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Human Immunodeficiency Virus, HIV

July 7, 2009 by bioamin

Retrovirus

HIV is a retrovirus that belongs to the viral family Retroviridae which is replicated in a host cell.
With the help of reverse transcriptase enzyme they produce DNA from their RNA genome. Then
the DNA is conjugated with the host’s genome by an integrase enzyme. The genome of HIV-1 is
a single stranded component of RNA which consist a string of around 10000 bases that can
encode at least 10 proteins. Therefore the virus replicates as part of the host cell’s DNA. The
DNA copy then inserts into the host cell chromosome randomly and remains there for the life of
the cell. Termin and Baltimore discovered the reverse transcription process which is a
fundamental step to understand the biology of retrovirus like HIV-1.  

Target cells

There are some target cells such as CD4+ T cells, dendritic cells, macrophages, CD8+ T cells,
natural killer T cells and natural killer cells.

CD4+ T cells The loss of CD4+ T cells is a distinctive feature of HIV-1 infection. The
eventually loss of CD4+ T cells cause for many manifestations of HIV disease. Subjective loss of
mucosal CD4+ T cells probably occurs in the initial stages of acute infection. The large number
of CD4+ T cells which are significant of the chronic immune activation. Recent studies have
shown that HIV-specific memory CD4+ T cells comprise more HIV DNA than memory CD4+ T
cells of other specificities in the all stages of the infection. Another practical aspect of CD4+ T
cells stop proliferating and enter a pole of infected T cells which may be other cellular reservoirs.
These reservoirs are long-lived. Generally their half-life is about 44 months even after7 seven
years of suppression of its replication. Dendritic cells In peripheral tissues the dendritic cells
capture antigens and then transfer them to lymphoid organs. In the lymphoid organs the dendritic
cell digests the antigens and displays the resulting peptides to T cells. These are reasonably
susceptible to HIV infection in vitro due to their low expression of CXCR4, CD4 and CCRS.
Actually infection of dendritic cells depends on the amount of CCRS they express. In the initial
phage of HIV infection, the dendritic cells may play a role by displaying a particular cell-surface
lectin. Dendritic cell-specific intercellular adhesion molecule3-grabbing nonintegrin (DC-SIGN)
that holds the carbohydrate moieties on the gp 120 of HIV and moderates clustering of dendritic
cells with T cells. Therefore DC-SIGN on the surface of dendritic cells holds HIV.
Macrophages The macrophages are important target cells of HIV. Macrophages and their
precursors express high amount of heparin sulfate proteoglycan and low amount CD4.
Macrophages express another receptor like CD91 which bind to heat shock proteins with HIV
virion membrane. Especially at the time of opportunistic infections, the macrophages may be the
initial target for virus production and infection. CD8+ T cells Particularly the patients with late
stage of HIV infection, found CD8+ T cells. Recent experiments have shown that the frequency
of infected CD8+memory T cells is very small in HIV infected patients by using high purity of
flow–cytometric sorting. Besides naïve CD8+ T cells are rarely infective which proposed that if
thymocytes express both CD4 and CD8, become infected with HIV. Natural killer T cells A
different subgroup of CD4+ T cells referred as natural killer T cells. These cells are shown to be
susceptible to infection by HIV. The receptor for natural killer T cells is constant and particular
for hydrophobic glycolipid antigens on dendritic cells. CCR5 expressed by CD4+natural killer T
cells which are largely prone to infection with CCR5-tropic strains of HIV. Natural killer cells
The cells which do not necessary early sensitization for reorganization and killing targets are
referred as natural killer cells. The natural killer cells express CD4 and can be infected by both
CCR5 and CXCR4 strains in vitro. In natural killer cells, the viral DNA can continue even after
one or two years of active highly active anti-retroviral therapy (HAART) which proposed that
the natural killer cells perform as a viral reservoir.

Virulence factors (gag, pol, env, reverse transcriptase etc)

All retroviruses including HIV-1 contain some virulence factors such as pol, gag, env, reverse
transcriptase etc. Every factor can encode a precursor protein that is cut to functional subunits.
The gag gene product provides three basic proteins such as capsid, nucleocapsid and matrix
which are able to produce the main parts of the virus particle. The polymerase enzyme as well as
integrase and protease are encoded by the pol gene. For example, the HIV-1 gag gene consists
the genetic information for the capsid, matrix and nucleocapsid proteins. These are primarily
translated to a long protein consisting of all three proteins linked together. The polymerase
enzymes carry out the reverse transcription process. The integrase enzyme deals the infusion of
the reverse transcribed viral DNA into the host genome. Another protease enzyme cuts viral
proteins to functional units by which they are able to carry out their functions. The env gene
encodes the outer coat of protein of virus that plays a crucial role of binding and infection of
CD41T cells. Env protein is a transmembrane protein like others transmembrane proteins but it
has different transmembrane, extracellular and cytoplasmic domains. HIV-1 infects not all the
cells but infects selectively host cells expressing CD4, a cell surface protein which is expressed
on the mature T cells. The HIV-1 env protein has a large affinity for CD4 resulting effects of the
tropism of HIV-1 for CD41 cells. In the rough endoplasmic reticulum, the env proteins are
synthesized as a precursor protein called gp 160 in the infected cells and are finally targeted to
the plasma membrane of the cells. Three gp 160 molecules gather into a trimetric structure in the
endoplasmic membrane. Each molecule of gp160 is splited to two subunits like gp41 and gp120
at the time of transport to the plasma membrane over the Golgi apparatus by a cellular protease
at a particular area of extracellular domain. The two subunits persist combined noncovalently.
The gp120 has binding sites for the CD4 which is existing in the outside of the virus particle can
noncovalently combined to the extracellular domain of gp41. At the time of the virus associate to
CD41 cells then a complex trimeric structure go through a remarkable series of structural
alteration which permits the virus to enter to the cells. Besides the pol, gag and env genes the
HIV-1 has others genes such as rev, tat, vpr, nef, vif and vpu. They can encode proteins which
control many aspects of the virus life cycle; reb and tat control the expression of viral genes at
the posttranscriptional and transcriptional levels respectively; vpr is able to cause cell cycle
arrest; vpu and nef affect host cell expression of CD4 and the functions of vif are not well
known.
Receptors and co-receptors

Several immune cell receptors can bind with HIV. The identification of CD4 as an essential
component of HIV-1 receptor. In 1984, CD4 molecule is recognized as an HIV receptor which
shows the main receptor for HIV. In 1996 Edward Berger and his colleagues emerged that
CXCR4 which is a seven transmembrane protein can act as a coreceptor for HIV-1. CXCR 4 also
acts as a receptor for chemokines. A recent study in the AIDS field discovered that for entry of
HIV into host coreceptor is required. Kemokine receptors are needed for the entry of HIV-1 into
host cell. The gp120 interacts with CD4 which binds with the kemokine receptors. This binding
influences a structural change in the in the Env protein which exposes a hydrophobic fusion
domain situated in the N-terminus of the gp41. By Env protein which exposes a hydrophobic
fusion domain situated in the N-terminus of the gp41 releasing of chemokines for example MIP-
1a, RANTES and MIP-1b the CTLs can regulate viral replication. These chemokines can check
HIV-1 replication by combing with the identical chemokine receptors. Chemokine receptor can
block the communication of the HIV-1 Env protein with other chemokine co-receptors CXCR4
and CCR5. Another receptor for HIV is integrin alpha 4 beta 7.

Life cycle

To maintain the life cycle of HIV it has to continue several steps. The high attraction of HIV-1
gp120 for CD4 allows viral strong attachment with macrophages and CD4+ T cell. This strong
attachment is the primary step of life cycle of HIV. A recent study in the AIDS field discovered
that for entry of HIV into host co receptors is required. In 1996 Edward Berger and his
colleagues emerged that CXCR4 which is a seven transmembrane protein can act as a coreceptor
for HIV-1. CXCR4 also acts as a receptor for chemotactic cytokines. In the host cell the viral
genetic information enters and requires the lyses of viral envelope to the host cell membrane.
Then the gp120 interacts with CD4 which again binds with the kemokine receptors. This binding
influences a structural change in the Env protein which exposes a hydrophobic fusion domain
situated in the N-terminus of the gp41. The hydrophobic domain then enters in the membrane of
target cells so that gp41can bind with the cell membrane. An extra structural change in gp41
pulls these two membranes combindly, approving fusion to occur and the viral genetic
information can enter into the host cell after fusion. After enter into the host body the next step
of life cycle is reverse transcription occurred by reverse transcriptase (RT) enzyme carried by
virion. Reverse transcription is an error prone process as the RT lacking proofreading functions.
So, it generates some mutations. Per cycle of replication of viral genome approximately one new
mutation may occur. Such mutations of viral genome permit the virus to develop very swiftly,
escaping away from the antiviral drugs and antiviral immune responses. Generally reverse
transcription happens in the large molecular weight component and forming preintegration
complex which gives a conformational framework for the reverse transcription. In the life cycle
this complex can be imported in the nucleus of host cell and integration of DNA copy of viral
genome occurs. In the host cell under suitable conditions the genes are transcribed to viral RNA
molecules. Some of them are integrated with new virus particles and the others are used as
mRNAs to produce viral proteins. Then the proteins assemble with genomic viral RNA at the
plasma membrane to make a virus particle which buds from the infected cells including some of
host cell membrane which acts as a viral envelope. The gp120/gp41 complexes are established in
the envelope can allow attachment with CD4+ cells in the next round of infection.
Treatment/antiviral agents drug resistance

Infection of HIV-1 can be treated by using some drugs which inhibit the viral enzyme like
protease and reverse transcriptase. The drugs which are currently used for the treatment of HIV-
1are classified into four classes. These are nucleotide and nucleoside analogues that can function
as inhibit reverse transcription of viral genome into DNA consequently the DNA chain
termination occurs which is the principal step at the initial stage of viral life cycle. The
nucleoside analogues are stavudine, didanosine, abacavir, zidovudine, lamivudine, and
zalcitabine. The nucleotide analogue is tenofovir.  Nonnucleoside reverse-transcriptase inhibitors
such as efavirenz, nevirapine and delavirdine can associate and stop the function of reverse
transcriptase. Another is protease inhibitor such as ritonavir, nelfinavir, lopinavir, saquinavir
indinavir and amprenavir act on viral protease which is necessary for the production of precursor
protein such as gag and gag-pol. Now for treatment of HIV the combined drug therapy are used
which is called the highly active antiretroviral therapy (HAART). In 1987, a reverse transcriptase
inhibitor zidovudine (3’-azido-2’, 3’-dideoxythymidine or AZT) that was approved to treat HIV-
1 infection. This inhibitor is structurally analogue to the nucleoside deoxythymidine. When the
nucleoside deoxythymidine are taken by cells and phosphorylated then it becomes to
deoxythymidine triphosphate (dTTP) which is a building block of DNA. The viral enzyme,
reverse transcriptase (RT) is a polymerase enzyme recognizes AZT and assimilates it to the
viable viral DNA chain at the time of reverse transcription processing. The AZT which is lack of
3´-OH cannot serve at the site for the adjoining of the adjacent nucleotide. Hence the
transcription of the growing chain is terminated and the activity of reverse transcriptase is
inhibited. AZT and some other nucleosides are correlative to RT inhibitors were the mainstay of
HIV-1 therapy up to 1996 while the two current classes of antiretroviral drugs became
obtainable, the protease inhibitors and the nonnucleoside RT inhibitors. These protease inhibitors
are devised to hindrance the viral protease enzyme which cleavages the HIV-1 Pol and Gag
precursor proteins to functional units. These types of cleavages are necessary for the treatment of
HIV-1 infection. Clinical trials and initial laboratory testing are ongoing with two variant types
of drugs which hindrance the access of the virus into cells. One class of drugs hampers by the
conformational alteration in the gp41 molecule which occur at the time of actual fusion reaction.
Another class of drugs expresses chemokine receptor antagonists which hindrance the
association of the HIV-1 ENV protein by the chemokine receptors CXCR4 and CCR5. More
over to the access hindrance agents, inhibitors of HIV-1 integrase are being evaluated.

Drug resistance

Two thoughts are significant to know about the development of drug resistance. The first one is,
the HIV infection is occurred due to large numbers of virus production and turnover. Most of the
cases the lymphoid tissue of untreated patients has been estimated 107 to 108 (Approx.) cells.
This number is relatively constant at the time of chronic phase of HIV infection which reflects
the equilibrium between the infection of new target cells and their clearance. The second one is
the viral population of an infected person is highly heterogeneous. In some conditions, the
substitution of an amino acid creates large levels of resistance. Low levels of resistance can be
induced by single mutation and large levels of resistance need the additional mutations.

Mechanisms of resistance: The mechanisms of resistance are related to the resistance to

nucleotide and nucleoside analogues, nonnucleoside reverse-transcriptase inhibitors and protease
inhibitors. The nucleotide analogues and nucleoside analogues discontinue the production of
viral DNA by reverse transcriptase. Two different mechanisms are related in HIV resistance to
these drugs: damage of the incorporation of the analogue into DNA and eradication of the
analogue from the immaturely terminated DNA chain is conjugated with a group of mutations
usually termed thymidine analogue mutations. Mutations of this group are commonly selected
after the decline of drug combinations which related thymidine analogues like stavudine and
zidovudine but they can build up resistance to almost all nucleotide and nucleoside analogues.
Thymidine analogue mutations raise resistance by fostering ATP or pyrophosphate mediated
eradication of nucleoside analogues. ATP and pyrophosphate that are enough in lymphocytes do
not take participation in the DNA polymerization reaction. The nonnucleoside reverse
transcriptase inhibitors are small components which belong to high affinity to a hydrophobic
catalytic domain of reverse transcriptase. The association with the inhibitors impresses the
flexibility of enzyme. Resistance of nevirapine is often conjugated to the Y181C mutation but
other mutations like V106A, Y188C, G190A and K103A also occur. Beginning resistance of
efavirenz is usually characterized by K103N mutation but the mutation of Y188L is also found.
Resistance of protease inhibitors is the resultant of amino acid substitutions which emerge at
distant site or inside the substrate binding domain of the enzyme. These changes directly or
indirectly modify the nature and the number of the points of the association among the protease
and the inhibitors hence reduce their affinity to the enzyme. Resistance mutations of protease
cause the overall enlargement to the catalytic site of the enzyme. All these mutations explain the
remarkably vast range of natural susceptibility and take part in the evolution of acquired
resistance to enfuvirtide. Such type of knowledge help to treatment of HIV infected patients that
acquire resistance to multiple classes of drugs.

Infection (3phases: primary infection, asymptomatic phase, AIDS)

Primary infection: The initial phase of infection caused by HIV is known as the primary HIV
infection. In primary infection, the virus present in the infecting inoculums replicate of host cells.
A transient sickness found 1-12 weeks after exposure. In case of primary infection only 50-70%
of individuals usually have symptoms. Characteristic primary symptoms of HIV infection are
enlarged lymph nodes, fever, rash, lethargy, muscle and joint pain and occasionally aseptic
meningitis. Symptoms are found for 1-2 weeks. At the time of primary infection, the amount of
infected cells and infectious viruses are both very large in the circulation. It can be more than 10 6
copies per milliliter and as high as 108 copies per milliliter. In primary HIV infection a high level
of viraemia developed (Figure 1). If the immune response for the HIV developed then a dramatic
falls of viraemia. In the blood the virus level reduced to a lower plateau (set point) range. Most
usually the set point values for plasma HIV-1 RNA are between 10 3 and 105 copies per milliliter.
At the time of symptomatic primary infection the CD4+ T cells are reduced. The primary
infection gives some clues which are helpful for regulating the replications of the virus. Recent
studies of SIV infection of rhesus monkeys already have proved that virus specific cytolytic T
lymphocytes (CTLs) show firstly and express a critical host factor in the regulation of acute
infection.

The asymptomatic phase The next phase of primary HIV infection is the asymptomatic phase.
This is long phase between primary infection and the development of clinical disease (Figure 1).
Generally the asymptomatic phase lasts for 8-10 years. One of the most prominent features of
this phase is the gradual but progressive losing of CD41 T cells. The loss of CD41 T cells
characteristic evidence which is primarily responsible for the progress of the opportunistic
infections which characterize AIDS. In the blood, the concentration of CD41 T cells delivers a
good symbol of the development of the disease. In an uninfected adult the CD4 is usually
approximately 1000 cells mL21 of blood. If the CD4 count has decrease to fewer than 200 cells

mL21then the opportunistic infection occurs. It

can be stressed that, although patients having no symptoms in the asymptomatic phase of the
infection, during the AIDS phase the virus replicates continuously. By appropriately sensitive
method the infected cells and free virus can be estimated in the circulation, although the ranges
are very low that those observed at the time of primary HIV-1 infection or the patient with AIDS.
Molecular determination of HIV-1 RNA in the plasma can be identified as important indicators
of disease development. With the increasing of plasma HIV-1 RNA, the patient will lose CD41 T
cells and develops to AIDS, because HIV-1 destroys CD41 T cells in vitro which indicate viral
cytopathic effects were accountable for the loss of CD41 T cells. At any intigated time only a
tiny fraction of CD41 T cells originally bear integrated HIV-1 (50.01%). Most of the infected
cells are present in the peripheral lymphoid organs, for example the spleen and the lymph nodes.
In the circulation the lymphocytes represent a few fractions (52%) of the total lymphocyte
pool. Complex factors that consist expression of adhesion molecules that determine the
trafficking of lymphocytes among these compartments. Besides the infected cells, the free virus
particles are seen in the circulation bound form in the specific locations of spleen and lymph
nodes which called germinal centers. In the germinal centers, the virus particles are seen
conjugated to the network of follicular dendritic cells (FDCs). These cells can acts as filters and
able to catch the virus particles so, in the circulation it lowers the level of virus infection. In
response to antigen, the FDCs play great roles for the activation of B lymphocytes. The loss of
FDCs is responsible for the aberrant function of B-cell in the HIV-1 infected individuals.

 AIDS: AIDS is the third and the last stage of HIV-1 infection. When the CD4 cells fall under
200 cells mL21then the affected cells become largely prone to many opportunistic infections and
set malignancies. Generally the CD4 count of 5200 cells mL21 is seem to be an AIDS-defining
status i.e. an HIV-1-affected person including a CD4 count of 5200 cells mL21 is seem to have
AIDS (Figure 1). Other conditions of AIDS are some associated disease such as The most
common diseases are HIV-1 associated wasting syndrome, chronic herpes simplex infection,
Kaposi sarcoma, tuberculosis, recurrent bacterial pneumonia, symptomatic cytomegalovirus
(CMV) infection toxoplasmosis etcetera. It can be emphasized that the present forms of
antiretroviral therapy can stop the development of AIDS and permits substantial degree of
immune reconstruction even CD4 counts of 510 cells mL21.

 CD-4 depletion

 Most usually the depletion of CD-4 T cells is viewed in case of the production and destruction
of these cells. When any individuals are infected then the rate of CD4 T-cell loss more than the
rate of CD41 T cells production by differentiation of T cell precursors in the thymus which is the
site for the production of new T cells and /or differentiation of developed CD41T cells in the
lymphoid organs. This is an imbalance which is responsible for the increased destruction and
decreased production. The characterized decrease in thymic output of new T cells in many HIV-
1 infected adults. Besides, increased CD41 T cells decrease is also a critical factor in CD41 T
cell depletion. Some cytopathic effects which regulate at the level of individuals infected cells
i.e. HIV-1-infected T cells seem to die. Other HIV-1 proteins comprising Vpr accused for the
death of infected cells. Another active process for the loss of CD41 T cells in HIV-1infection
comprises the damage of these cells by the components of immune system specially CTLs.
Activated T cells are liable to apoptosis that is programmed cell death which are responsible for
the loss of CD41 T cells in HIV-1 infected cells. Inspite of the correct mechanisms of CD41 T
cells depletion is not clear but it is true that replication of virus is the main driving force behind
CD41 T cells depletion.

 Immune response

The immunological aberrancies of HIV-1-infected cells can be seen in the connection of the
immune response to the virus. Although the presence of T lymphocytes and detectable antibody
responses to HIV-1. All the infected cells progress antibody against of proteins of virus. The
most infected cells have large levels of virus-specific CTL movement. Generally HIV-1infection
convinces actively B and T-lymphocyte responses and these responses play a great role in
antiviral effects. Inspite of the infected cells are able to produce antibodies in response to some
different proteins, only the antibodies which are produced in response to extracellular portion of
the Env protein have beneficial neutralizing effects. Usually the neutralizing effects of antibodies
to HIV-1 are low, even when high levels then it indicates that many of anti-Env antibodies are
not neutralizing. Initially the X-ray crystallographic studies showed that the crucially significant
CD4-binding site on gp120 is situated in the comparatively hidden region of the molecule which
is limited by carbohydrates groups as well by the variable loops of gp 120 which is able to
accommodate mutations that permit run away from neutralizing antibodies. Therefore the
antibody response to the HIV-1 virus is not as efficient as the antibody response to other viruses.
The immune response of the component against HIV-1has been fairly exposed to have an active
antiviral issue is the HIV-1-specific CTL response. In most infected individuals the CD8 1 CTLs
are easily marked. As mentioned before, CTLs appear at the initial stage of HIV-1 infection and
it can help to regulate the large range of viraemia properties of this phase of infection by lysing
efficiently infected cells. By releasing of chemokines for example MIP-1a, RANTES and MIP-
1b the CTLs can regulate viral replication. These chemokines can check HIV-1 replication by
combing with the identical chemokine receptors. Now it is clear evidence in the SIV system that
CTL cells help to regulate viraemia. All these evidences maintain the concept that the HIV-1-
specific CTL response CD81employs a characteristic antiviral effect in vivo which is helpful to
the host. One of the most important components for the immune response to HIV-1 which is not
freely demonstrable many of affected people is the CD41 helper T-cell that is response to HIV-1
proteins. It shows that HIV-1-specific CD41 T cells are wiped initially in the infection. They can
be easily detected only in the rare individuals who are not fully affected by HIV-1. Recent
studies have proved that the treatment of infected cells by antiviral therapy initially HIV-1
infection permits preservation of the HIV-1-particular immune response. There are two other
mechanisms which permit HIV-1 to escape host immune response. The first one is the rapid rate
of mutation that permits the virus to change regions of viral proteins which are designed by the
immune system and the second one is the latency. Latency is the ability of a virus to dormant in a
silent stage in some infected individuals.