Clinical group
The Biology of HIV Infection
Duangrat Inthorn
Mahidol University
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Duangrat Inthorn
The Biology of HIV Infection
This report includes general information on HIV history, the classes of
retroviruses, and HIV composition and structure. It will also provide basic
information on the HIV life cycle and identify possible targets for drug development.
The HIV viral genome and the cause of the disease are also described. If you want
more detailed information you can find it in the subsequent reports from the clinical
group.
Introduction
History
We know now that AIDS is caused by the Human Immunodeficiency Virus
(HIV), but it was originally observed by its effects on the immune system. An
important clue was that AIDS patients often developed a lung infection (or
pneumonia) caused by fungus called Pneumocystis carinii. This infection is very rare
in healthy individuals, but patients with cancers of the immune system itself
(lymphomas) were known to be susceptible to this disease. In 1981, a cluster of cases
of Kaposi's sarcoma were observed in patients in San Francisco and New York.
Kaposi's sarcoma normally occurs in elderly Jewish men but these patients were all
young male homosexuals. Other diseases associated with immuno-compromisation
also occurred in this same population; particularly of note was the occurrence of
Pneumocystis pneumonia (which is an opportunistic infection) and lymphadenopathy.
Later, a similar immunodeficiency was found in intravenous drug users who shared
needles, persons who received blood transfusions and hemophiliaces. Moreover, the
sex partners of these patients also got the disease. The disease was originally termed
Gay-Related Immune Deficiency (GRID) but we now know it as Acquired ImmunoDeficiency Syndrome (AIDS).
HIV causes disease insidiously. The early stages of infection are often not
apparent, without visible symptoms. The infected person may feel healthy and appears
to be completely normal during that time (the incubation period) but such a person is
able to transmit the infection. The HIV incubation period is of variable duration and
can be quite long (on average 8 to 10 years). In contrast, for most common virus
infections, such as colds or influenza, an incubation period of a few days or weeks
will be followed by apparent disease. This adds greatly to the difficulty of studying
and controlling AIDS, because many people infected with the virus have not yet
developed the disease.
Retrovirus Family
HIV-1 is the predominant AIDS virus and is found worldwide, primarily in
Central Africa , Europe and North and South America. A second virus HIV-2, closely
related to the simian immunodeficiency virus (SIV), is shown to be endemic in parts
of West Africa with limited spread in Western Europe. HIV-2 is only now beginning
to appear in the Americas, mainly in the United States, Canada, and Brazil. Infection
with either HIV-1 or HIV-2 results in a number of biologic and pathologic changes
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leading to a spectrum of immune dysfunctions, neurologic disorders, enteropathy and
AIDS.
The human immunodeficiency viruses are members of the retrovirus family of
viruses. The retroviruses are so called because at the beginning of their life cycle
they reverse the usual flow of genetic information in a cell. In all living organism
and in many other viruses, genetic information is stored as DNA and later
transcribed into RNA. By contrast, retroviruses store their genetic information as
RNA and contain a unique enzyme, reverse transcriptase (RT), which catalyzes the
reverse transcription of the RNA genome (its entire complement of genes) into a
DNA copy.
The retrovirus family is composed of three subfamilies : oncoviruses,
spumaviruses and lentiviruses (Table 1). The oncoviruses cause cancer and are
called cancer-causing viruses. The lentiviruses and spumaviruses do not cause
cancer and do not integrate into the host's germ cell line. Both the lentiviruses and
the spumaviruses produce a persistent lifelong infection of the host cells. Of the two,
only the lentiviruses have been identified as causes of human and animal diseases.
Classification of HIV as a lentivirus is based on its fine structure, biologic
properties, protein and nucleic acid sequence homology (Table 2).
Table 1 Subfamilies of retroviruses (3) .
Subfamily
Examples
Oncoviruses: associated with the activation of certain cell genes leading to tumor develop
Type A
Mouse intracisternal type A
Type B
Mouse mammary tumor virus
Type C
Murine leukemia virus
Human T cell leukemia virus type I and II
Feline leukemia virus
Bovine leukemia virus
Type D
Mason-Pfizer virus
SAIDS virus
Spumavirus: readily isolated from humans and other primates, but have not been associated with any
specific disease
Simian foamy virus
Human foamy virus
Lentiviruses: produce acute cytocidal infection followed by a slowly developing multisystem disease
Visna maedi virus
Caprine arthritis encephalitis virus
Equine infectious anemia virus
Feline immunodeficiency virus
Bovine immunodeficiency virus
Simian immunodeficiency virus
Human immunodeficiency virus type 1 (HIV-1) and type (HIV-2)
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Table 2 HIV characteristics resembling those of lentiviruses (3).
Biologic characteristics
Persistent or latent infection
Cytopathic effects (syncytia formation) on selected cells
Capable of infecting macrophages
Associated with immune suppression
Long incubation period
Central nervous system involvement
Affects hematopoietic system
Molecular biologic characteristics
Similar genomic organization
Morphology of virus (cone nucleoid)
Accumulation of unintegrated proviral DNA
Polymorphism, particularly in the envelope gene
Primer binding site (tRNAlys)
Origins of HIV-1 and HIV-2
The genetic similarity between HIV-1 and HIV-2 is significantly less (40-50%
nucleotide identity) than is found among different HIV-1 isolates (>85% nucleotide
identity). HIV-1 and HIV-2 and other lentiviruses have been discovered in a wide
variety of nonhuman primates (Table 3). The nonhuman primate lentiviruses are
collectively know as simian immunodeficiency viruses (SIVs). To date, natural SIV
infections have not been shown to cause disease in the infected animal. HIV-1 and
HIV-2 appear to be closely related to the primate lentiviruses isolated from
chimpanzees and sooty mangabey monkeys.
Table 3 Primate lentiviruses (3)
Virus
Host
HIV-1
HIV-2
SIVCPZ
SIVSM
SIVMAC
SIVMNE
SIVSTMver
SIVAGMgri
SIVAGMsab
SIVAGMtan
SIVAGM
SIVMND
SIVSYK
Human
Human
Chimpanzee
Sooty mangabey
Rhesus macaque
Pig-tailed macaque
Stump-tailed macaque
Vervet monkey
Grivet monkey
Sabaeus monkey
Tantalus monkey
Mandrill
Sykes' monkey
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Studies of the African green monkey and
their related simian virus (SIVagm) yield
important information in our understanding
of HIV-1 and HIV-2. As see in Fig.1 there are
three major species of African green monkeys
indigenous to Africa.
Fig. 1 African green monkeys (2)
Fig. 2 Geographic domain of African
green monkeys (2)
Fig. 2 shows a map of Africa and indicates
the native locations of different species
of the African green monkey. Within
each species, a unique family of SIVagm
has been show to exist
Structure of HIV
The structure of HIV resembles that
of all retroviruses but particularly that
of the lentiviruses (Fig.3). HIV
has a cycindrical eccentric nucleoid
or core. The nucleoid contains the
HIV genome, which is diploid.
Outer lipid bilayer coat studded with
Surface (SU, gp120), transmembrane
(TM, gp41) glycoprotein complexes.
Beneath the lipid bilayer are matrix
proteins (MA), the virion consist of
Internal capsular (CA) and nuclear
Capsular (NC) proteins which
surround the single stranded RNA
genome.
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Fig. 3 Structure of HIV (2)
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HIV virion
Fig. 4 shows the components and their
genetic source, the matrix (MA) internal
capsular (CA), and nuclear capsid (NC)
proteins produced by the gag region
contain gene products of the pol
region-RT, integrase and protease.
Fig. 4 HIV Virion (2)
Life cycle of the human immunodeficiency virus
Fig. 4 Life cycle of HIV (2)
HIV and related lentiviruses have growth cycles that are typical of all retroviruses. It
is convenient to think of viral growth as four distinct stages:
 Infection: The HIV-1 virus binds to the CD4 receptor complex on the
surface of CD4+ cells. The virion then enters the cell, and uncoats.
 reverse transcription and integration : The HIV-1 virus undergoes the
process of reverse transcription in which viral RNA is transcribed into
complementary DNA. This is the portion of the life cycle at which all
currently available antiretroviral agents are designed to intercede.
 viral gene expression : After reverse transcription, the DNA becomes
double-stranded and migrates to the cell nucleus, where it is integrated into
the host genomic DNA as a provirus.
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
virus assembly and maturation: The virus can then be transcribed back into
mRNA and genomic RNA, and the resultant proteins and genomic RNA
are assembled near the surface of the cell and packaged into a new virion,
which buds from the cell membrane (2).
Soon after infection of the cells, the viral RNA genome is reverse transcribed
into a DNA copy, transported to the nucleus and integrated at random sites in
the chromosome. Once integrated, the proviral genome is subject to
transcriptional regulation by the host cell, as well as its own transcriptional
control mechanisms. The later stages of the life cycle involve expression of the
viral genes and eventual assembly and release of virus particles
How it might be stopped (Drug develpoment )
 RNA is converted into double strand DNA by RT
-Drugs called RT inhibitors can interrupt this process. ART inhibitor drugs,
such as AZT and 3TC, can disrupt the early stage of viral reproduction.
 The integrase enzyme incorporates the virus genetic material into the T
cell's DNA
-Drugs called integrase inhibitors, which are designed to halt this process, are
in development
 Disrupting the assembly line
The protease enzyme cuts viral proteins into shorter pieces so that they can
become functional proteins and allow the infection of other cells.
-Protease inhibitors block this stage of reproduction by neutralizing the
enzyme. They are even more effective when combine with RT inhibitors.
In this electron micrograph
(see Fig. 5), the virus can be seen
budding forth from the surface of
a cell. Note how the outer membrane
of the virus is composed of the lipid
bilayer membrane of the host cell
studded with integrated protein
products (envelop proteins) of
the virus (2).
Fig. 5 show viral budding (2)
The Genome of HIV
The HIV genome is 9749 nucleotides, about the same size as any other
retrovirus, for example Rous sarcoma virus (RSV). But the genome of HIV is
more complex than RSV since it has extra open reading frames that clearly
code for small proteins. Some of these are protein synthesis controlling
proteins.
The HIV genome has nine open reading frames but 15 proteins are
made in all.
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The GAG/POL polyprotein and the ENV polyprotein are cleaved into several
proteins:
GAG is cleaved to : MA (matrix), CA (capsid), NC (nucleocapsid), p6
POL is cleaved to: PR (protease), RT (reverse transcriptase), IN (integrase)
ENV is cleaved to: SU (gp120) and TM (gp41)
Of the other proteins, three are incorporated into the virus (Vif, Vpr
and Nef) while three are not found in the mature virus: Tat and rev are
regulatory proteins and Vpu indirestly assists in assembly.
TAT: Trans-Activator of Transcription
REV: Regulator of Virion protein expression
NEF: Negative Regulatory Factor
VIF: Virion Infective Factor
VPU: Viral Protein U
VPR: Viral Protein R
These genes encode small proteins. They overlap with the structural
genes (especially ENV) but are different reading frames. Note some are
encoded by two exons (unlike the structural genes) and therefore their mRNAs
can be derived by alternative splicing of structure gene mRNAs. Mutants in
the TAT and REV genes show that they are both vital to any production of
virus.
TAT gene product binds to a sequence in all the genes and positively
stimulates transcription. It is thus a positive regulator of protein synthesis,
including its own synthesis.
REV bind to an element only in the mRNA of structural proteins
(GAG/POL/ENV) and regulates the ratio of GAG/POL/ENV to non-structural,
controlling protein (TAT/REV) synthesis.
NEF despite its small size NEF has several functions
a) Homeostasis leads to several problem for the parasitic: superinfection by other HIV particles.
b) By a different mechanism from its down regulation of CD4
antigen, NEF reduces surface expression of MHC class molecules.
This alters antigen presentation by the infected cell and is proposed
to protect the infected cell from attack by cytotoxic T cells.
c) NEF is important for HIV replication in vivo but there seems to be
little effect of NEF in an in vitro cell culture situation.
Fig. 6
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HIV genomic map (2)
Duangrat Inthorn
This genetic map of the HIV-1 viral genome depicts the structural and
regulatory genes in their relative position as well as their products and functions. The
9-kb RNA virus is flanked by a long terminal repeat (LTR) section on both the 5' and
3' ends of the virus, which serves as a promoter and binding site for host and viral
transactivating factors. The TAR element exists within the R region of the LTR and
serves as a binding point for the tat gene product (a potent transcriptionalactivator).
The gag region encodes the nucleocapsid core and matrix proteins. The pol gene
codes the reverse transcriptase, protease, and integrase enzyme. The envelope region
(env) is responsible for the viral-coat glycoproteins, gp120 and gp41, which mediate
CD4 binding and membrane fusion. The remaining genes (vif, vpr, vpu, rev and nef)
are regulatory genes whose products play critical roles in controlling viral expression,
trafficking of viral gene products within the infected cell, and viral infectivity. The
rev-responsive element (RRE) is the binding site for the rev gene product, which is
important for the transport of unspliced and singly spliced RNA massage from the
nucleus (2).
HIV subtype
The two types of HIV can be distinguished genetically and antigenically.
HIV-1 is the cause of the current pandemic while HIV-2 is found in west Africa and
rarely elsewhere. The HIV-2 type is closely related to simian immunodeficiency virus
(SIV) found in west Africa. There are also 10 different HIV-1 subtypes. The major
one in the US and Europe is type B. In some countries, mosaics between different
subtypes have been found.
HIV binding via CD4 receptor
The HIV virus binds to the cell surface of a CD4
Lymphocyte. The binding attachment occurs
through an interaction of the viral glycoprotein
gp120/gp41 and the CD4 receptor complex on
the cell surface (see in Fig. 7).
Fig. 7 HIV binding via CD4 receptor (2)
The gp41 fragment consists of cytoplasmic
tail and a hydrophobic membrane-spanning
domain and is joined with the larger gp120
component via a fusion domain. The gp120
glycoprotein has several glycosylation sites
and hypervariable loops (eg. V3), which lead
to antigenic variation between viral strains.
The cd4-binding region is located toward
the center of the complex and consists of
components from both the gp120 and gp41
fragment.
Fig.8 Envelope glycoprotein complex of HIV-1 (2)
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The couse of the disease (5)
Usually from the time of infection till the clinical manifestation of AIDS a period
of 8-10 years goes by. However, in certain cases this period may be two year or less.
Approximately 10% of patients succumb to AIDS within 2 to 3 years.

Acute infection (acute retroviral syndrome)
HIV infection produces a mild disease that is self-limiting. This is not seen in all
patients. In the period immediately after infection, virus titer rises (about 4 to 11 days
after infection) and continues at a high level over a period of a few weeks. The patient
experiences some mononucleosis-like symptom (fever, rash, swollen lymph glands
but none of these are life-threatening. The result is an initial fall in the number of
CD4+ cells and a rise in CD8+ cells but the numbers quickly return to near normal
levels.

A strong cell-mediated and humoral anti-HIV immune defense
Cytotoxic B and T lymphocytes mount a strong defense and the virus largely
disappears from circulation. During this period, more than 10 billion new particles are
produced each day but they are rapidly cleared by the immune system and have a half
life of only 5-6 hours. The infected cells that are producing this virus are destroyed
either by the immune system or by the virus (half life about 1 day). However, the rate
of production of CD4+ cells can compensate for the loss of cells and a steadstate is set
up in which a very small fraction of the resting memory CD4+ cells carry an
integrated HIV genome. Most CD4 cells at this stage are uninfected.
The virus disseminates to other regions including lymphoid and nervous tissue.
This is the most infectious phase of the disease. Seroconversion occurs between one
and four weeks after infection.

A latent reservoir
As a result of the strong immune defense, the number of viral particles in the
blood stream declines and the patient enters clinical latency. Little virus can be found
in the bloodstream or peripheral blood lymphocytes. Nevertheless, the virus persists
elsewhere, particularly in follicular dendrite cells in lymph nodes and here viral
replication continues.
Although the number of HIV particles in the bloodstream falls during clinical
latency, the virus is detectable. Most patients with more than 100,000 copies per ml,
lose their CD4+ cells more rapidly and progress to AIDS before 10 years. Most
patients have between 10,000 and 100,000 copies per ml in the clinical latency phase.

Loss of CD4+ cells and abortion of the immune response
The major reason that the immune system fails to control HIV infection is that the
CD4+ T helper cells are the target of the virus. Also follicular dendrite cells can be
infected with HIV and these also diminish in number over time.
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
Onset of AIDS
The period of clinical latency varies in length from as little as 1-2 years to more
than 15 years but, eventually, the virus can no longer be controlled as the virus and
cytotoxic T (CD8+) cells destroy helper CD4+ (T4) cells. The killer cells needed to
control HIV also damage the helper T cells that need to function efficiently. With the
lack of CD4+ cells, new cytotoxic T cell response cannot occur as helper cells are
lacking and such new responses are demanded as the virus mutates. As T4 cells fall
below 200 per c mm, virus titers rise rapidly and immune activity drops to zero. It is
the loss of immune competence that titers rise rapidly and immune activity drops to
zero. Once AIDS develops, patients rarely survive more than two years without
chemotherapeutic intervention.
Reference
1. Fan H., Conner R.F. and Villarreal L.P. 1996. AIDS Science and Society. Jones
and Bartlett Publishers , Inc., Sudbury, Massachusetts.
2. Mandell G.L. 1995. Atlas of Infectious Diseases. Volume 1. AIDS. Churchill
Livingstone.
3. Schochetman G. and George J.R. 1994. AIDS testing. Second Edition. SpringerVerlag.
4. Karn J. 1995. HIV a Practical Approach. Biochemistry, Molecular Biology, and
Drug Discovery. Oirl Press at Oxford University Press.
5. Lecture from Dr. Hunt R., HIV and AIDS. University of South Carolina School of
Medicine, Department of Microbiology and immunology. From the Web site.
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