor stimulates the T cells to continue growing, thus
increasing the likelihood that the cells will become malignant.
Clinical Symptoms:

Malignant T cells are non-functional and infiltrate various organs (Metastasis).

Loss of function of transformed T cells, which became the majority of T cells, leads to the
collapse of the immune system and consequently leas for various opportunistic bacterial, viral and
fungal infections (as in AIDS).

Most individuals the develop ATL, die in about 6 months.
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HTLV-1-Associated Myelopathy (HAM):
Another rare clinical condition that is caused by HTLV-1 is HAM, which may develop in few years after
infection.
Pathogenesis of HAM:
 The disease is believed to be induced as a result of the immune response to HTLV-1 infection,
while the immune system is trying to clear the HTLV-I infection.
 The HAM patients exhibit evidence of inflammation in the spinal cord, with many lymphocytes
infiltration to the infection site.
 It is believed that the inflammatory cytokines plays a central role in the pathogenesis process.
Clinical symptoms of HAM:
 Lymphocytic infiltration and demyelination of the spinal cord (thoracic region)
 Brain lesions
 Progressive weakness of the extremities
 Urinary and fecal incontinence
 Hyper-reflexia
 Some peripheral sensory loss
Note: The presence of anti-HTLV-1 antibody in the CSF confirm the diagnosis of HAM
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HTLV-2:

Most infections with HTLV-1 are asymptomatic

In rare cases, HTLV-2 causes Hairy Cell Leukemia, which is a rare form of malignant
lymphocytic leukemia of B cell origin.

The transformed malignant B cells (which have a characteristic ciliated appearance), infiltrate
bone marrow and other organs such as the spleen.

In the bone marrow, the cancerous B cells replace the bone marrow and thus abolishing the
production of all types of blood cells.
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