Retroviruses and Human Immunodeficiency Virus (HIV) (Final Version)

MINISTRY OF EDUCATION AND TRAINING CAN THO UNIVERSITY INSTITUTE OF BIOTECHNOLOGY RESEARCH AND DEVELOPMENT
VIROLOGY REPORT
RETROVIRUSES AND HUMAN IMMUNODEFICIENCY VIRUS (HIV)

LECTURER BI TH MINH DIU STUDENTS 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
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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

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V.2 V.3 VI.
Special feature of HIV-1...........................................................................................33 Functions of HIV additional proteins .......................................................................34 TREATMENT AND PREVENTION OF AIDS .....................................................40
VI.1 Treatment ..................................................................................................................40 VI.2 Prevention .................................................................................................................45 CONCLUSION .....................................................................................................................48 REFERENCES .....................................................................................................................49
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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
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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
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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.
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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 Figure 1 Peyton Rous
independently in the laboratories of in 1971 demonstrated
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
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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 Alpharetrovirus Betaretovirus Gammaretrovirus Deltaretrovirus Epsilonretrovirus Lentivirus Examples of virus Rous sarcoma virus Mouse mammary virus Murine leukemia virus Human T-cell leukemia virus type 1 Walleye dermal sarcoma virus Human immunodeficiency virus type 1 Simian immunodeficiency virus Feline immunodeficiency virus Spumavirus Simian foamy virus Host Chickens Mice Mice Humans Fish Humans Monkeys Cats 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
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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
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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 thinsectioning 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 HIVlike 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
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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
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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-tohead 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
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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 membraneanchored trans-membrane component (TM). Thus the env protein is what enables the retrovirus to be infectious.
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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
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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 strongstop 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).
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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 plusstrand 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 minusstrand 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.
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Figure 7 Reverse transcription

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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 viral DNA.
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Figure 8 Integration of proviral DNA into host cell

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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.
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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 All one mRNA
molecule.
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.
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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 translation termination generation of the Gag/Pol polyprotein. The 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
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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
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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 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 13 Two assembly pathways in retroviruses
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Figure 14 Retrovirus life cycle
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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.
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(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 Feline immunodeficiency virus Equine infectious anemia virus Caprine arthritis-encephalitis virus Visna-maedi virus Apes and old world monkeys Cats Horses Goats 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.
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(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
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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
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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 WestCentral 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
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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 HIV infection (adults and children) 31.6 million 35.2 million 21.6 million 24.1 million 3.6 million 4.5 million 1.3 million 1.7 million 1.2 million 1.7 million 1.0 million 1.9 million 580,000 1.1 million 770,000 930,000 adult child Adult and prevalence deaths (%)
during 2010 Worldwide Sub-Saharan Africa South and South-East Asia Eastern Europe & Central Asia Latin America North America East Asia Western & Central Europe 1.6 -1.9 million 1.2 million 250,000 90,000 67,000 20,000 56,000 9,900 0.8 5.0 0.3 0.9 0.4 0.6 0.1 0.2
Source: UNAIDS World Aids Day Report

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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 Figure 17 Map of HIV prevalence in Africa in 2007
Source: UNAIDS
Africa
is
the
hardest hit region, with adult 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,
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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
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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
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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 Figure 18 Diagram of an HIV-1 virion
For clarity, only one of the two RNA molecules is shown covered by NC proteins
microscopy are at the upper end of this range or greater. Generally, there is one capsid per virion, though virions with two 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).
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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
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Table 4 HIV-1 structural proteins

Alternative name Name Matrix Capsid Nucleocapsid Protease Reverse transcriptase Integrase Surface protein Virion protein R Abbreviation MA CA NC PR RT IN SU Vpr (M. Wt. in KDa) p17 p24 p7 p14 p66/p51 p32 gp120 p15
Table 5 HIV-1 non-structural proteins

Alternative name Name Viral infectivity factor Virion protein unique for HIV-1 Transactivator for transcription Regulator of expression of virion protein Negative effector Abbreviation Vif Vpu Tat Rev Nef (M. Wt. in KDa) p23 p16 p15 p19 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.
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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 and helper T
lymphocytes
macrophages.
Thus HIV-1 attacks at the very heart of the immune system, as both CD4positive 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 CXCR4) for to CCR5; block SDF-1 virus for entry
demonstrates their signicant role in the infection process. Viruses using CXCR4 are
Figure 20 Model of HIV-1 entry
designated X4 (or T cell-tropic) 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
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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.
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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

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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 2kb 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
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(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.
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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
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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
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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 CD4positive 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-
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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.
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Table 6 Classes of antiretrovirals

Class Nucleoside analog reverse-transcriptase inhibitors (NRTIs) Mode(s) of Act Inhibit viral reverse transcription by competing with natural nucleotides for the viral RT. Examples - Zidovudine or azidothymidine (AZT) - Lamivudine (3TC) Drawbacks Able to inhibit cellular DNA polymerase responsible for synthesis of mitochondrial DNA, leading to adverse sideeffects (as lactic acidosis, neuropathy, pancreatitis) Non-nucleoside RT inhibitors (NNRTIs) Bind tightly to viral RT close to the polymerase active site, and cause allosteric inhibition Nevirapine (NVP), efavirenz (EFV) - Side-effects of the drugs such as insomnia, vivid dreams, and rash - Ineffective against HIV-2 and mutants with high-level resistance to the drugs Protease Inhibitors (PIs) Act as competitive inhibitors of the protease, and prevent the cleavage of Gag/Pol protein, thereby preventing maturation into a fully infectious viral particle Entry inhibitors Inhibit fusion between the membranes of HIV-1 virion and host cell by binding to gp41 and inhibiting the conformational change. Intergrase inhibitors Inhibit strand transfer - Fusion inhibitors: enfuvirtide (ENF) - CCR5 inhibitors: maraviroc, vicriviroc RAL Exhibit a low barrier to the emergence of resistance and viruses with mutation at intergrase gene - Production costs are high - Vulnerable to loss of activity through the rapid emergence of resistance Ritonavir Frequent and severe sideeffects (hyperlipidaemia, insulin resistance, and lipodystrophy)
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)
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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
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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
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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
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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.
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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.
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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.
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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.
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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): 935946. 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.
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Retroviruses and Human Immunodeficiency Virus (HIV) (Final Version)

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MINISTRY OF EDUCATION AND TRAINING CAN THO UNIVERSITY INSTITUTE OF BIOTECHNOLOGY RESEARCH AND DEVELOPMENT

RETROVIRUSES AND HUMAN IMMUNODEFICIENCY VIRUS (HIV)

Can Tho, March, 2014

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II. METHODS TO STUDY RETROVIRUSES .................................................................3 III. RETROVIRUS VIRION .............................................................................................6

V. HIV REPLICATION ....................................................................................................31 V.1 Receptors of HIV-1...................................................................................................32

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V.2 V.3 VI.

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independently in the laboratories of in 1971 demonstrated

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

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Figure 4 A typical retrovirus virion III.2. Genome structure

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Figure 5 Structure of retrovirus RNA

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RETROVIRUS LIFE CYCLE

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Figure 7 Reverse transcription

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Figure 8 Integration of proviral DNA into host cell

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Figure 11 Ribosomal frameshifting

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