Retroviruses and Human Immunodeficiency Virus (HIV)

MINISTRY OF EDUCATION AND TRAINING
CAN THO UNIVERSITY

INSTITUTE OF BIOTECHNOLOGY RESEARCH AND DEVELOPMENT
VIROLOGY REPORT
RETROVIRUSES
AND HUMAN IMMUNODEFICIENCY VIRUS (HIV)
LECTURER STUDENTS
BI TH MINH DIU TRN HONG (3112449)
LM TN HO (3112459)
HUNH L BO NGC (3118301)
TRN HNH PHC (3118059)
HONG NGUYN PHNG TRINH (3112563)
L HONG TUN (3112573)
CLASS
ADVANCED BIOTECHNOLOGY COURSE 37
Can Tho, March, 2014

Virology Report Can Tho University
TABLE OF CONTENT
TABLE OF CONTENT ......................................................................................................... I
LIST OF FIGURES ............................................................................................................ III
LIST OF TABLES .............................................................................................................. IV
INTRODUCTION ..................................................................................................................1
PART 1: RETROVIRUSES ..................................................................................................2
I. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES .....................2
II. METHODS TO STUDY RETROVIRUSES.................................................................3
III. RETROVIRUS VIRION .............................................................................................6
III.1. Virion structure ...........................................................................................................6
III.2. Genome structure ........................................................................................................7
III.3. Viral proteins ..............................................................................................................8
IV. RETROVIRUS LIFE CYCLE....................................................................................9
IV.1. Early phase..................................................................................................................9
IV.2. Late phase .................................................................................................................14
PART 2: HUMAN IMMUNODEFICIENCY VIRUS (HIV) ...........................................20
I. THE DISCOVERY OF HIV ........................................................................................20
II. SIGNS AND SYMPTOMS OF HIV INFECTION ....................................................21
III. AIDS TRANSMISSION AND EPIDEMIOLOGY .................................................24
III.1 Transmission .............................................................................................................24
III.2 Epidemiology ............................................................................................................25
IV. HIV VIRION ..............................................................................................................29
V. HIV REPLICATION ....................................................................................................31
V.1 Receptors of HIV-1 ..................................................................................................32
Advanced Biotechnology Class Course 37 i Institute of Biotechnology Research and Development

V.2 Special feature of HIV-1...........................................................................................33
V.3 Functions of HIV additional proteins .......................................................................34
VI. TREATMENT AND PREVENTION OF AIDS .....................................................40
VI.1 Treatment ..................................................................................................................40
VI.2 Prevention .................................................................................................................45
CONCLUSION .....................................................................................................................48
REFERENCES .....................................................................................................................49
Advanced Biotechnology Class Course 37 ii Institute of Biotechnology Research and Development

LIST OF FIGURES
Figure 1 Peyton Rous ...............................................................................................................2
Figure 2 (a) Howard Temin and (b) David Baltimore .............................................................2
Figure 3 Cryo-EM micrographs of immature and mature HIV-1 particles .............................6
Figure 4 A typical retrovirus virion .........................................................................................7
Figure 5 Structure of retrovirus RNA ......................................................................................8
Figure 6 Early phase of retrovirus life cycle ............................................................................9
Figure 7 Reverse transcription ...............................................................................................12
Figure 8 Integration of proviral DNA into host cell ..............................................................13
Figure 9 Production of retrovirus RNA .................................................................................15
Figure 10 Suppression of translation termination ..................................................................16
Figure 11 Ribosomal frameshifting .......................................................................................16
Figure 12 Retrovirus translation and post-translational modifications ..................................17
Figure 13 Two assembly pathways in retroviruses ................................................................18
Figure 14 Retrovirus life cycle ...............................................................................................19
Figure 15 (a) Luc Montagnier, (b) Barr-Sinoussi, and (c) Robert Gallo .............................21
Figure 16 Events associated with progression to AIDS .........................................................22
Figure 17 Map of HIV prevalence in Africa in 2007 .............................................................26
Figure 18 Diagram of an HIV-1 virion ..................................................................................29
Figure 19 Genome structure and RNA splicing pattern of HIV-1 .........................................30
Figure 20 Model of HIV-1 entry ............................................................................................32
Figure 21 Mechanism of Tat function ....................................................................................34
Figure 22 Mechanism of Rev function...................................................................................35
Figure 23 Down-regulation of CD4 expression .....................................................................40
Figure 24 A model for the mechanism of RNA inteference ..................................................43
Advanced Biotechnology Class Course 37 iii Institute of Biotechnology Research and Development
LIST OF TABLES
Table 1 Retrovirus genera ........................................................................................................3
Table 2 Lentiviruses ...............................................................................................................21
Table 3 Prevalence rate of HIV/AIDS infection in 2010 .......................................................25
Table 4 HIV-1 structural proteins ..........................................................................................31
Table 5 HIV-1 non-structural proteins ...................................................................................31
Table 6 Classes of antiretrovirals ...........................................................................................41
Advanced Biotechnology Class Course 37 iv Institute of Biotechnology Research and Development

INTRODUCTION
Retroviruses are best-known viruses that use reverse transcriptase to produce DNA
copy of their RNA genome. Until the discovery of these viruses, the central dogma by
Francis Crick had formalized the one-way direction of genetic information from DNA to
RNA, and to protein, so finding that some viruses carry out transcription backwards
caused something of a revolution.
The discovery of human immunodeficiency viruses (HIV) in the late 20th century
brought to the public awareness of retroviruses. There are two types of HIV (HIV-1 and
HIV-2), and HIV-1 is much more prevalent. HIV infection damages the immune system,
leaving the body susceptible to infection with a variety of pathogens. This condition is
called acquired immune deficiency syndrome (AIDS). It is estimated that in the early 21st
century that AIDS has killed approximately 3 million people, which has become the fourth
biggest cause of mortality in the world, and still remains unchecked despite the availability
of effective anti-HIV chemotherapy.
This report is divided into 2 main parts. The first one aims to provide a general
introduction to the retroviruses, which have been found in all classes of vertebrate animal,
with the emphasis on the viral and genome structures, as well as their life cycle. The second
part is devoted entirely to HIV-1, which has been studied more intensively than HIV-2.
Advanced Biotechnology Course 37 1 Institute of Biotechnology Research and Development

PART 1: RETROVIRUSES
I. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES

The first discovery of a retrovirus was made as
long ago as 1910 by Peyton Rous (Figure 1), working
at the Rockefeller Institute for Medical Research in
New York. This agent, avian sarcoma virus, induced
tumors in muscle, bone, and other tissues of chickens. He
received the Nobel Prize for this discovery, but it was
not until the 1930s that other retroviruses, causing
tumors in mice and other mammals, were discovered.
The discovery of reverse transcriptase
independently in the laboratories of in 1971 demonstrated Figure 1 Peyton Rous
that retroviruses integrate a DNA copy of their RNA genome into the chromosomes of
infected cells. Howard Temin (Figure 2a) and David Baltimore (Figure 2b) both received
Nobel Prizes for their spectacular discovery of this enzyme, which overturned a central
dogma of molecular biology genetic information flows in one direction only, from
DNA RNA protein.
(a) (b)
Figure 2 (a) Howard Temin and (b) David Baltimore

Classification
Retroviruses are presently grouped into seven genera (Table 1), based on differences
in morphology and genome organization. A previous but related classification was based on
the pathology associated with infection: oncoviruses (many viruses in the Alpha- to
Epsilonretrovirus genera) are tumor-inducing viruses; lentiviruses induce slowly
progressing, wasting disease; and spumaviruses (foamy viruses) induce persistent
infection without any associated pathology.
Table 1 Retrovirus genera
Genus Examples of virus Host
Alpharetrovirus Rous sarcoma virus Chickens
Betaretovirus Mouse mammary virus Mice
Gammaretrovirus Murine leukemia virus Mice
Deltaretrovirus Human T-cell leukemia virus type 1 Humans
Epsilonretrovirus Walleye dermal sarcoma virus Fish
Lentivirus Human immunodeficiency virus type 1 Humans
Simian immunodeficiency virus Monkeys
Feline immunodeficiency virus Cats
Spumavirus Simian foamy virus Monkeys
II. METHODS TO STUDY RETROVIRUSES
Many previous researches about retroviruses have utilized methods applied

extensively in virology. Until the successful crystallization and X-ray diffraction on
spherical viruses in the last decade, structural information was gained largely by
fractionation of the components of purified viruses, by electron microscopy, and indirectly
by genetic analysis. For viruses which useful crystals have not been obtained for, such as
many retroviruses, these techniques remain the basis upon which implications about
structure are built.
Retroviral particles are usually purified on the basis of their size and density. Because
the particles are scattered into the extracellular medium, purification is simple and efficient
if disruption of cells can be avoided. The virus is first collected by centrifugation of the

growth medium. The resulting pellet is redissolved and the particles are sedimented to
equilibrium, usually by centrifugation in a gradient of sucrose. The density of retroviruses is
approximately 1.16 g/ml, corresponding to about 35% w/w sucrose. Higher levels of
purification can be achieved by selecting not only for particle density, but also for particle
size, for example, by rate zonal sedimentation. The most concentrated and clean source of a
retrovirus is from the plasma of chicks infected with avian myeloblastosis virus (AMV),
which can contain as much as several milligrams of virus per milliliter of plasma (1 mg is
about 1012 virions). For this reason, many of the early biochemical studies of retroviral
structural proteins and of reverse transcriptase were carried out with this member of the
ASLV genus.
Not all of the virions in a preparation are infectious. Typically for retroviruses, the
ratio of physical to infectious particles is 100:1 or greater. Thus, in most biochemical or cell
biological studies, the measurements in fact reflect the properties of the inactive particles,
since these are the predominant population. Interpretations that do not take cognizance of
the vast excess of inactive virions may be flawed. Infectious particles are rapidly inactivated
by standard disinfecting treatments like detergents. These facts have obviously important
implications for those retroviruses that cause animal or human diseases.
Particle size for viruses typically is measured either by electron microscopy or by
rate zonal sedimentation, but neither method is very accurate. Thin-section techniques
require harsh fixation, and the final appearance of the particles depends on the plane of
sectioning. Negative staining can cause deformations in particles. Sedimentation is rather
inaccurate, with a doubling in size resulting. In addition, several assumptions must be made
to allow calculation of the size of a particle from its sedimentation rate. In thin-section
electron microscopy, retroviral particles measure about 80120 nm in diameter. Since very
few studies have compared different viruses in the same experiment, it is uncertain if size
differs among the retroviral genera or being affected by other factors. In rate zonal
sedimentation, viral particles sediment at about 600S.
Electron microscopy is also applied to define morphology, one of the major criteria for
classification of viruses. The technique of negative staining shows the perimeter and
sometimes the center of the virion outlined by the surrounding accumulation of heavy
metal. In this rapid procedure, virus is simply adsorbed to a coated grid and then exposed
briefly to the solution of heavy metal before viewing. For structures that can be penetrated

by the heavy metal, negative staining usually allows excellent visualization of structural
details, but the lipid membrane of enveloped viruses typically is not penetrated by the stain,
limiting the usefulness of this technique for retroviruses. For many purposes, the thin-
sectioning technique provides more information, but it requires fixation of virus or cells by
a crosslinking reagent, dehydration, staining, and embedding into plastic before sectioning
and viewing.
Both negative staining and thin-section techniques show various projections from the
viral envelope, which comprise the viral envelope glycoproteins. The great variability
among different viruses and even among different strains or isolates of the same virus is
poorly understood and often is attributed to the propensity of the surface glycoprotein to fall
off during purification or storage. However, in some cases, even freshly isolated viruses
show few projections, and these viral preparations also contain little envelope. In contrast,
some retroviruses, for example, spumaviruses, typically are densely studded with
glycoproteins.
Cryoelectron microscopy (cryo-EM) obviates the problems of electron microscopic
thin-section techniques, since the virus is observed directly as an unstained particle in a thin
sheet of noncrystalline ice at the temperature of liquid nitrogen. Although such images have
low contrast, if the virus has detectable symmetry, computer-assisted averaging can be used
to construct a three-dimensional image of the virus. Detailed high-resolution reconstructions
have been published for numerous spherical viruses, including the alphaviruses, which, as
simple enveloped RNA viruses, can serve as models for retroviruses. Cryo-EM analyses of
retroviruses have been reported only recently for mature and immature MLVs and for HIV-
like Gag particles expressed in insect cells (Figure 3). Immature particles show a spoke-like
structure inside the envelope for both HIV and MLV. Mature particles of MLV simply show
a spherical core, with no obvious symmetrical features.
In contrast to mature cores, immature cores are quite stable to weak detergents, and
thus can be isolated readily and studied by negative-staining techniques, for example, from
mutant viruses with a defective protease. Negative-stain electron microscopy of immature,
HIV particles shows evidence of a hexagonal arrangement of subunits in local areas but this
does not necessarily imply icosahedral symmetry as suggested by other microscopic
evidence. Also, cryo-EM pictures of immature particles do not reveal clear icosahedral
symmetry of HIV, suggesting that if such symmetry features exist, they may be unstable

after virion formation. Besides, an alternative model for the structure of immature retroviral
particles postulates a helical symmetry. Thus, a more complete understanding of the
molecular structure of retroviral particles thus may have to wait for the development of new
techniques, for instance, computer programs to help interpret the cryo-EM images of
nonicosahedral viruses.
(a) (b)
Figure 3 Cryo-EM micrographs of immature and mature HIV-1 particles

To sum up, the exact arrangement of the components of the retroviral particle remains
uncertain, and hence models are necessary to represent the structure of the virion. The most
useful models represent in a pictorial form what is known about the relative positions of
components of the particle, as well as other aspects of their structure and function.
Predictions may also be incorporated into models if appropriate. Numerous models for
virions have been published, some highly detailed, but all are based to some extent on
conjecture and analogy with other viruses. One of the earliest and perhaps most influential,
presented in 1978 presaged much of what was learned later from biochemical studies about
the internal organization of the virion. Modern versions of this model (Figure 18)
incorporate newer information about structural proteins. The drawing is for HIV-1, but it
can apply to other retroviruses as well with some minor modifications.
III. RETROVIRUS VIRION
III.1. Virion structure

Retroviruses are roughly spherical and approximately 100 nm in diameter (Figure 4).
The envelope contains the external surface protein (SU), bound by non-covalent interactions

to the transmembrane protein (TM), which traverses the lipid bilayer. Coating the inner
surface of the membrane is the viral matrix protein (MA). The capsid protein (CA) forms an
icosahedral or conical core, depending on the virus strain. Three virus-coded enzymes a
protease (PR), an integrase (IN), and a reverse transcriptase (RT) are associated with the
virus core. The viral structural proteins are often identified by their glycosylation status and
their molecular weights; for example, the HIV-1 SU protein is called gp120 (glycoprotein
with molecular weight of 120), TM is gp41, and CA is p24.
Figure 4 A typical retrovirus virion

III.2. Genome structure
The virus genome (Figure 5) is a positive-strand RNA 7 to 10 kb long, complexed

with the nucleocapsid protein (NC). Genome RNAs are capped at their 5 termini and
polyadenylated at their 3 termini, as are eukaryotic mRNAs. A 150- to 200-nt (nucleotide)
repeated sequence (R) is present at both the 5 and 3 ends of the genome RNA. Adjacent to
the repeated sequences at either end are unique regions designated U5 (80200 nt) and U3
(2401200 nt).
Unlike most other viruses, retroviruses package two identical copies of the genome in
each virion. Within the virion, the two RNAs exist as a dimer, held together in a head-to-
head configuration by interaction of sequences known as a kissing loop located in the U5
region. A specific cellular transfer RNA is bound to the genome RNA by base pairing

between the primer binding sequence (PBS), located just downstream of U5, and 18
nucleotides at the 3 end of the tRNA. Different virus strains bind different cellular tRNAs.
Viral proteins are generated from three genes designated gag (for group-specific antigen),
pol (for polymerase), and env (for envelope proteins).
Figure 5 Structure of retrovirus RNA

Beginning at the left end, features are: methylated cap; repeat region (R); untranslated 5
sequence (U5); primer binding sequence (PBS); 5 splice site (5 ss); psi () packaging
sequence; gag, pol, and env reading frames for viral structural genes; 3 splice site (3 ss);
polypurine tract (ppt) used during reverse transcription; untranslated 3 sequence (U3);
repeat region (R), poly(A) tail
III.3. Viral proteins

Retroviral proteins consist of gag proteins, pol proteins and env proteins. Gag proteins
are major components of the viral capsid, which are about 20004000 copies per virion.
Protease is expressed differently in different viruses. It functions in proteolytic cleavages of
gag and pol proteins during virion maturation to produce mature and functional forms.
Reverse transcriptase and intergrase are responsible for synthesis of viral DNA and
integration into host DNA after infection, respectively. Finally, env proteins play a role in
association and entry of virion into the host cell. Possessing a functional copy of an env
gene is what makes retroviruses distinct from retroelements. The env gene serves three
distinct functions: enabling the retrovirus to enter and exit host cells through endosomal
membrane trafficking, protection from the extracellular environment via the lipid bilayer,
and the ability to enter cells. The ability of the retrovirus to bind to its target host cell using
specific cell-surface receptors is given by the surface component (SU) of the env, while the
ability of the retrovirus to enter the cell via membrane fusion is imparted by the membrane-
anchored trans-membrane component (TM). Thus the env protein is what enables the
retrovirus to be infectious.

IV. RETROVIRUS LIFE CYCLE
The retrovirus life cycle takes place in early and late phase.
IV.1. Early phase

During the early phase (Figure 6), there are three main steps. First, the retrovirus
enters the cell. Then, they make a DNA copy of their RNA genome and finally insert those
copies into the host cell genome.
Figure 6 Early phase of retrovirus life cycle

IV.1.a. Attachment and Entry
Retrovirus can only attach and infect certain species and certain cell types. Fusion is
initiated by the interaction between SU and receptor on the host cell. Next, there is a
conformational shift in the SU protein that exposes the hydrophobic amino terminus of the
TM protein. Thus, the TM protein changes its conformation which allows a hydrophobic
fusion sequence to fuse the virion membrane and cell membrane. The structure that is
released into the cytoplasm loses some proteins and a reverse transcription complex is
formed. Furthermore, viral envelope can fuse directly with the host plasma membrane, or

the virus undergoes receptor-mediated endocytosis and fusion is initiated by a decrease in

pH within the endosome.
IV.1.b. Reverse transcription

The enzyme responsible for this conversion is reverse transcriptase, exists as a dimer
that has two distinct activities: an RNA/DNA-dependent DNA polymerase activity, and a
ribonuclease H activity. Ribonuclease H is an enzyme that selectively hydrolyses the RNA
part of an RNA-DNA hybrid, but does not degrade unhybridized RNA. The cellular tRNA
molecule bound to the primer-binding site (PBS) on the viral RNA serves as a primer for
the initiation of synthesis of DNA complementary to the genome RNA. Reverse
transcription is a complex procedure with 9 steps that converts RNA into DNA (Figure 7):
1. Synthesis of minus-strand strong-stop DNA: DNA synthesis initially extends from

the tRNA primer up to the 5 end of the viral RNA, resulting in a short DNA
molecule that is a copy of the U5 and R regions. This is called minus-strand strong-
stop DNA because it is a complementary copy of part of the positive-strand genome
RNA, and DNA synthesis stops abruptly at the end of the RNA template during in
vitro reactions.
2. Removal of template RNA: RNAse H digests the RNA part of the newly made
DNA-RNA hybrid (but not the RNA-RNA hybrid at the primer binding site),
removing the RNA template and exposing the DNA copy of the U5 and R sequences.
3. Strand transfer: The DNA copy of the R sequence hybridizes with the R sequence at
the 3 end of the genome RNA. This is called the rst strand transfer, since the
strong-stop DNA strand is transferred from the 5 end to the 3 end of the genome
RNA. The actual geometry of how this transfer takes place within the virus core
during reverse transcription is not clear.
4. Copying of full-length genome: The strong-stop DNA is extended by reverse
transcriptase to copy the entire remaining part of the genome RNA up through the
primer-binding site, making a full-length minus-strand copy of the genome. Because
of the strand transfer, this DNA molecule contains a copy of the R sequence
sandwiched in between the U3 sequence, originally at the right end of the viral RNA,
and the U5 sequence, originally at the left end. The U3-R-U5 sequence is called a
long terminal repeat (LTR).

5. Removal of template RNA: As it is copied into DNA, most of the genome RNA is
digested by RNAse H. However, an RNA sequence just to the left of U3, consisting
of a polypurine tract (ppt), is resistant to digestion, and remains hybridized to the
newly synthesized minus-strand DNA. This residual RNA serves as a primer for the
subsequent synthesis of plus-strand DNA by reverse transcriptase.
6. Synthesis of plus-strand strong-stop DNA: Synthesis is initiated by the ppt RNA
primer and extends through the U3-R-U5 long terminal repeat just formed, and on
through the 18 nucleotides of the tRNA that were initially hybridized to the primer
binding site on genome RNA. The short DNA intermediate made is designated plus-
strand strong-stop DNA.
7. Removal of tRNA and ppt primer: RNAse H digestion of the 3 end of the tRNA,
now part of an RNA-DNA hybrid, removes the tRNA from the minus-strand DNA
copy and exposes the primer binding site on the plus-strand strong-stop DNA. The
ppt primer is also removed.
8. Second strand transfer: This exposed primer binding site (PBS) can hybridize with
its complementary PBS sequence at the other end of the newly synthesized minus-
strand DNA. This is called the second strand transfer since, like the rst strand
transfer, the plus-strand strong-stop DNA is transferred from one end of the template
to the other end.
9. Extension of both DNA strands: Both the minus and plus DNA strands are then
extended by reverse transcriptase to the ends of their respective template strands.
This results in a linear, double-stranded DNA with long terminal repeats at both
ends. This DNA is called proviral DNA.

Figure 7 Reverse transcription

The reverse transcriptase of retroviruses lacks the 3-to-5 exonuclease activity that
cellular DNA polymerases use for proofreading. Therefore, about 1 to 10 nucleotide errors
could be produced during synthesis of each proviral DNA molecule, which leads to the
incompletely uniform of retrovirus populations as they have a lot of variants or
quasispecies.
The linear double-stranded viral DNA resulting from reverse transcription remains
associated with components of the virus core in a preintegration complex. The large size
of this complex prevents its entry through the nuclear pores until the host nuclear envelope
is disappeared in cell division. For this reason, the retroviruses can only productively infect
cells that undergo mitosis. Exceptionally, HIV-1 and other lentiviruses can transfer their
DNA in all stages of host cell life through nuclear pores.
IV.1.c. Intergration
Integrase is the viral enzyme used in this
step which presents in the core of the infecting
virion. This enzyme binds to the two ends of
linear viral DNA and brings them together and
in close proximity to cellular DNA. Integration
step has some major points (Figure 8):
1. The integrase removes the two 3

terminal nucleotides of each strand of
the linear viral DNA.
2. Viral DNA is inserted into host DNA by
cleavage and ligation reaction. The
integrase brings the two 3-OH ends of
viral DNA close to two phosphodiester
linkages 4 to 6 nucleotides apart on the
host DNA, and joins viral to cellular
DNA strands. This leaves a 4-to 6-nt
single-stranded gap on the target host
DNA, and a 2-nt unpaired region on the
Figure 8 Integration of proviral
viral DNA. DNA into host cell

3. Host enzymes carry out repair synthesis of the gap, simultaneously removing the
terminal 2 unpaired nucleotides of the viral DNA. This generates a direct repeat of
host DNA (46 bp depending on the virus) and results in the loss of the terminal 2 bp
of viral DNA without any effect on progeny virus because the ends are not used in
the synthesis of viral RNA.
Integration sites appear to be distributed randomly over the host genome. Once
integrated, the proviral DNA becomes part of a host cell chromosome and is replicated
along with host DNA, just like any cellular gene. Consequently, spread of the infection
within an animal can be achieved by infection of new cells with progeny virus and by
multiplication of cells already containing proviral DNA. Furthermore, virus infections can
be transmitted from parent to offspring if an egg or sperm cell becomes infected and
contains integrated proviral DNA.
IV.2. Late phase

The late phase involves expression of viral RNA, synthesis of viral proteins, and
assembly of viral virions. The U3 region contains transcriptional enhancers which interact
with cellular transcription factors and determine in which cell type and to which extent
transcription takes place. The mix of transcription factor presence in turn may also be
affected by external stimuli.
IV.2.a. Expression of viral mRNA
A TATA box just upstream of the U3/R junction directs the initiation of transcription
by cellular RNA polymerase II (Figure 9). Transcription begins precisely at the U3/R
junction within the left LTR and proceeds through the entire genome and the right LTR. A
highly conserved AUAAAA signal in the right LTR directs cleavage of the transcript and
polyadenylation of RNA 3 end by the host cell enzymes precisely at the R/U5 boundary.
This gives rise to full-length RNA identical to the genome RNA of the infecting virus.
There are two identical LTRs, one at each end of the proviral DNA. RNA polymerases
can dislodge the binding of transcription factors to the right LTR, inactivating its ability to
initiate transcription (promoter occlusion). This makes sure transcription only begins at the
left LTR.

Similarly, only the right LTR is used for signaling cleavage and polyadenylation
because some viruses position the AUUAAA signal within the U3 region so that only the
copy present in the right LTR is transcribed. However, the AAUAAA is located within the
R region of other retroviruses, and therefore their U3 region contains additional sequences
that enhance recognition of the polyadenylation signal near the 3 end of viral RNAs. In
another way, thay can also possess sequence elements adjacent to the polyadenylation signal
near the 5' end that repress recognition of that AAUAAA. These two mechanisms ensure
that cleavage and polyadenylation take place only at that end.
IV.2.b. Synthesis of viral proteins
Splicing of the primary

transcript enables the virus to
produce numerous viral
proteins, which are encoded
in different reading frames,
from only one mRNA
molecule. All retroviruses
make at least two mRNAs:
unspliced RNA is used for
synthesis of the Gag and
Figure 9 Production of retrovirus RNA Gag/Pol proteins, and a singly
spliced form, from which the
Gag/Pol reading frames have been removed, is used for synthesis of the Env proteins
(Figure 9). In some retroviruses, more complex splicing patterns generate additional
mRNAs. For example, for HIV-1, a typical member of the lentivirus subfamily, viral RNA
can undergo multiple splicing events to generate mRNAs encoding regulatory proteins.
The unspliced RNA is used to synthesize Gag and Gag/Pol polyproteins, the
precursors of the MA, CA, NC, PR, RT, and IN proteins. Only a few molecules of reverse
transcriptase, protease, and intergrase are needed, but many structural protein molcules
encoded by Gag are required to form a single virion. Therefore, to ensure the synthesis of
Gag and Gag/Pol in a particular ratio, the generation of these two polyproteins from a single
mRNA requires 2 mechanisms of modification of the normal translation process.

The first one is suppression of

transcription termination (Figure 10). The
stop codon UAG separating the gag and pol
reading frames is occasionally misread by
Gln-tRNAGln as CAG about 1/20 times, and
glutamine is inserted at that site. This allows
translational readthrough, permitting the
Figure 10 Suppression of generation of the Gag/Pol polyprotein. The
translation termination
misreading process is stimulated by a
particular secondary structure called a pseudoknot, located just beyond the termination
codon in the mRNA.
The second mechanism is ribosomal frameshifting (Figure 11), in which the ribosome
shifts its reading frame at a precise position within the RNA prior to the termination codon.
Ribosomal frameshifting is induced by the presence of two sequence elements within the
RNA: a heptamer sequence (for example U UUU UUA in HIV-1), where the ribosome
stalls, and a secondary structure downstream of the heptamer that induces ribosome stalling.
Because of the similar strength of base pairing interactions between the codons on mRNA at
the heptamer sequence and the anticodon sequences of the two tRNAs, the stalled ribosome
is able to shift the reading frame back one nucleotide occasionally, and resumes translation
of the sequence. In the new reading frame, the gag termination codon is no longer
recognized and the pol region is translated, resulting in the generation of the Gag/Pol
protein.
Figure 11 Ribosomal frameshifting

The Env protein is translocated directly into the lumen of the endoplasmic reticulum as
it is being synthesized. It is subsequently transported through the Golgi apparatus and the
endosome compartment, and finally arrives at the plasma membrane. In the course of these
events, the protein undergoes glycosylation and cleavage by host enzymes to generate the
mature forms of SU and TM. In contrast to Env, both Gag and Gag/Pol proteins are released
into the cytosol upon translation. The Gag protein is targeted to the plasma membrane by
the fatty acid myristate, linked post-translationally to its N-terminal amino acid. The Gag
and Gag/Pol proteins interact with each other to initiate assembly of the virus core.
The translation and post-translational modifications to generate retroviral proteins is

summarized in Figure 12.
Figure 12 Retrovirus translation and post-translational modifications

IV.2.c. Assembly and release of virions
Two different assembly

pathways have been elucidated, based
on the relative occurrence of the core
assembly and the budding. In B-
and D-type viruses, the core is first
assembled within the cytoplasm,
generating spherical structures called
A-type particles, and then bud
through the plasma membrane in
regions where the SU and TM
proteins have accumulated, acquiring
an envelope. For C-type viruses, as Figure 13 Two assembly pathways in
retroviruses
well as lentiviruses, assembly of the
core occurs simultaneously with budding at the plasma membrane. Certain defective
endogenous retroviruses have a similar pathway except that they bud exclusively from the
ER membrane to produce intracisternal A-type particles (IAPs).
Selective encapsidation of only unspliced full-length viral RNA is achieved by

position the packing signal psi (), to which the NC portion of Gag binds, downstream the
5 splice site. The Gag/Pol polyprotein is incorporated into the assembling core by
interaction between its CA region and the corresponding region of Gag. Finally, tRNA is
incorporated into the core by binding to the RT and NC portions of the Gag/Pol protein.
As virions are assembled and extruded from the cell, the viral protease becomes
activated. The protease then cleaves the Gag and Gag/Pol polyproteins into the individual
structural (MA, CA, and NC) and enzymatic (PR, RT, and IN) proteins, and they rearrange
to form mature virions. It is only at this stage that virions become infectious; therefore, the
protease is an important target of antiviral chemotherapy directed against retroviruses.
Retroviral life cycle is summarized in Figure 14.

Figure 14 Retrovirus life cycle

PART 2: HUMAN IMMUNODEFICIENCY VIRUS (HIV)
I. THE DISCOVERY OF HIV
The earliest known case
The first case of HIV infection in a human was identified in 1959. (The transfer of the
HIV disease from animal to human likely occurred several decades earlier, however.) The
infected individual lived in the Democratic Republic of the Congo. He did not know (and
research could not identify) how he was infected.
The controversy surrounding the discovery of AIDS virus
In 1981, the term acquired immunodeficiency syndrome (AIDS) was coined to

describe a condition in a group of previously healthy young males within the Los
Angeles/San Francisco area who showed a marked depletion of their immune CD4-positive
T lymphocytes, rendering them immune-incompetent. As a consequence, they suffered
from a number of opportunistic infections (the most prevalent being Pneumocystis carinii
pneumonia, as reported by The Centers for Disease Control in Atlanta) that were often fatal.
Subsequent epidemiological studies suggested that the syndrome was due to a transmissible
agent that was acquired through sexual contact or blood exchange; hemophiliacs, recipients
of blood transfusions, and intravenous drug users were also affected.
In 1983, a retrovirus isolated from the blood of individuals with AIDS was
characterized by groups led by Luc Montagnier (Figure 15a) and Barr-Sinoussi (Figure
15b) at the Pasteur Institute in Paris and Robert Gallo (Figure 15c) in Maryland. This virus,
subsequently named human immunodeficiency virus type 1 (HIV-1) was demonstrated
(despite much controversy and debate) to be the causative agent of AIDS. HIV-1 is
characteristic of a subfamily of retroviruses named the lentiviruses (Table 2), so named
because of the slow progression of diseases caused by lentiviruses. Another type of human
immunodeficiency virus, HIV-2 was isolated from mildly immune suppressed patients in
West Africa and appears to be less pathogenic than HIV-1. Fewer people succumb to HIV-2
than HIV-1 and prior infection with HIV-2 may even help to prevent infection with HIV-1.
However, the incidence of HIV-2 is growing.

(a) (b) (c)
Figure 15 (a) Luc Montagnier, (b) Barr-Sinoussi, and (c) Robert Gallo
Table 2 Lentiviruses
Virus Host
Human immunodeficiency virus type 1 Humans
Human immunodeficiency virus type 2 Humans
Simian immunodeficiency virus Apes and old world monkeys
Feline immunodeficiency virus Cats
Equine infectious anemia virus Horses
Caprine arthritis-encephalitis virus Goats
Visna-maedi virus Sheep
II. SIGNS AND SYMPTOMS OF HIV INFECTION
The course of the infection can be roughly divided into three phases: (1) acute
infection, (2) clinical latency, and (3) AIDS (Figure 16). Two to six weeks following
exposure to the virus, individuals can develop a mononucleosis or influenza-like syndrome
(fever, malaise, lethargy, nausea, diarrhea, headaches, stiff neck, or swelling of lymph
nodes) that requires hospitalization in a minority of individuals.

(a)
Entry of virus into the host
Localized replication at site of infection
Release of virus into the circulation
Seeding of lymph nodes throughout body
Immune clearance of virus from peripheral circulation; continued replication in lymph nodes
Replication and destruction of lymph node architecture
Release of virus into the circulation
Loss of immune response; susceptibility to opportunistic infections.
(b)
Figure 16 Events associated with progression to AIDS

(a) Change in viral RNA load and CD4+ T cell level in the peripheral circulation from acute
infection to end-stage disease. (b) Stages of HIV infection
The first organ system to be affected by the infection is the gut associated lymphoid
tissue (GALT). There is a significant depletion of CD4-positive T cells in this lymphoid
tissue during acute infection, which is not restored even after resolution of the initial
viremia. Given the role of GALT in regulating intestinal flora, it is has been suggested that
its depletion may result in release of bacterial products such as lipopolysaccharide into the
circulation, including a state of chronic immune activation known to persist in the chronic
phase of HIV disease.
Increased numbers of T cells from HIV-infected individuals undergo spontaneous

apoptosis even though they are not directly infected. Within 1 to 2 months, the primary
infection resolves but there is little recovery of the GALT. Virus titers drop as the immune
system responds with both cytotoxic T lymphocytes and antibodies. However, infection
within the lymph nodes persists throughout the course of the disease.
Several course of disease following acute infection have been documented in the
absence of treatment:
1. Rapid progressors (1015% of infected individuals) develop late stage symptoms in

2 to 3 years.
2. Slow progressors (7080%) develop late stage symptoms in 8 to 10 years.
3. Long-term non-progressors (5%) show no decline in CD4-positive T-cell levels.
Several factors help predict clinical outcome. After resolution of the acute infection,
varying levels of viral RNA genomes can be detected in the blood of different individuals
(virus load set point, Figure 16). The higher the basal level of viral RNA, the more rapidly
patients progress to full-blown AIDS. Also important is the nature of the virus itself.
The nature of the immune response is also crucial. Patients who develop a
predominantly cytotoxic T-cellbased immune response have a better chance of long-term
survival. The diversity of the epitopes recognized by the immune system also appears to
play a role: recognition of a limited number of epitopes is associated with a poor prognosis.
Over the course of clinical latency, virus replication persists in the lymph nodes,
resulting in a gradual depletion in the level of circulating CD-4 positive T cells and
destruction of the lymph node architecture. Individuals progressing toward end-stage
disease have high levels of virus in the blood, indicative of the failure of the immune system
to contain the infection. Patients exhibit chronic fever, night sweats, diarrhea, a number of
infections such as cytomegalovirus, pneumonia, oral thrush, herpes simplex, neoplasm such
as Kaposis sarcoma, and neurological syndromes including dementia and neuromuscular
disorder. Neurological symptoms correlate with virus replication in the central nervous

system. While current therapies delay or prevent disease progression, they do not eradicate
the infection. Consequently, withdrawal from therapy results in reemergence of the virus
and continued disease progression.
III. AIDS TRANSMISSION AND EPIDEMIOLOGY
The relatively recent discovery that HIV induces fatal human diseases has reinforced
the need to understand the epidemiology and transmission of all pathogenic retroviruses.
The niche these agents occupy in nature and the ways in which they are maintained within
the host population are not always emphasized by studies conducted in tissue culture and
laboratory animal models. However, these features influence the frequency with which
disease arises and they provide clues to methods that may control and eventually eliminate
the virus.
III.1 Transmission
HIV-1 was probably transmitted to humans from chimpanzees infected with SIVcpz.
Many species of African monkeys and apes are hosts for specific strains of simian
immunodeficiency virus (SIV), closely related to HIV. These viruses have been isolated and
their nucleotide sequences compared. As a result of these studies, it has been determined
that HIV-1 is a zoonotic infection likely transmitted in the early 1900s from butchered
chimpanzees infected with the chimpanzee strain of SIV (SIVcpz) to humans in West-
Central Africa.
Among humans, HIV is transmitted by three main routes: sexual contact, exposure to
infected body fluids or tissues, and from mother to child during pregnancy, delivery, or
breastfeeding (known as vertical transmission). In the majority of cases, HIV is
transmitted upon exposure to mucous membranes, usually during sex (currently the most
frequent mode of transmission of HIV) or ingestion of breast milk (the third most common
way in which HIV is transmitted globally).
Only certain fluids blood, semen, rectal fluids, vaginal fluids, and breast milk from
an HIV-infected person can transmit HIV. These fluids must come in contact with a mucous
membrane or damaged tissue or be directly injected into the bloodstream (from a needle or
syringe) for transmission to possibly occur. There is no risk of acquiring HIV if exposed to
feces, nasal secretions, saliva, sputum, sweat, tears, urine, or vomit unless these are

contaminated with blood. It is possible to be co-infected by more than one strain of HIV a
condition known as HIV superinfection.
III.2 Epidemiology
HIV/AIDS is a global pandemic. According to UNAIDS (Joint United Nations

Programme on HIV/AIDS), in 2010, there are approximately 35.3 million people living
with HIV globally (Table 3). Of these, about 17.2 million are men, 16.8 million are women
and 3.4 million are less than 15 years old. There were about 1.8 million deaths from AIDS
in 2010, down from 2.2 million in 2005.
The pandemic is not similar within regions, with some countries more afflicted than
others. Even at the country level, there are wide variations in infection levels among
different areas. The number of people infected with HIV continues to increase in most parts
of the world, despite the implementation of prevention strategies, Sub-Saharan Africa is the
worst-affected region, with about 22.9 million at the end of 2010, 68% of the global total.
South and South East Asia have an estimated 12% of the global total. The rate of new
infections has fallen slightly since 2005 after a more rapid decline between 1997 and 2005.
Annual AIDS deaths have been continually declining since 2005 as antiretroviral therapy
has become more widely available.
Table 3 Prevalence rate of HIV/AIDS infection in 2010

World region Estimated prevalence of Estimated Adult
HIV infection adult and prevalence
(adults and children) child deaths (%)
during 2010
Worldwide 31.6 million 35.2 million 1.6 -1.9 million 0.8

Sub-Saharan Africa 21.6 million 24.1 million 1.2 million 5.0
South and South-East Asia 3.6 million 4.5 million 250,000 0.3
Eastern Europe & Central Asia 1.3 million 1.7 million 90,000 0.9
Latin America 1.2 million 1.7 million 67,000 0.4
North America 1.0 million 1.9 million 20,000 0.6
East Asia 580,000 1.1 million 56,000 0.1
Western & Central Europe 770,000 930,000 9,900 0.2
Source: UNAIDS World Aids Day Report

III.2.a. Sub-Saharan Africa

Sub-Saharan Africa
remains the highest region.
HIV infection is becoming
endemic in sub-Saharan
Africa, which is home to just
over 12% of the worlds
population but two-thirds of
all people infected with HIV.
The adult HIV prevalence
rate is 5.0% and between
21.6 million and 24.1 million
total are affected. However,
the actual prevalence varies
between regions. Presently,
Southern Africa is the
Figure 17 Map of HIV prevalence in Africa in 2007
hardest hit region, with adult
Source: UNAIDS
prevalence rates exceeding
20% in most countries in the region, and 30% in Swaziland and Botswana (Figure 17).
Eastern Africa also experiences relatively high levels of prevalence with estimates
above 10% in some countries, although there are signs that the pandemic is declining in this
region. West Africa on the other hand has been much less affected by the pandemic. Several
countries reportedly have prevalence rates around 2 to 3%, and no country has rates above
10%. In Nigeria and Cte d'Ivoire, two of the region's most populous countries, between 5
and 7% of adults are reported to carry the virus.
Across Sub-Saharan Africa, more women are infected with HIV than men, with 13
women infected for every 10 infected men. This gender gap continues to grow. Throughout
the region, women are being infected with HIV at earlier ages than men. The differences in
infection levels between women and men are most pronounced among young people (aged
1524 years). In this age group, there are 36 women infected with HIV for every 10 men.
The widespread prevalence of sexually transmitted diseases, the practice of scarification,

unsafe blood transfusions, and the poor state of hygiene and nutrition in some areas may all
be facilitating factors in the transmission of HIV.
Mother-to-child transmission is another contributing factor in the transmission of HIV

in developing nations. Due to a lack of testing, a shortage in antenatal therapies and through
the feeding of contaminated breast milk, 590,000 infants born in developing countries are
infected with HIV-1 per year. In 2000, the World Health Organization estimated that 25%
of the units of blood transfused in Africa were not tested for HIV, and that 10% of HIV
infections in Africa were transmitted via blood.
Poor economic conditions (leading to the use of dirty needles in healthcare clinics) and
lack of sex education contribute to high rates of infection. In some African countries, 25%
or more of the working adult population is HIV-positive. Poor economic conditions caused
by slow onset-emergencies, such as drought, or rapid onset natural disasters and conflict can
result in young women and girls being forced into using sex as a survival strategy. Worse
still, research indicates that as emergencies, such as drought, take their toll and the number
of potential 'clients' decreases, women are forced by clients to accept greater risks, such as
not using contraceptives.
AIDS-denialist policies have impeded the creation of effective programs for

distribution of antiretroviral drugs. Denialist policies by former South African President
Thabo Mbeki's administration led to several hundred thousand unnecessary deaths.
UNAIDS estimates that in 2005, there were 5.5 million people in South Africa infected with
HIV 12.4% of the population. This was an increase of 200,000 people since 2003.
Although HIV infection rates are much lower in Nigeria than in other African
countries, the size of Nigeria's population meant that by the end of 2003, there were an
estimated 3.6 million people infected. On the other hand, Uganda, Zambia, Senegal, and
most recently Botswana have begun intervention and educational measures to slow the
spread of HIV, and Uganda has succeeded in actually reducing its HIV infection rate.
III.2.b. South and South-East Asia
The HIV prevalence rate in South and South-East Asia is less than 0.35%, with total of
4.2 4.7 million adults and children infected. More AIDS deaths (480,000) occur in this
region than in any other except sub-Saharan Africa. The geographical size and human

diversity of South and South-East Asia have resulted in HIV epidemics differing across the
region. The AIDS picture in South Asia is dominated by the epidemic in India.
In South and Southeast Asia, the HIV epidemic remains largely concentrated in
injecting drug users, men who have sex with men (MSM), sex workers, and clients of sex
workers and their immediate sexual partners. In the Philippines, in particular, sexual
contacts between males comprise the majority of new infections. An HIV surveillance study
conducted by Dr. Louie Mar Gangcuangco and colleagues from the University of the
Philippines Philippine General Hospital showed that out of 406 MSM tested for HIV in
Metro Manila, HIV prevalence was 11.8%.
Particularly, migrants are vulnerable, and 67% of those infected in Bangladesh and
41% in Nepal are migrants returning from India. This is in part due to human trafficking and
exploitation, but also because those migrants who willingly go to India in search of work
are often afraid to access state health services due to concerns over their immigration status.
Vietnam
In Vietnam, the estimated number of people living with HIV rose drastically from
3,000 in 1992 to 220,000 in 2007, claiming 0.47% of the population. Among these, 5,670
are children. This trend is placing Vietnam at the threshold of moving the disease from the
high-risk groups of drug users and sex workers to the general population.
Injecting drug users (IDU) account for up to 65% of people living with HIV. The HIV
prevalence among male IDU is estimated to be 23.1%. Drug injection is reported as the
major cause for doubling the number of HIV/AIDS patients from 2000 to 2005. Although
there appears widespread awareness of using sterile needles among IDU (88% reported
doing so in the last injection) sharing needles is common among those who have already
contracted HIV/AIDS. In a survey of 20 provinces in Vietnam, 35% of IDU living with HIV
shared needles and syringes. Besides, IDU often engage in risky sexual behaviors. 25% of
male IDU in Hanoi is reported to buy sex and do not use condoms. Meanwhile, female IDU
often sell sex to finance their drug need. This raises the risk of spreading HIV/AIDS to the
general population.
While HIV/AIDS remain an epidemic only within the high-risk groups, women in the
general population may be more exposed to the risk of contracting HIV than reported. One

study estimates that reported HIV transmission among women may reflect as low as 16% of
the real number due to the lack of HIV screening. The number of women with HIV
infection is estimated to increase from less than 30,000 in 2000 to 90,000 in 2007.
Women may contract HIV/AIDS through partners who are undisclosed IDU. Men
having pre-marital or extra-marital sexual relationships with female sex workers inevitably
expose their wives to HIV/AIDS risk. Particularly in provinces with mobile populations,
migrant husbands who, being away from home, are likely buy sex and use drugs may
contract HIV and transmit to their wives.
With potentially high HIV prevalence among women, perinatal transmission presents
another channel of HIV transmission. It is reported that more than 1% of pregnant women
in some provinces are found HIV positive.
IV. HIV VIRION
The virion has the general

characteristics of retroviruses but, in
contrast to most retroviruses, the capsid is
cone shape with a diameter of 4060 nm
at the wide end and about 20 nm at the
narrow end. The diameter of the HIV
virion measured in negatively stained
preparations is in the range 80110 nm,
while results from cryo-electron
microscopy are at the upper end of this
range or greater. Generally, there is one Figure 18 Diagram of an HIV-1 virion
capsid per virion, though virions with two For clarity, only one of the two RNA molecules is
shown covered by NC proteins
or more capsids have been reported.
Sequence analysis of the genome of HIV-1 revealed it to be considerably more

complex than many other retroviruses. In addition to the standard gag, pol, and env genes,
six additional reading frames were identified: vif, vpr, vpu, tat, rev, and nef (Figure 18 and
Figure 19, Table 4 and Table 5).

In contrast to simpler retroviruses, which make only two mRNAs (unspliced and
singly spliced), splicing of the HIV-1 primary transcript generates more than 25 mRNAs
that fall into three size classes (Figure 19):
1. The unspliced 9-kb full-length RNA, used to produce Gag and Gag-Pol proteins
2. The singly spliced 4-kb class of RNAs, which encode Vif, Vpr, Vpu, or Env
3. The doubly spliced 2-kb class of RNAs, which encode Tat, Rev, or Nef
In each class of spliced RNA there are multiple species, generated by the presence of
several different 3 and 5 splice sites.
Figure 19 Genome structure and RNA splicing pattern of HIV-1

Table 4 HIV-1 structural proteins
Alternative name
Name Abbreviation
(M. Wt. in KDa)
Matrix MA p17
Capsid CA p24
Nucleocapsid NC p7
Protease PR p14
Reverse transcriptase RT p66/p51
Integrase IN p32
Surface protein SU gp120
Virion protein R Vpr p15
Table 5 HIV-1 non-structural proteins
Alternative name
Name Abbreviation
(M. Wt. in KDa)
Viral infectivity factor Vif p23
Virion protein unique for HIV-1 Vpu p16
Transactivator for transcription Tat p15
Regulator of expression of virion protein Rev p19
Negative effector Nef p27
V. HIV REPLICATION
The basic replication pattern of lentiviruses as well as HIV-1 is identical to that of

other retroviruses. This section emphasizes only on some specific features and functions of
additional proteins in HIV-1.

V.1 Receptors of HIV-1
There are two types of receptors for HIV-1 virus, primary receptors and chemokine
receptors which vary from different host cells.
Primary receptor for HIV-1 is

the CD4 antigen, found on the
surface of both helper T
lymphocytes and macrophages.
Thus HIV-1 attacks at the very heart
of the immune system, as both CD4-
positive T cells and macrophages are
vital for development of both
humoral antibody and cell-mediated
immunity.
Beside the presence of CD4
alone on the cell surface, infection
also requires the presence of either
the CCR5 or CXCR4 chemokine
receptor. The ability of ligands for
these receptors (Mip1, Mip1, and
Rantes for CCR5; SDF-1 for
CXCR4) to block virus entry
demonstrates their signicant role in
the infection process.
Viruses using CXCR4 are
designated X4 (or T cell-tropic)
Figure 20 Model of HIV-1 entry
viruses, whereas those using CCR5
are termed R5 (or macrophage-tropic) viruses. These strain differences depend on variations
in the SU protein (gp 120), particularly in a region that undergoes a high rate of evolution,
designated variable domain 3. Although both forms of HIV-1 may be present in an
inoculum, only the R5 strain is sexually transmitted. Natural resistance to HIV-1 infection is
associated with a mutation in CCR5 that results in a loss of cell surface expression of the

protein. In contrast to CD4+ T cells, HIV-1 infection of macrophages results in a low level
of virus replication, with the bulk of the virus accumulating in intracellular vacuoles.
Release of the virus occurs upon fusion of the vacuoles with the plasma membrane.
Binding to CD4 (Figure 20a) induces a conformational change in gp120 that exposes
regions that interact with the chemokine receptor. This binding triggers a conformational
change in the envelope protein TM (gp41) that induces the fusion of the viral envelope with
the plasma membrane (Figure 20b), allowing release of the nucleocapsid into the cytoplasm
(Figure 20c).
Once released into the cytoplasm, the viral nucleocapsid partially breaks down to
permit access to nucleotide pools within the cell. The viral capsid associates with cellular
microlaments and reverse transcription of the viral genome begins. Experiments in several
species have identied host proteins (Ref1, Lv1) that can block this stage of the infection.
Designated restriction factors, they either accelerate capsid breakdown or block transport
of the viral preintegration complex into the nucleus. Old world monkeys experimentally
infected with HIV-1 express Trim5, a protein that promotes rapid degradation of the
capsid before reverse transcription can occur. Unfortunately, the human Trim 5 homolog
fails to recognize HIV-1.
V.2 Special feature of HIV-1
Most retroviruses cannot productively infect non-dividing cells because the

preintegration complex, containing proviral DNA, is unable to enter the intact nucleus.
Integration of proviral DNA must therefore await the disintegration of the nuclear
membrane when the cell divides. In contrast, HIV-1 is able to transport the preintegration
complex into the nucleus via the nuclear pores, and can therefore infect cells that are not
actively dividing. Three virus-encoded proteins in the preintegration complex facilitate this
transport: MA, Vpr, and IN. MA encodes a classical nuclear import signal that interacts
with the importin family of proteins. In contrast, both Vpr and IN interact directly with
components of the nuclear pore.

V.3 Functions of HIV additional proteins
V.3.a. Tat
The Tat protein increases HIV-1 transcription by stimulating elongation by RNA

polymerase II.
Tat, which is localized in the cell nucleus, is a highly basic 86-amino acid protein
produced by doubly spliced mRNA. Expression of this protein dramatically increases the
amount of viral RNA, thus its name, abbreviated from transactivator of transcription.
The function of Tat is achieved by its binding to Tat-responsive element (TAR) on

nascent RNAs, which located just downstream the transcription start site. TAR forms a
stem-loop structure with two regions essential for its function: (1) a bulge in the stem,
which forms the recognition element for Tat binding; and (2) the nucleotide sequence within
the loop. Tat increases viral RNA abundance by increasing the elongation efficiency of
RNA polymerase molecules.
The form of RNA polymerase II that participates in initiation contains few phosphate
groups within its carboxy-terminal domain (CTD), so it has low efficiency in elongation
(Figure 21a). Increasing the extent of phosphorylation of CTD promote the movement of
the polymerase away from the point of initiation and facilitate the elongation stage. Tat
increases phosphorylation of CTD by recruitment of cyclin-dependent kinase (cdk)-
9/cyclin T to the transcription complex (Figure 21b).
Figure 21 Mechanism of Tat function

V.3.b. Rev
The Rev protein mediates cytoplasmic transport of viral RNA that code for HIV-1
structural proteins.
Rev, abbreviated from regulator of expression of virion proteins, is required for the
transport of unspliced and 4-kb (singly spliced) class of viral RNAs from the nucleus to the
cytoplasm. However, export and translation of the 2-kb (doubly spliced) one is not
dependent on Rev.
A 240-nucleotide sequence within env, termed the Rev response element (RRE), where
Rev binds is required for Rev action (Figure 22). The 116-amino acid Rev protein contains
both a nuclear localization signal and a nuclear export signal. Transport to the cytoplasm
involves binding of the nuclear export signal on Rev to the cellular protein exportin 1,
which mediates the docking of Rev to the nuclear pore. If Rev is simultaneously bound to
an mRNA via its RRE, the export of Rev results in the export of the mRNA. Transport of
Rev back into the nucleus requires dissociation of the Rev/RNA complex. Subsequently,
Rev binds to importin , which docks Rev to the cytoplasmic face of the nuclear pore. Rev
is returned to the nucleus, where the cycle is repeated.
Together, the Tat and Rev proteins strongly upregulate viral protein expression.
Tat and Rev are essential for
virus replication because they regulate
HIV-1 transcription and transport of
mRNAs that code for viral structural
proteins. Their action results in the
expression of viral proteins in two
stages. Following integration of
proviral DNA and its transcription at a
basal level, only the doubly spliced 2-
kb RNAs are transported to the
cytoplasm. This permits the synthesis
of Tat, Rev, and Nef. Both Tat and
Figure 22 Mechanism of Rev function Rev are then transported to the
nucleus where they augment
transcription of provirus DNA (Tat) and the transport of viral mRNAs to the cytoplasm
(Rev), allowing the expression of proteins encoded by the 9-kb and 4-kb classes of mRNAs
(Gag, Gag/pol, Env, Vif, Vpr, and Vpu).
V.3.c. Vif
Vif increases virion infectivity by counteracting a cellular deoxcytidine deaminase.
Vif (viral infectivity factor) is a 193-amino acid protein found in the cytoplasm of
infected cells and incorporated at low levels in virions via an interaction with viral genome
RNA. Deletion of the Vif gene reduces infectivity of HIV-1 in cell cultures and in animal
models used to test pathogenicity. Virus lacking Vif enters cells normally but generates a
lower level of proviral DNA than wild-type virus. The absence of Vif within infecting
virions cannot be compensated by expressing it in the cells being infected.
Vif is required to overcome the action of a host cell protein, APOBEC3G.
APOBEC3G is a member of a family of cellular proteins that deaminate cytidines (in RNA)
or deoxycytidines (in DNA) to either uridine or deoxyuridine. The original member of this
family, APOBEC1, was so named because it deaminates a specic cytidine residue in the
mRNA coding for Apolipoprotein B, allowing two proteins to be made from the same gene
using either the native or edited messenger RNA.
APOBEC3G is incorporated into virions during assembly, and can induce deamination
of multiple deoxycytidine residues in the DNA product of reverse transcription made during
a subsequent infection. This leads to mutations in viral structural and regulatory proteins,
with a corresponding reduction in infectivity. APOBEC3G therefore functions to defend the
cell against infection by mutating the DNA copy of the HIV-1 genome. Vif acts by binding
to APOBEC3G and inducing ubiquitination and degradation of this protein by
proteasomes. This prevents its incorporation into virions, and therefore counteracts this
cellular antiviral defense mechanism.
However, mutants of APOBEC3G that lack deoxycytidine deaminase activity retain
some antiviral activity. Recent studies have shown that APOBEC3G also directly impairs
the reverse transcription reaction, signicantly reducing the yield of proviral DNA.
V.3.d. Vpr
Vpr (virion protein R) is a 100-amino acid protein that is recruited into virions (10100
molecules per virion) by virtue of its interaction with the carboxy-terminal region of Gag.

One of its major effects is to permit the infection of non-dividing cells by serving as a signal
for the active transport of the preintegration complex into the cell nucleus (Section V.2).
Vpr also facilitates packaging within the virion of the cellular enzyme uracil DNA
glycoslase. This enzyme can remove deoxyuridine residues incorporated into viral DNA
during reverse transcription because of high levels of dUTP in the cell, which makes it
unavailable for the synthesis of viral DNA.
Vpr can also arrest and delay infected cells in the G2 stage of the cell cycle. Vpr may
do this by targeting for degradation cellular proteins that are needed to pass from the G2
phase to mitosis, which may be beneficial for virus replication since HIV-1 transcription by
is the most active at this stage of the cell cycle.
V.3.e. Vpu
Vpu protein enhances release of progeny virions from infected cells.
Vpu (virion protein unique to HIV-1) is an 81-amino acid protein that is inserted into
membranes via its amino-terminal domain. This protein accumulates in the Golgi apparatus
and the endosome compartment of the cell. No homologs have been identied in related
lentiviruses such as HIV-2 and simian immunodeciency virus. Vpu has two known
activities within the cell.
Degradation of CD4: The cellular CD4 protein is a receptor for HIV that interacts
with gp120 at the cell surface. However, both CD4 and gp160, the precursor of gp120, are
made in the endoplasmic reticulum, and they can bind to each other at that intracellular site.
The aggregate that forms retains gp160 inside the cell and therefore reduces gp120
incorporation into the virions released (Figure 23a). Vpu acts by binding to CD4 and to the
cellular protein -TrCP. This induces the ubiquitination of CD4 and its subsequent
degradation by proteasomes, thus releasing gp160 and increasing surface expression of its
cleavage products, gp 41 and gp 120.
Enhancement of virus release from the plasma membrane: This activity is dependent
upon the transmembrane portion of Vpu. In the absence of Vpu, virions accumulate on the
cell surface in a partially budded state. Expression of Vpu results in enhanced release of
virus from the cell surface. Remarkably, this effect is not restricted to HIV-1; Vpu also
enhances the release of other, unrelated viruses. Recent work has determined that Vpu

induces degradation of tetherin, a host cell protein located on the plasma membrane that is
believed to interact with budding virions and promote their endocytosis.
V.3.f. Nef
Nef protein is an important mediator of pathogenesis.
Nef (negative effector) is a 210-amino acid protein that is localized at the inner face of
the plasma membrane via a residue of myristate added to its N-terminal amino acid.
Infection of monkeys with simian immunodeciency virus containing point mutations in the
Nef gene resulted in the rapid generation of revertant viruses with a functional Nef gene,
showing that there is considerable selection pressure for an active Nef protein. Simian
immunodeciency virus mutants with deletions of the Nef gene are viable, but have lower
titers and fail to induce disease in infected monkeys. Expression of Nef in mouse T cells and
macrophages causes a disease that resembles the late stages of AIDS. These ndings
implicate Nef as an important determinant of disease in infected animals. Three activities
have been attributed to Nef, but it is unclear which of these activities is important for
disease.
Decrease in the surface expression of CD4 and MHC 1: Nef expression decreases the
levels of CD4 and the major histocompatibility complex protein MHC 1 on the cell
surface. Because these are important mediators of immune responses, their absence can be
important in disease progression. The loss of surface CD4 is caused by an increase in the
cycling of CD4 between the cell surface and the endosome compartment. Nef binds to CD4
and to the adaptor protein AP2 on the plasma membrane, and this complex is recruited into
clathrin-coated pits and endosomes (Figure 23b).
In contrast, Nef-induced loss of MHC 1 from the cell surface is due to a block in
trafcking of MHC 1 from the Golgi apparatus to the plasma membrane. This activity of
Nef requires its interaction with another adaptor protein, AP1. The loss of cell surface MHC
1 means that the cell cannot present viral antigens to circulating cytotoxic T lymphocytes,
thus masking the infection from the immune system.
Enhancement of virus infectivity: HIV Nef mutants make virus particles that have
reduced capacity to infect cells. This effect cannot be reversed by expression of Nef in cells
infected with Nef-minus virus. Nef may enhance infectivity by modication of virion
structure; however, no difference in the structure of virions produced in the presence or
absence of Nef has been detected. Virions produced in the absence of Nef appear to have a
reduced ability to complete proviral DNA synthesis upon infection of target cells. There has
been a suggestion that the presence of Nef might facilitate the passage of the nucleocapsid
from virions into the cytoplasm by altering the structure of the actin matrix that lines the
inner surface of the plasma membrane, where nucleocapsids are released after fusion.
Modication of cell signaling: Nef has been implicated in alterations of signaling in T
cells, resulting in general activation of the cell and promoting virus replication. However,
unlike T cells activated by antigens, T cells activated by Nef cannot effectively mount an
immune response. Activation of T cells by Nef is caused by modulation of the activity of a
number of cellular protein kinases involved in signaling pathways.
One such target is the host serine/threonine protein kinase Pak2, known to be involved
in stimulation of cell growth and inhibition of apoptosis. Nef also prevents apoptosis of the
infected cell by inhibition of Ask-1, a kinase that links death receptors with cellular
caspases involved in initiating apoptosis. By stimulating PI-3 kinase, Nef also inactivates
Bad, a pro-apoptotic factor. Expression of FasL on the surface of the infected cell is also
increased by Nef, inducing apoptosis of surrounding uninfected CD8-positive and CD4-
positive T cells by interaction between FasL and Fas. In so doing, Nef acts to kill cells that
could otherwise help to clear the infection, prolonging the lifetime of the infected cell and
maximizing production of new virus.
Nef also interacts via its proline-rich domain with members of the Src family of
tyrosine protein kinases and alters their activity. Activation of the kinase Hck results in
increased expression of interleukin-6, tumor necrosis factor-, and interleukin-1, all
activators of HIV-1replication. This also results in increased release of chemokines from
infected cells, recruiting uninfected T cells to the sites of virus infection and activating
them, thus making them susceptible to productive infection by HIV-1.
At present, it is unclear which of the multiple activities of Nef are directly involved in
pathogenesis in infected animals. However, the demonstration that point mutations within
Nef can result in selective inactivation of particular functions provides a means of
separating the contributions of the various activities to the disease process. The initial
failure to detect pathogenesis with HIV-1 lacking Nef resulted in the proposal such a virus
could be used as an attenuated virus vaccine. Initial studies yielded promising results in
adult monkeys; vaccinated animals displayed resistance to subsequent challenge with wild-

type virus. However, infection of young animals with virus lacking Nef induced disease,
and adults experienced complications over a prolonged period of time.
Figure 23 Down-regulation of CD4 expression

VI. TREATMENT AND PREVENTION OF AIDS
VI.1 Treatment
VI.1.a. Chemotherapy
Five classes of antiretrovirals are currently available in clinical practice (Table 6),
targeting virus entry, reverse transcription, integration and protein cleavage.

Table 6 Classes of antiretrovirals

Class Mode(s) of Act Examples Drawbacks
Nucleoside analog Inhibit viral reverse - Zidovudine or Able to inhibit cellular

reverse-transcriptase transcription by competing azidothymidine DNA polymerase
inhibitors (NRTIs) with natural nucleotides for (AZT) responsible for synthesis of
the viral RT. - Lamivudine (3TC) mitochondrial DNA,
leading to adverse side-
effects (as lactic acidosis,
neuropathy, pancreatitis)
Non-nucleoside RT Bind tightly to viral RT Nevirapine (NVP), - Side-effects of the drugs
inhibitors (NNRTIs) close to the polymerase efavirenz (EFV) such as insomnia, vivid
active site, and cause dreams, and rash
allosteric inhibition - Ineffective against HIV-2
and mutants with high-level
resistance to the drugs
Protease Inhibitors Act as competitive inhibitors Ritonavir Frequent and severe side-
(PIs) of the protease, and prevent effects (hyperlipidaemia,
the cleavage of Gag/Pol insulin resistance, and
protein, thereby preventing lipodystrophy)
maturation into a fully
infectious viral particle
Entry inhibitors Inhibit fusion between the - Fusion inhibitors: - Production costs are high
membranes of HIV-1 virion enfuvirtide (ENF) - Vulnerable to loss of
and host cell by binding to - CCR5 inhibitors: activity through the rapid
gp41 and inhibiting the maraviroc, emergence of resistance
conformational change. vicriviroc
Intergrase inhibitors Inhibit strand transfer RAL Exhibit a low barrier to the
emergence of resistance
and viruses with mutation
at intergrase gene
Because each class of drug only targets one step of HIV replication and each has its
own disadvantages, current therapy requires the simultaneous use of multiple drugs to
generate a higher barrier for the virus to overcome. The most effective combination involves
three drugs: two NRTIs (usually two nucleoside analogs, such as AZT and 3TC) and a PI
(Highly active antiretroviral therapy HAART)

It is now possible to quantify effects of drug treatment by assaying the amount of viral
genome in the plasma of the patient. Drug combinations can reduce the load to undetectable
levels and therefore, there is some optimism that HIV may be held in check by such
complex drug treatments. Although it is still too early to tell whether eradication can be
achieved, many AIDS patients have benefited from the effects of these new combinations of
drugs and can even return to work.
VI.1.b. Immunotherapy
A safe, efficacious vaccine that prevented HIV infection would provide the most
important means of limiting the AIDS pandemic. Many approaches to developing vaccines
have been attempted, but unfortunately, there is no imminent prospect of developing a
prophylactic vaccine, because HIV may repair its fitness, and recombine with incoming
viruses. In the absence of such vaccine, effort has been turned towards immunotherapy.
Although immunotherapy for chronic, persistent infections is more problematic, the
treatment of rhesus macaques indicates that monoclonal antibodies show much promise in
clearing infection with a hybrid form of the simian immunodeficiency virus (SIV) that bears
the envelope antigens of HIV-1 and SIV (SHIV). For patients whom antiretroviral treatment
has failed, a combination of conventional drugs and immunotherapy may be better than
either alone. One of the problems with antibody therapy is the need for repeated injections
of the monoclonal antibody in order to maintain levels sufficient to control the virus. An
alternative is to deliver the genes encoding the heavy and light chains of the monoclonal
antibody so that the patient can generate it internally.
Nonetheless, experimental protection of macaques against challenge by the same virus
strain as the immunogen has been achieved. For example, passive transfer of neutralizing
antibody in sufficient concentration can block infection if administered at the time of
challenge. SHIV may be useful in testing future envelope-based vaccine candidates. Much
effort will continue to be placed on vaccine discovery and development.
VI.1.c. RNA Interference
The trigger of RNA interference (RNAi) in response to the double stranded RNA has
become a genetic tool in the gene function studies as well as the development of
therapeutics for various diseases. The control of the gene function helps in the regulation of
the different developmental stages in the life cycle of an organism as well as in the
progression of the various stages of a particular disease. The first target of the RNAi was
HIV infection may be due to extensive research in this area leading to accumulation of
knowledge regarding the life cycle of the virus.
Several HIV-encoded RNAs both early and late have been targeted by the expressed
shRNAs (short hairpin RNAs) and the small interfering RNA (siRNAs) prepared
synthetically. In certain cases, RNAi has been illustrated in the prevention of HIV infection
in cells. However, in cases where the cells are infected by the HIV retrovirus, the RNAi
mechanism proceeds via the following steps (Figure 24):
1. Artificially synthesized siRNA specific to the HIV mRNA in a particular stage of the
virus life cycle are introduced into the cell by injection or through lentivirus vectors.
2. These siRNAs insert into the RNA-Induced Silencing complex (RISC) whereby only
a single strand of siRNA remains that binds to the specific HIV mRNA and cleaves
it. RNases within the cell then remove these fragments.
Thus, the siRNAs help in the neutralization of the HIV mRNAs thereby reducing the
chance of synthesis of HIV proteins and preventing the progression of the infection.
Figure 24 A model for the mechanism of RNA interference

Although the inhibition of HIV-encoded RNAs by RNAi has been made possible, the
direct targeting of the HIV virus faces numerous challenges for clinical application due to
an increased rate of mutation in the virus enabling some mutants to escape from being
targeted. Hence, complementary approach of targeting on cellular transcripts that encode for
functions has been carried out. For instance, the down-regulation of the various cofactors
present within the cell by RNAi necessary for the progress of HIV infection was studied.
Down-regulation of various cellular cofactors such as the HIV receptor CD4, NFB,
and the co-receptors CCR5 and CXCR4 have proved successful in the inhibition of viral
replication as well as its cell entry. However, the CXCR4 receptor was found to be essential
for the hematopoietic stem cell formation in the bone marrow as well as subsequent T cell
differentiation and the CD4 was also found to be an essential cellular receptor. Targeting
only the CCR5 co-receptor may also present problems, since HIV-1 switches to CXCR4
tropism during the course of AIDS, creating a more virulent infection. Therefore, viral
targets became essential for the successful study of RNAi based therapy for HIV. The
mixture of shRNAs with several antiviral genes has become a potent alternative anti-HIV
approach, which is becoming an active area of research.
The introduction of the siRNAs has posed great challenge as the vectors used for the
delivery initiated immunological reactions within the body. It was overcome partly by an
approach involving the isolation of the T-cells of patients, its transduction with lentiviral
vector carrying the anti-HIV antisense RNAs and expansion, followed by re-infusion into
the patients blood stream. Another significant progress in this area is the use of the
hematopoietic progenitor stem cells, which are isolated, transduced with the vector carrying
the therapeutic genes, followed by reinfusion.
Although similar to siRNA, miRNAs are derived from endogenous RNAs that contain
stem-loop structures. Some miRNAs function to regulate developmental timing, signal
transduction, apoptosis, cell proliferation and tumorigenesis. Experiments to investigate the
ability of miRNA inhibiting the infection of HIV have been carried out and obtained some
different results. A cellular miRNA (miR-32) was recently identified to inhibit infection by
the primate foamy virus type 1 (PFV-1) and this finding provides the first evidence that
cells may use miRNA as an anti-viral defense. However, in a different, the human miRNA,
miR-122 is specifically expressed in liver cells and was found to be required for efficient
Hepatitis C virus (HCV) replication in hepatocytes. These contrary results emerged
questions that: Are there some cellular miRNAs that target HIV or other cellular miRNAs
contribute to facilitated replication of pathogens?
In this way, it can be noted that compared to the ribozymes or the antisense
approaches, the RNAi based therapy is more potent. The pre-clinical study of this approach

on the human trials in near future will mark a revolution in the therapeutics for the HIV
based infection.
VI.2 Prevention
VI.2.a. Mother-to-Child Transmission
There is a linear correlation between maternal viral load and risk of transmission.
Treatment of the mother, who has a low viral load, with AZT during the last trimester of
pregnancy and the infant for the first six weeks of life reduces 6070% in vertical
transmission. HAART is not only recommended in pregnant women who require treatment
for their own health, have a high viral load (>10,000 copies ml-1) or have drug resistance,
but should also be given to infants born to untreated mothers. Exclusive formula-feeding is
also recommended to all HIV-positive mothers. With these combined strategies, vertical
transmission of HIV can be reduced to negligible levels.
VI.2.b. Sexually Transmitted Infections

Sexually transmitted infections are a risk factor for acquisition of HIV. In addition,
local genital tract inflammation increases HIV infecting. It follows that control of sexually
transmitted infections may be an important and cost-effective method for reducing
transmission of HIV. Therefore, safe sex messages remain the cornerstone of any
prevention campaign.
VI.2.c. Microbicides
Topical administration of microbicides to vagina and/or rectum has been proposed as
appropriate for women in particular, who otherwise may not be able to convince sexual
partners to adopt safer sex practices. Compounds in development include polyanions, such
as cellulose sulfate and PRO-2000, and non-ionic surfactants such as nonoxynol-9. These
are thought to act by disrupting the viruscell interaction. However, progress in the field
was slowed, since recent research indicated that microbicides may cause inflammatory
effect on genital epithelium, alterations to epithelial permeability and/or alterations to
natural genital microbial flora. Nevertheless, further work is being undertaken, including the
topical use of antiretroviral drugs, within the microbicides programme.

VI.2.d. Post-exposure Prophylaxis (PEP)

Post-exposure prophylaxis (PEP) was initially addressed in the context of occupational
exposure to HIV-1, such as needle stick injuries. Epidemiological studies have indicated
that the average risk for HIV transmission after percutaneous exposure to HIV-infected
blood in healthcare settings is about 3 per 1000 injuries. After a mucocutaneous exposure,
the average risk is estimated at less than 1 in 1000. It has been considered that there is no
risk of HIV transmission where intact skin is exposed to HIV-infected blood. More recently,
attention has turned to post-exposure prophylaxis following sexual exposure (PEPSE),
where the risk of acquisition is increased in the passive partner in anal intercourse. The
administration of ZDV prophylaxis to healthcare workers occupationally exposed to HIV
was associated with an 81% reduction in the risk for occupationally acquired HIV infection.
Four factors were associated with increased risk of occupationally acquired HIV infection:
(i) deep injury, (ii) visible blood on the needle, (iii) injury with a needle which had been
placed in a source patients artery or vein and (iv) terminal HIV-related illness in the source
patient (now explained through a high viral load). SIV/macaque animal models
demonstrated a protective effect of TDF when administered within 72 hours of inoculation,
and such protection was enhanced by treatment for more than 10 days. Antenatal treatment
of the pregnant woman with ZDV was omitted (through choice or limited clinical care),
neonatal ZDV started within 48 hours of birth was associated with an HIV transmission rate
of 9.3%, compared with a rate of 18.4% when ZDV was started at a later time. Current
guidance suggests truvada (TDF and FTC) and kaletra (LPV/r) as the PEP of choice, to be
taken over four weeks.
VI.2.e. Pre-exposure Prophylaxis (PREP)
There is increasing interest in the use of antiretroviral drugs with low toxicity prior to
possible exposure. Such an approach is relevant for, for example, sex workers. Trials of
TDF, with or without FTC, are ongoing. Concerns with this approach include the risk of
resistance in cases where the recipient is already HIV infected, or indeed, rapid
development of resistance in cases of transmission, and also the potential increase in risky
behavior consequent on the reassurance given by use of this approach.

Remained problems in treatment of HIV/AIDS

Successful long-term treatment of HIV-1 infection remains an unrealized goal for
many reasons.
The first reason is due in part to the high degree of variation in the virus, both within
one individual and within a population, because of errors generated during reverse
transcription. Reverse transcriptases do not have highly efficient proofreading mechanisms,
resulting in about 1 10 mutations per one proviral DNA molecule, and thus render HIV-1
a difficult target for both the immunotherapy and drug treatment strategies. Besides, the
rapid emergence of drug-resistant strains, which currently represent approximately 10% of
new infections in develop countries, has complicated HIV treatment.
Another difficulty is the ability of HIV-1 to direct the transport of proviral DNA into
the cell nucleus, which presents a problem for the immune system. To generate an immune
response, T cells are activated by the presence of antigen fragments during contact with
dendritic cells. However, dendritic cells collect HIV-1 virions on their surface.
Consequently, T cells that would support an immune response against HIV-1 are exposed to
virus while interacting with dendritic cells, facilitating entry of proviral DNA into the
nucleus, and eventually lead to infection and death of the T cells.
The third problem is that chemotherapy, although it appears promising for treating
HIV-1 infections, will be of little use in the developing countries, where the majority of
AIDS cases exist. In fact, the kinds of HIV-1 drug therapies are both too complex and too
expensive for use where the need is the greatest. Besides, part of the difficulty is also
associated with an attempt to develop inhibitors that are both potent and safe. This means a
sufficient dosage of inhibitors is needed for efficient reduction of HIV-1 viral load but it can
bring about toxicity and some severe side-effects to patients.
Latent infection complicates the elimination of HIV-1. About 1% of infected cells
remained latent, which viral RNA is not expressed, after HIV-1 proviral DNA integrates
into the host cell genome. They represent a substantial obstacle to treatment and a cure,
because they do not express viral proteins, and thus cannot be readily distinguished from
uninfected cells by the immune system. Removal of patients from chemotherapy invariably
results in reemergence of the infection, so treatment for HIV-1 must be continued for life.

CONCLUSION
The discovery of retroviruses and reverse transcriptase was phenomenal because it

proves that the flow of genetic information is not simply from DNA to RNA and to protein.
Retroviruses pack two identical copies of positive-strand RNA along with three important
common retroviral enzymes: reverse transcriptase, intergrase, and protease in a 100 nm
spherical enveloped virion. Its life cycle can be conveniently divided into two phases: The
early phase comprising of entry of virus into the host cell, reverse transcription to make the
proviral DNA, and integration of proviral DNA to the host genome; and the late phase
consisting of all steps for the synthesis of viral proteins and eventually the assembly of
virions.
HIV-1, which belongs to the sub-family lentiviruses, is a characteristic member of

retroviruses. HIV-1 has caused major global pandemic, termed acquired immunodeficiency
syndrome (AIDS) that affects males and females equally. In response to health crisis,
considerable resources have been committed to understanding HIV-1biology and pathology,
rendering it perhaps the most intensively studied disease agent of our time. HIV-1 possesses
6 additional proteins, rendering it some special features that benefit their replication in the
host cell. The poor efficiency of reverse transcriptase cause a high degree of mutation in the
virus, which is the most challenging obstacle that the scientists has yet to overcome in an
attempt to develop an efficacious vaccine or drug to completely eradicate HIV.

REFERENCES
Acheson, Nicholas H. Fundamentals of Molecular Virology. 2nd. Wiley, 2011.
Carter, John, and Venetia Saunders. Virology: Principles and Applications. Wiley,
2007.
Coffin, John M, Stephen H Hughes, and Harold E Varmus. Retroviruses. Cold

Spring Harbor Laboratory Press, 1997.
Rossi, John J. "RNAi as a treatment for HIV-1 infection." BioTechniques 40, no. 4
(2006): 25-29.
UNAIDS World AIDS Day Report 2011. Joint United Nations Programme on
HIV/AIDS (UNAIDS), 2011.
Yeung, Man Lung, Yamina Bennasser, Shu Yun Le, and Kuan Teh Jeang. "siRNA,
miRNA and HIV: promises and challenges." Cell Research 15, no. 11 (2005): 935-
946.
Zuckerman, Arie J., Jangu E. Banatvala, John R. Pattison, Paul D. Griffiths, and
Barry D. Schoub. Principles and Practice of Clinical Virology. 5th. John Wiley &
Sons Ltd,, 2004.

Retroviruses and Human Immunodeficiency Virus (HIV)

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MINISTRY OF EDUCATION AND TRAINING

CAN THO UNIVERSITY

Can Tho, March, 2014

TABLE OF CONTENT ......................................................................................................... I

LIST OF FIGURES ............................................................................................................ III

LIST OF TABLES .............................................................................................................. IV

PART 1: RETROVIRUSES ..................................................................................................2

I. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES .....................2

II. METHODS TO STUDY RETROVIRUSES.................................................................3

III. RETROVIRUS VIRION .............................................................................................6

III.1. Virion structure ...........................................................................................................6

III.2. Genome structure ........................................................................................................7

III.3. Viral proteins ..............................................................................................................8

IV. RETROVIRUS LIFE CYCLE....................................................................................9

IV.1. Early phase..................................................................................................................9

IV.2. Late phase .................................................................................................................14

PART 2: HUMAN IMMUNODEFICIENCY VIRUS (HIV) ...........................................20

I. THE DISCOVERY OF HIV ........................................................................................20

II. SIGNS AND SYMPTOMS OF HIV INFECTION ....................................................21

III. AIDS TRANSMISSION AND EPIDEMIOLOGY .................................................24

III.1 Transmission .............................................................................................................24

III.2 Epidemiology ............................................................................................................25

IV. HIV VIRION ..............................................................................................................29

V. HIV REPLICATION ....................................................................................................31

V.1 Receptors of HIV-1 ..................................................................................................32

Advanced Biotechnology Class Course 37 i Institute of Biotechnology Research and Development

V.2 Special feature of HIV-1...........................................................................................33

V.3 Functions of HIV additional proteins .......................................................................34

VI. TREATMENT AND PREVENTION OF AIDS .....................................................40

VI.1 Treatment ..................................................................................................................40

VI.2 Prevention .................................................................................................................45

Advanced Biotechnology Class Course 37 ii Institute of Biotechnology Research and Development

Advanced Biotechnology Class Course 37 iv Institute of Biotechnology Research and Development

Advanced Biotechnology Course 37 1 Institute of Biotechnology Research and Development

I. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES

Figure 2 (a) Howard Temin and (b) David Baltimore

Advanced Biotechnology Course 37 2 Institute of Biotechnology Research and Development

Alpharetrovirus Rous sarcoma virus Chickens

Betaretovirus Mouse mammary virus Mice

Gammaretrovirus Murine leukemia virus Mice

Deltaretrovirus Human T-cell leukemia virus type 1 Humans

Epsilonretrovirus Walleye dermal sarcoma virus Fish

Lentivirus Human immunodeficiency virus type 1 Humans

Simian immunodeficiency virus Monkeys

Feline immunodeficiency virus Cats

Spumavirus Simian foamy virus Monkeys

II. METHODS TO STUDY RETROVIRUSES

Many previous researches about retroviruses have utilized methods applied

Advanced Biotechnology Course 37 3 Institute of Biotechnology Research and Development

Advanced Biotechnology Course 37 4 Institute of Biotechnology Research and Development

Advanced Biotechnology Course 37 5 Institute of Biotechnology Research and Development

Figure 3 Cryo-EM micrographs of immature and mature HIV-1 particles

III. RETROVIRUS VIRION

III.1. Virion structure

Advanced Biotechnology Course 37 6 Institute of Biotechnology Research and Development

Figure 4 A typical retrovirus virion

The virus genome (Figure 5) is a positive-strand RNA 7 to 10 kb long, complexed

Advanced Biotechnology Course 37 7 Institute of Biotechnology Research and Development

Figure 5 Structure of retrovirus RNA

III.3. Viral proteins

Advanced Biotechnology Course 37 8 Institute of Biotechnology Research and Development

IV. RETROVIRUS LIFE CYCLE

IV.1. Early phase

Figure 6 Early phase of retrovirus life cycle