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

VIROLOGY REPORT

RETROVIRUSES AND HUMAN IMMUNODEFICIENCY VIRUS (HIV)
LECTURER BÙI THỊ MINH DIỆU STUDENTS TRẦN HOÀNG ĐỆ (3112449) LÂM TẤN HÀO (3112459) HUỲNH LÊ BẢO NGỌC (3118301) TRẦN HẠNH PHƯỚC (3118059) HOÀNG NGUYỄN PHƯƠNG TRINH (3112563) LÝ HOÀNG TUẤN (3112573) CLASS ADVANCED BIOTECHNOLOGY COURSE 37

Can Tho, March, 2014

Virology Report

Can Tho University

TABLE OF CONTENT
TABLE OF CONTENT ......................................................................................................... I LIST OF FIGURES ............................................................................................................ III LIST OF TABLES .............................................................................................................. IV INTRODUCTION ..................................................................................................................1 PART 1: RETROVIRUSES ..................................................................................................2 I. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES .....................2

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

III.1. Virion structure ...........................................................................................................6 III.2. Genome structure ........................................................................................................7 III.3. Viral proteins ..............................................................................................................8 IV. RETROVIRUS LIFE CYCLE ....................................................................................9

IV.1. Early phase..................................................................................................................9 IV.2. Late phase .................................................................................................................14 PART 2: HUMAN IMMUNODEFICIENCY VIRUS (HIV) ...........................................20 I. THE DISCOVERY OF HIV ........................................................................................20

II. SIGNS AND SYMPTOMS OF HIV INFECTION ....................................................21 III. AIDS TRANSMISSION AND EPIDEMIOLOGY .................................................24

III.1 Transmission .............................................................................................................24 III.2 Epidemiology............................................................................................................25 IV. HIV VIRION ..............................................................................................................29

V. HIV REPLICATION ....................................................................................................31 V.1 Receptors of HIV-1...................................................................................................32
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Institute of Biotechnology Research and Development

Advanced Biotechnology Class Course 37

Virology Report

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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

Advanced Biotechnology Class Course 37

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Institute of Biotechnology Research and Development

Virology Report

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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) Barré-Sinoussi, and (c) Robert Gallo .............................21 Figure 16 Events associated with progression to AIDS .........................................................22 Figure 17 Map of HIV prevalence in Africa in 2007 .............................................................26 Figure 18 Diagram of an HIV-1 virion ..................................................................................29 Figure 19 Genome structure and RNA splicing pattern of HIV-1 .........................................30 Figure 20 Model of HIV-1 entry ............................................................................................32 Figure 21 Mechanism of Tat function ....................................................................................34 Figure 22 Mechanism of Rev function...................................................................................35 Figure 23 Down-regulation of CD4 expression .....................................................................40 Figure 24 A model for the mechanism of RNA inteference ..................................................43

Advanced Biotechnology Class Course 37

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Institute of Biotechnology Research and Development

Virology Report

Can Tho University

LIST OF TABLES
Table 1 Retrovirus genera ........................................................................................................3 Table 2 Lentiviruses ...............................................................................................................21 Table 3 Prevalence rate of HIV/AIDS infection in 2010 .......................................................25 Table 4 HIV-1 structural proteins ..........................................................................................31 Table 5 HIV-1 non-structural proteins ...................................................................................31 Table 6 Classes of antiretrovirals ...........................................................................................41

Advanced Biotechnology Class Course 37

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Institute of Biotechnology Research and Development

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

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. were discovered.Virology Report Can Tho University PART 1: RETROVIRUSES I. avian sarcoma virus. which overturned a central dogma of molecular biology – genetic information flows in one direction only. induced tumors in muscle. (a) (b) Figure 2 (a) Howard Temin and (b) David Baltimore Advanced Biotechnology Course 37 2 Institute of Biotechnology Research and Development . Howard Temin (Figure 2a) and David Baltimore (Figure 2b) both received Nobel Prizes for their spectacular discovery of this enzyme. but it was not until the 1930s that other retroviruses. bone. This agent. causing tumors in mice and other mammals. working at the Rockefeller Institute for Medical Research in New York. THE DISCOVERY AND CLASSIFICATION OF RETROVIRUSES The first discovery of a retrovirus was made as long ago as 1910 by Peyton Rous (Figure 1). and other tissues of chickens. from DNA → RNA → protein. He received the Nobel Prize for this discovery.

such as many retroviruses. The virus is first collected by centrifugation of the Advanced Biotechnology Course 37 3 Institute of Biotechnology Research and Development . METHODS TO STUDY RETROVIRUSES Many previous researches about retroviruses have utilized methods applied extensively in virology. Because the particles are scattered into the extracellular medium. wasting disease. by electron microscopy. based on differences in morphology and genome organization. Retroviral particles are usually purified on the basis of their size and density. A previous but related classification was based on the pathology associated with infection: oncoviruses (many viruses in the Alpha. For viruses which useful crystals have not been obtained for.to Epsilonretrovirus genera) are tumor-inducing viruses. 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.Virology Report Can Tho University Classification Retroviruses are presently grouped into seven genera (Table 1). structural information was gained largely by fractionation of the components of purified viruses. lentiviruses induce slowly progressing. and indirectly by genetic analysis. these techniques remain the basis upon which implications about structure are built. Until the successful crystallization and X-ray diffraction on spherical viruses in the last decade. purification is simple and efficient if disruption of cells can be avoided.

the ratio of physical to infectious particles is 100:1 or greater. usually by centrifugation in a gradient of sucrose.Virology Report Can Tho University growth medium. in most biochemical or cell biological studies. Higher levels of purification can be achieved by selecting not only for particle density. but also for particle size. The technique of negative staining shows the perimeter and sometimes the center of the virion outlined by the surrounding accumulation of heavy metal. These facts have obviously important implications for those retroviruses that cause animal or human diseases. viral particles sediment at about 600S. Particle size for viruses typically is measured either by electron microscopy or by rate zonal sedimentation.16 g/ml. and the final appearance of the particles depends on the plane of sectioning. In rate zonal sedimentation. virus is simply adsorbed to a coated grid and then exposed briefly to the solution of heavy metal before viewing. Thin-section techniques require harsh fixation. For structures that can be penetrated Advanced Biotechnology Course 37 4 Institute of Biotechnology Research and Development . Typically for retroviruses. The resulting pellet is redissolved and the particles are sedimented to equilibrium. one of the major criteria for classification of viruses. corresponding to about 35% w/w sucrose. Not all of the virions in a preparation are infectious. retroviral particles measure about 80–120 nm in diameter. Infectious particles are rapidly inactivated by standard disinfecting treatments like detergents. with a doubling in size resulting. In addition. Sedimentation is rather inaccurate. by rate zonal sedimentation. many of the early biochemical studies of retroviral structural proteins and of reverse transcriptase were carried out with this member of the ASLV genus. The most concentrated and clean source of a retrovirus is from the plasma of chicks infected with avian myeloblastosis virus (AMV). Thus. which can contain as much as several milligrams of virus per milliliter of plasma (1 mg is about 1012 virions). the measurements in fact reflect the properties of the inactive particles. it is uncertain if size differs among the retroviral genera or being affected by other factors. Negative staining can cause deformations in particles. The density of retroviruses is approximately 1. Since very few studies have compared different viruses in the same experiment. Electron microscopy is also applied to define morphology. for example. since these are the predominant population. For this reason. In this rapid procedure. Interpretations that do not take cognizance of the vast excess of inactive virions may be flawed. several assumptions must be made to allow calculation of the size of a particle from its sedimentation rate. but neither method is very accurate. In thin-section electron microscopy.

if the virus has detectable symmetry. for example. but the lipid membrane of enveloped viruses typically is not penetrated by the stain. with no obvious symmetrical features. 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. typically are densely studded with glycoproteins. Cryoelectron microscopy (cryo-EM) obviates the problems of electron microscopic thin-section techniques. but it requires fixation of virus or cells by a crosslinking reagent. spumaviruses. Also. cryo-EM pictures of immature particles do not reveal clear icosahedral symmetry of HIV. and embedding into plastic before sectioning and viewing. they may be unstable Advanced Biotechnology Course 37 5 Institute of Biotechnology Research and Development . the thinsectioning technique provides more information. and these viral preparations also contain little envelope. suggesting that if such symmetry features exist. 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.Virology Report Can Tho University by the heavy metal. even freshly isolated viruses show few projections. Mature particles of MLV simply show a spherical core. since the virus is observed directly as an unstained particle in a thin sheet of noncrystalline ice at the temperature of liquid nitrogen. 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). computer-assisted averaging can be used to construct a three-dimensional image of the virus. including the alphaviruses. immature cores are quite stable to weak detergents. in some cases. can serve as models for retroviruses. and thus can be isolated readily and studied by negative-staining techniques. Although such images have low contrast. dehydration. However. Immature particles show a spoke-like structure inside the envelope for both HIV and MLV. In contrast to mature cores. staining. Negative-stain electron microscopy of immature. as simple enveloped RNA viruses. In contrast. from mutant viruses with a defective protease. negative staining usually allows excellent visualization of structural details. some retroviruses. Detailed high-resolution reconstructions have been published for numerous spherical viruses. Both negative staining and thin-section techniques show various projections from the viral envelope. which comprise the viral envelope glycoproteins. For many purposes. which. for example. limiting the usefulness of this technique for retroviruses.

(a) (b) Figure 3 Cryo-EM micrographs of immature and mature HIV-1 particles To sum up.1. bound by non-covalent interactions Advanced Biotechnology Course 37 6 Institute of Biotechnology Research and Development . for instance. but all are based to some extent on conjecture and analogy with other viruses. a more complete understanding of the molecular structure of retroviral particles thus may have to wait for the development of new techniques. some highly detailed.Virology Report Can Tho University after virion formation. as well as other aspects of their structure and function. III. computer programs to help interpret the cryo-EM images of nonicosahedral viruses. and hence models are necessary to represent the structure of the virion. an alternative model for the structure of immature retroviral particles postulates a helical symmetry. RETROVIRUS VIRION III. One of the earliest and perhaps most influential. The most useful models represent in a pictorial form what is known about the relative positions of components of the particle. The envelope contains the external surface protein (SU). Numerous models for virions have been published. the exact arrangement of the components of the retroviral particle remains uncertain. Modern versions of this model (Figure 18) incorporate newer information about structural proteins. The drawing is for HIV-1. Thus. Besides. but it can apply to other retroviruses as well with some minor modifications. presented in 1978 presaged much of what was learned later from biochemical studies about the internal organization of the virion. Virion structure Retroviruses are roughly spherical and approximately 100 nm in diameter (Figure 4). Predictions may also be incorporated into models if appropriate.

which traverses the lipid bilayer. Adjacent to the repeated sequences at either end are unique regions designated U5 (80–200 nt) and U3 (240–1200 nt).Virology Report Can Tho University to the transmembrane protein (TM). for example. Within the virion.to 200-nt (nucleotide) repeated sequence (R) is present at both the 5 and 3 ends of the genome RNA. held together in a head-tohead configuration by interaction of sequences known as a ―kissing loop‖ located in the U5 region. Coating the inner surface of the membrane is the viral matrix protein (MA). Genome structure The virus genome (Figure 5) is a positive-strand RNA 7 to 10 kb long. and CA is p24. depending on the virus strain. an integrase (IN). A specific cellular transfer RNA is bound to the genome RNA by base pairing Advanced Biotechnology Course 37 7 Institute of Biotechnology Research and Development . TM is gp41. as are eukaryotic mRNAs. complexed with the nucleocapsid protein (NC). Figure 4 A typical retrovirus virion III. Unlike most other viruses. Genome RNAs are capped at their 5 termini and polyadenylated at their 3 termini. the HIV-1 SU protein is called gp120 (glycoprotein with molecular weight of 120). Three virus-coded enzymes – a protease (PR). retroviruses package two identical copies of the genome in each virion. and a reverse transcriptase (RT) – are associated with the virus core.2. The capsid protein (CA) forms an icosahedral or conical core. The viral structural proteins are often identified by their glycosylation status and their molecular weights. the two RNAs exist as a dimer. A 150.

repeat region (R). It functions in proteolytic cleavages of gag and pol proteins during virion maturation to produce mature and functional forms. pol. The env gene serves three distinct functions: enabling the retrovirus to enter and exit host cells through endosomal membrane trafficking.Virology Report Can Tho University between the primer binding sequence (PBS). pol proteins and env proteins. gag. primer binding sequence (PBS). repeat region (R). Reverse transcriptase and intergrase are responsible for synthesis of viral DNA and integration into host DNA after infection. Protease is expressed differently in different viruses. Viral proteins are generated from three genes designated gag (for ―group-specific antigen‖). 3 splice site (3 ss). untranslated 5 sequence (U5). and env reading frames for viral structural genes. features are: methylated cap. Finally. and env (for envelope proteins). which are about 2000–4000 copies per virion. Gag proteins are major components of the viral capsid. Possessing a functional copy of an env gene is what makes retroviruses distinct from retroelements. respectively. while the ability of the retrovirus to enter the cell via membrane fusion is imparted by the membraneanchored trans-membrane component (TM). polypurine tract (ppt) used during reverse transcription. untranslated 3 sequence (U3). Advanced Biotechnology Course 37 8 Institute of Biotechnology Research and Development .3. protection from the extracellular environment via the lipid bilayer. Figure 5 Structure of retrovirus RNA Beginning at the left end. 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. psi () packaging sequence. Thus the env protein is what enables the retrovirus to be infectious. and 18 nucleotides at the 3 end of the tRNA. Viral proteins Retroviral proteins consist of gag proteins. located just downstream of U5. pol (for polymerase). env proteins play a role in association and entry of virion into the host cell. poly(A) tail III. 5 splice site (5 ss). Different virus strains bind different cellular tRNAs. and the ability to enter cells.

they make a DNA copy of their RNA genome and finally insert those copies into the host cell genome.Virology Report Can Tho University IV. Early phase During the early phase (Figure 6). Next. there is a conformational shift in the SU protein that exposes the hydrophobic amino terminus of the TM protein.1. Then. Fusion is initiated by the interaction between SU and receptor on the host cell. The structure that is released into the cytoplasm loses some proteins and a reverse transcription complex is formed. IV.1. Furthermore. Thus. RETROVIRUS LIFE CYCLE The retrovirus life cycle takes place in early and late phase. the TM protein changes its conformation which allows a hydrophobic fusion sequence to fuse the virion membrane and cell membrane. viral envelope can fuse directly with the host plasma membrane. there are three main steps. Attachment and Entry Retrovirus can only attach and infect certain species and certain cell types. or Advanced Biotechnology Course 37 9 Institute of Biotechnology Research and Development .a. First. Figure 6 Early phase of retrovirus life cycle IV. the retrovirus enters the cell.

This is called the ―first strand transfer‖. resulting in a short DNA molecule that is a copy of the U5 and R regions. since the strong-stop DNA strand is transferred from the 5 end to the 3 end of the genome RNA. 2. This is called ―minus-strand strongstop DNA‖ because it is a complementary copy of part of the positive-strand genome RNA. removing the RNA template and exposing the DNA copy of the U5 and R sequences. The U3-R-U5 sequence is called a ―long terminal repeat‖ (LTR). 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. making a full-length minus-strand copy of the genome. originally at the right end of the viral RNA. and a ribonuclease H activity. Because of the strand transfer. and the U5 sequence. and DNA synthesis stops abruptly at the end of the RNA template during in vitro reactions. this DNA molecule contains a copy of the R sequence sandwiched in between the U3 sequence. Strand transfer: The DNA copy of the R sequence hybridizes with the R sequence at the 3 end of the genome RNA. originally at the left end. IV.b.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.Virology Report Can Tho University the virus undergoes receptor-mediated endocytosis and fusion is initiated by a decrease in pH within the endosome. Advanced Biotechnology Course 37 10 Institute of Biotechnology Research and Development . exists as a dimer that has two distinct activities: an RNA/DNA-dependent DNA polymerase activity. but does not degrade unhybridized RNA. 3. 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). Reverse transcription The enzyme responsible for this conversion is reverse transcriptase. Reverse transcription is a complex procedure with 9 steps that converts RNA into DNA (Figure 7): 1. 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. Ribonuclease H is an enzyme that selectively hydrolyses the RNA part of an RNA-DNA hybrid. 4. The actual geometry of how this transfer takes place within the virus core during reverse transcription is not clear.

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 is called the ―second strand transfer‖ since. an RNA sequence just to the left of U3. The ppt primer is also removed. Removal of tRNA and ppt primer: RNAse H digestion of the 3 end of the tRNA. is resistant to digestion. 7. consisting of a polypurine tract (ppt). This residual RNA serves as a primer for the subsequent synthesis of plus-strand DNA by reverse transcriptase. the plus-strand strong-stop DNA is transferred from one end of the template to the other end. double-stranded DNA with long terminal repeats at both ends. most of the genome RNA is digested by RNAse H. removes the tRNA from the minus-strand DNA copy and exposes the primer binding site on the plus-strand strong-stop DNA. The short DNA intermediate made is designated ―plusstrand strong-stop DNA‖. now part of an RNA-DNA hybrid. However. Removal of template RNA: As it is copied into DNA. 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.Virology Report Can Tho University 5. This DNA is called proviral DNA. 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. Advanced Biotechnology Course 37 11 Institute of Biotechnology Research and Development . like the first strand transfer. 8. 6. 9. This results in a linear. and remains hybridized to the newly synthesized minus-strand DNA. and on through the 18 nucleotides of the tRNA that were initially hybridized to the primer binding site on genome RNA.

Virology Report Can Tho University Figure 7 Reverse transcription Advanced Biotechnology Course 37 12 Institute of Biotechnology Research and Development .

This leaves a 4-to 6-nt single-stranded gap on the target host DNA. Exceptionally.Virology Report Can Tho University The reverse transcriptase of retroviruses lacks the 3-to-5 exonuclease activity that cellular DNA polymerases use for proofreading.c. the retroviruses can only productively infect cells that undergo mitosis. Therefore. and a 2-nt unpaired region on the viral DNA. and joins viral to cellular DNA strands. 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. which leads to the incompletely uniform of retrovirus populations as they have a lot of variants or quasispecies. Viral DNA is inserted into host DNA by cleavage and ligation reaction. For this reason. 2. Integration step has some major points (Figure 8): 1. about 1 to 10 nucleotide errors could be produced during synthesis of each proviral DNA molecule. Intergration Integrase is the viral enzyme used in this step which presents in the core of the infecting virion.1. The integrase removes the two 3 terminal nucleotides of each strand of the linear viral DNA. This enzyme binds to the two ends of linear viral DNA and brings them together and in close proximity to cellular DNA. The large size of this complex prevents its entry through the nuclear pores until the host nuclear envelope is disappeared in cell division. 13 Figure 8 Integration of proviral DNA into host cell Institute of Biotechnology Research and Development Advanced Biotechnology Course 37 . HIV-1 and other lentiviruses can transfer their DNA in all stages of host cell life through nuclear pores. The linear double-stranded viral DNA resulting from reverse transcription remains associated with components of the virus core in a preintegration complex. IV.

This generates a direct repeat of host DNA (4–6 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.2. Once integrated. Host enzymes carry out repair synthesis of the gap. Consequently. and assembly of viral virions. just like any cellular gene. Advanced Biotechnology Course 37 14 Institute of Biotechnology Research and Development . 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. Transcription begins precisely at the U3/R junction within the left LTR and proceeds through the entire genome and the right LTR. There are two identical LTRs. inactivating its ability to initiate transcription (promoter occlusion). This gives rise to full-length RNA identical to the genome RNA of the infecting virus. This makes sure transcription only begins at the left LTR. Furthermore. synthesis of viral proteins.a. The mix of transcription factor presence in turn may also be affected by external stimuli.Virology Report Can Tho University 3. Integration sites appear to be distributed randomly over the host genome. one at each end of the proviral DNA. IV. RNA polymerases can dislodge the binding of transcription factors to the right LTR. 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). IV. 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.2. 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 proviral DNA becomes part of a host cell chromosome and is replicated along with host DNA. virus infections can be transmitted from parent to offspring if an egg or sperm cell becomes infected and contains integrated proviral DNA. simultaneously removing the terminal 2 unpaired nucleotides of the viral DNA. Late phase The late phase involves expression of viral RNA.

However. NC. and a singly spliced form. 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. which are encoded in different reading frames. for HIV-1. and IN proteins. For example. protease. Advanced Biotechnology Course 37 15 Institute of Biotechnology Research and Development . the generation of these two polyproteins from a single mRNA requires 2 mechanisms of modification of the normal translation process. RT. the precursors of the MA. Synthesis of viral proteins Splicing of the primary transcript enables the virus to produce numerous viral proteins. the AAUAAA is located within the R region of other retroviruses.b. Therefore. to ensure the synthesis of Gag and Gag/Pol in a particular ratio. In some retroviruses. from which the Gag/Pol reading frames have been removed. more complex splicing patterns generate additional mRNAs. 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 intergrase are needed.2. a typical member of the lentivirus subfamily.Virology Report Can Tho University Similarly. is used for synthesis of the Env proteins (Figure 9). The unspliced RNA is used to synthesize Gag and Gag/Pol polyproteins. viral RNA can undergo multiple splicing events to generate mRNAs encoding regulatory proteins. Only a few molecules of reverse transcriptase. CA. These two mechanisms ensure that cleavage and polyadenylation take place only at that end. In another way. thay can also possess sequence elements adjacent to the polyadenylation signal near the 5' end that repress recognition of that AAUAAA. PR. but many structural protein molcules encoded by Gag are required to form a single virion. and therefore their U3 region contains additional sequences that enhance recognition of the polyadenylation signal near the 3 end of viral RNAs. IV. from only All one mRNA molecule.

where the ribosome stalls. the stalled ribosome is able to shift the reading frame back one nucleotide occasionally. resulting in the generation of the Gag/Pol protein. in which the ribosome shifts its reading frame at a precise position within the RNA prior to the termination codon. and glutamine is inserted at that site.Virology Report Can Tho University The first one is suppression of transcription termination (Figure 10). The second mechanism is ribosomal frameshifting (Figure 11). and resumes translation of the sequence. located just beyond the termination codon in the mRNA. The misreading process is stimulated by a particular secondary structure called a pseudoknot. Figure 11 Ribosomal frameshifting Advanced Biotechnology Course 37 16 Institute of Biotechnology Research and Development . 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. permitting the Figure 10 Suppression of translation termination generation of the Gag/Pol polyprotein. and a secondary structure downstream of the heptamer that induces ribosome stalling. The stop codon UAG separating the gag and pol reading frames is occasionally misread by Gln-tRNAGln as CAG about 1/20 times. 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). This allows translational readthrough. In the new reading frame. the gag termination codon is no longer recognized and the pol region is translated.

In contrast to Env. Figure 12 Retrovirus translation and post-translational modifications Advanced Biotechnology Course 37 17 Institute of Biotechnology Research and Development . The Gag and Gag/Pol proteins interact with each other to initiate assembly of the virus core. The Gag protein is targeted to the plasma membrane by the fatty acid myristate.Virology Report Can Tho University The Env protein is translocated directly into the lumen of the endoplasmic reticulum as it is being synthesized. both Gag and Gag/Pol proteins are released into the cytosol upon translation. In the course of these events. linked post-translationally to its N-terminal amino acid. the protein undergoes glycosylation and cleavage by host enzymes to generate the mature forms of SU and TM. and finally arrives at the plasma membrane. It is subsequently transported through the Golgi apparatus and the endosome compartment. The translation and post-translational modifications to generate retroviral proteins is summarized in Figure 12.

tRNA is incorporated into the core by binding to the RT and NC portions of the Gag/Pol protein. assembly of the core occurs simultaneously with budding at the plasma membrane. and IN) proteins. CA.c. It is only at this stage that virions become infectious. For ―C-type‖ viruses. to which the NC portion of Gag binds. based on the relative occurrence of the core assembly and the budding. As virions are assembled and extruded from the cell. Figure 13 Two assembly pathways in retroviruses Advanced Biotechnology Course 37 18 Institute of Biotechnology Research and Development . The protease then cleaves the Gag and Gag/Pol polyproteins into the individual structural (MA.2. acquiring an envelope. the protease is an important target of antiviral chemotherapy directed against retroviruses. Finally. downstream the 5 splice site. Certain defective endogenous retroviruses have a similar pathway except that they bud exclusively from the ER membrane to produce intracisternal A-type particles (IAPs). RT. as well as lentiviruses. the core is first assembled within the cytoplasm. Retroviral life cycle is summarized in Figure 14.Virology Report Can Tho University IV. and then bud through the plasma membrane in regions where the SU and TM proteins have accumulated. and they rearrange to form mature virions. therefore. The Gag/Pol polyprotein is incorporated into the assembling core by interaction between its CA region and the corresponding region of Gag. and NC) and enzymatic (PR. In ―B-‖ and ―D-type‖ viruses. Selective encapsidation of only unspliced full-length viral RNA is achieved by position the packing signal psi (). generating spherical structures called ―A-type‖ particles. Assembly and release of virions Two different assembly pathways have been elucidated. the viral protease becomes activated.

Virology Report Can Tho University Figure 14 Retrovirus life cycle Advanced Biotechnology Course 37 19 Institute of Biotechnology Research and Development .

Virology Report Can Tho University PART 2: HUMAN IMMUNODEFICIENCY VIRUS (HIV) I. Another type of human immunodeficiency virus. This virus. As a consequence. Subsequent epidemiological studies suggested that the syndrome was due to a transmissible agent that was acquired through sexual contact or blood exchange. HIV-1 is characteristic of a subfamily of retroviruses named the lentiviruses (Table 2). recipients of blood transfusions. Fewer people succumb to HIV-2 than HIV-1 and prior infection with HIV-2 may even help to prevent infection with HIV-1.) 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. However. 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. they suffered from a number of opportunistic infections (the most prevalent being Pneumocystis carinii pneumonia. so named because of the slow progression of diseases caused by lentiviruses. hemophiliacs. subsequently named human immunodeficiency virus type 1 (HIV-1) was demonstrated (despite much controversy and debate) to be the causative agent of AIDS. as reported by The Centers for Disease Control in Atlanta) that were often fatal. the incidence of HIV-2 is growing. Advanced Biotechnology Course 37 20 Institute of Biotechnology Research and Development . however. In 1983. a retrovirus isolated from the blood of individuals with AIDS was characterized by groups led by Luc Montagnier (Figure 15a) and Barré-Sinoussi (Figure 15b) at the Pasteur Institute in Paris and Robert Gallo (Figure 15c) in Maryland. (The transfer of the HIV disease from animal to human likely occurred several decades earlier. THE DISCOVERY OF HIV The earliest known case The first case of HIV infection in a human was identified in 1959. HIV-2 was isolated from mildly immune suppressed patients in West Africa and appears to be less pathogenic than HIV-1. rendering them immune-incompetent. and intravenous drug users were also affected.

and (3) AIDS (Figure 16). (b) Barré-Sinoussi. Two to six weeks following exposure to the virus. diarrhea. 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. Advanced Biotechnology Course 37 21 Institute of Biotechnology Research and Development . SIGNS AND SYMPTOMS OF HIV INFECTION The course of the infection can be roughly divided into three phases: (1) acute infection. individuals can develop a mononucleosis or influenza-like syndrome (fever. headaches. lethargy. or swelling of lymph nodes) that requires hospitalization in a minority of individuals. malaise. stiff neck. (2) clinical latency.Virology Report Can Tho University (a) (b) (c) Figure 15 (a) Luc Montagnier. nausea.

it is has been suggested that Advanced Biotechnology Course 37 22 Institute of Biotechnology Research and Development . continued replication in lymph nodes Replication and destruction of lymph node architecture Release of virus into the circulation Loss of immune response. (b) Stages of HIV infection The first organ system to be affected by the infection is the gut associated lymphoid tissue (GALT). Given the role of GALT in regulating intestinal flora. (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.Virology Report Can Tho University (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. 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. susceptibility to opportunistic infections.

night sweats. herpes simplex. a number of infections such as cytomegalovirus. and neurological syndromes including dementia and neuromuscular disorder. oral thrush. 3. virus replication persists in the lymph nodes. varying levels of viral RNA genomes can be detected in the blood of different individuals (―virus load set point‖. infection within the lymph nodes persists throughout the course of the disease. Increased numbers of T cells from HIV-infected individuals undergo spontaneous apoptosis even though they are not directly infected. 2. However. The higher the basal level of viral RNA. Patients who develop a predominantly cytotoxic T-cell–based immune response have a better chance of long-term survival. the primary infection resolves but there is little recovery of the GALT. Slow progressors (70–80%) develop late stage symptoms in 8 to 10 years. Also important is the nature of the virus itself. Figure 16). Virus titers drop as the immune system responds with both cytotoxic T lymphocytes and antibodies. the more rapidly patients progress to full-blown AIDS. indicative of the failure of the immune system to contain the infection. Patients exhibit chronic fever.Virology Report Can Tho University its depletion may result in release of bacterial products such as lipopolysaccharide into the circulation. The nature of the immune response is also crucial. diarrhea. Within 1 to 2 months. After resolution of the acute infection. Neurological symptoms correlate with virus replication in the central nervous Advanced Biotechnology Course 37 23 Institute of Biotechnology Research and Development . pneumonia. Individuals progressing toward end-stage disease have high levels of virus in the blood. including a state of chronic immune activation known to persist in the chronic phase of HIV disease. Several factors help predict clinical outcome. Several course of disease following acute infection have been documented in the absence of treatment: 1. Rapid progressors (10–15% of infected individuals) develop late stage symptoms in 2 to 3 years. neoplasm such as Kaposi‘s sarcoma. Over the course of clinical latency. resulting in a gradual depletion in the level of circulating CD-4 positive T cells and destruction of the lymph node architecture. Long-term non-progressors (5%) show no decline in CD4-positive T-cell levels. 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.

While current therapies delay or prevent disease progression.Virology Report Can Tho University system. delivery. III. nasal secretions. Only certain fluids – blood. 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). these features influence the frequency with which disease arises and they provide clues to methods that may control and eventually eliminate the virus.1 Transmission HIV-1 was probably transmitted to humans from chimpanzees infected with SIVcpz. As a result of these studies. 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. However. closely related to HIV. These viruses have been isolated and their nucleotide sequences compared. or vomit unless these are Advanced Biotechnology Course 37 24 Institute of Biotechnology Research and Development . semen. 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. sputum. 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. In the majority of cases. and from mother to child during pregnancy. Among humans. III. HIV is transmitted upon exposure to mucous membranes. they do not eradicate the infection. withdrawal from therapy results in reemergence of the virus and continued disease progression. or breastfeeding (known as vertical transmission). tears. 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. sweat. rectal fluids. exposure to infected body fluids or tissues. Consequently. urine. HIV is transmitted by three main routes: sexual contact. saliva. Many species of African monkeys and apes are hosts for specific strains of simian immunodeficiency virus (SIV). There is no risk of acquiring HIV if exposed to feces. and breast milk – from an HIV-infected person can transmit HIV. vaginal fluids.

6 -1.9 0.000 9.0 million – 1.7 million 1. III. Even at the country level. South and South East Asia have an estimated 12% of the global total.Virology Report Can Tho University contaminated with blood. down from 2.2 million 250.000 67. 68% of the global total.3 million people living with HIV globally (Table 3).1 million 770.000 90.6 0.000 – 930.2 million 21.000 – 1.000 20.8 million deaths from AIDS in 2010.4 million are less than 15 years old. Annual AIDS deaths have been continually declining since 2005 as antiretroviral therapy has become more widely available.2 million are men.2 Source: UNAIDS World Aids Day Report Advanced Biotechnology Course 37 25 Institute of Biotechnology Research and Development . despite the implementation of prevention strategies.3 million – 1.2 million – 1.9 million 1. 16. It is possible to be co-infected by more than one strain of HIV – a condition known as HIV superinfection.4 0.0 0. with some countries more afflicted than others. in 2010. There were about 1.6 million – 24. with about 22.5 million 1.8 5.6 million – 4.1 million 3.1 0.2 Epidemiology HIV/AIDS is a global pandemic.7 million 1. there are approximately 35.9 million 580. The rate of new infections has fallen slightly since 2005 after a more rapid decline between 1997 and 2005. Of these.000 56.900 0.9 million at the end of 2010. The pandemic is not similar within regions.3 0. Sub-Saharan Africa is the worst-affected region. about 17.8 million are women and 3.6 million – 35. The number of people infected with HIV continues to increase in most parts of the world.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. According to UNAIDS (Joint United Nations Programme on HIV/AIDS). there are wide variations in infection levels among different areas.2 million in 2005. Table 3 Prevalence rate of HIV/AIDS infection in 2010 World region Estimated prevalence of Estimated HIV infection (adults and children) 31.

although there are signs that the pandemic is declining in this region. with adult prevalence rates exceeding 20% in most countries in the region. The differences in infection levels between women and men are most pronounced among young people (aged 15–24 years). and 30% in Swaziland and Botswana (Figure 17). Eastern Africa also experiences relatively high levels of prevalence with estimates above 10% in some countries. Presently.6 million and 24.2. In this age group. women are being infected with HIV at earlier ages than men. The widespread prevalence of sexually transmitted diseases. In Nigeria and Côte d'Ivoire.Virology Report Can Tho University III. which is home to just over 12% of the world‘s population but two-thirds of all people infected with HIV.0% and between 21. the practice of scarification. Across Sub-Saharan Africa. with 13 women infected for every 10 infected men. This gender gap continues to grow. Sub-Saharan Africa Sub-Saharan Africa remains the highest region. there are 36 women infected with HIV for every 10 men. and no country has rates above 10%. two of the region's most populous countries. However. between 5 and 7% of adults are reported to carry the virus. West Africa on the other hand has been much less affected by the pandemic. Advanced Biotechnology Course 37 26 Institute of Biotechnology Research and Development . more women are infected with HIV than men. Throughout the region.a.1 million total are affected. The adult HIV prevalence rate is 5. Several countries reportedly have prevalence rates around 2 to 3%. HIV infection is becoming endemic in sub-Saharan Africa. Southern Figure 17 Map of HIV prevalence in Africa in 2007 Source: UNAIDS Africa is the hardest hit region. the actual prevalence varies between regions.

590. Senegal. Poor economic conditions (leading to the use of dirty needles in healthcare clinics) and lack of sex education contribute to high rates of infection.35%. This was an increase of 200. UNAIDS estimates that in 2005. On the other hand. a shortage in antenatal therapies and through the feeding of contaminated breast milk. III.5 million people in South Africa infected with HIV – 12. such as drought.000 infants born in developing countries are infected with HIV-1 per year. The geographical size and human Advanced Biotechnology Course 37 27 Institute of Biotechnology Research and Development . Poor economic conditions caused by slow onset-emergencies. such as drought. Uganda. 25% or more of the working adult population is HIV-positive.7 million adults and children infected. and Uganda has succeeded in actually reducing its HIV infection rate. the size of Nigeria's population meant that by the end of 2003.2. Worse still. and that 10% of HIV infections in Africa were transmitted via blood. and the poor state of hygiene and nutrition in some areas may all be facilitating factors in the transmission of HIV. or rapid onset natural disasters and conflict can result in young women and girls being forced into using sex as a survival strategy. women are forced by clients to accept greater risks. take their toll and the number of potential 'clients' decreases. More AIDS deaths (480. there were an estimated 3.000) occur in this region than in any other except sub-Saharan Africa. Mother-to-child transmission is another contributing factor in the transmission of HIV in developing nations. AIDS-denialist policies have impeded the creation of effective programs for distribution of antiretroviral drugs. the World Health Organization estimated that 25% of the units of blood transfused in Africa were not tested for HIV. Although HIV infection rates are much lower in Nigeria than in other African countries.6 million people infected. In 2000.Virology Report Can Tho University unsafe blood transfusions. South and South-East Asia The HIV prevalence rate in South and South-East Asia is less than 0. such as not using contraceptives.4% of the population. with total of 4. Denialist policies by former South African President Thabo Mbeki's administration led to several hundred thousand unnecessary deaths.b. Zambia. there were 5.2 – 4. In some African countries. research indicates that as emergencies. and most recently Botswana have begun intervention and educational measures to slow the spread of HIV. Due to a lack of testing.000 people since 2003.

and 67% of those infected in Bangladesh and 41% in Nepal are migrants returning from India. women in the general population may be more exposed to the risk of contracting HIV than reported. Injecting drug users (IDU) account for up to 65% of people living with HIV. the estimated number of people living with HIV rose drastically from 3. IDU often engage in risky sexual behaviors. claiming 0.47% of the population. The HIV prevalence among male IDU is estimated to be 23.670 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. 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.8%. sex workers. migrants are vulnerable.000 in 1992 to 220. Drug injection is reported as the major cause for doubling the number of HIV/AIDS patients from 2000 to 2005.000 in 2007. The AIDS picture in South Asia is dominated by the epidemic in India. Besides. Vietnam In Vietnam.1%. 5. 35% of IDU living with HIV shared needles and syringes. Among these. men who have sex with men (MSM). sexual contacts between males comprise the majority of new infections. In the Philippines. In South and Southeast Asia. female IDU often sell sex to finance their drug need.Virology Report Can Tho University diversity of South and South-East Asia have resulted in HIV epidemics differing across the region. HIV prevalence was 11. Meanwhile. and clients of sex workers and their immediate sexual partners. 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. In a survey of 20 provinces in Vietnam. 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. the HIV epidemic remains largely concentrated in injecting drug users. While HIV/AIDS remain an epidemic only within the high-risk groups. This raises the risk of spreading HIV/AIDS to the general population. An HIV surveillance study conducted by Dr. One Advanced Biotechnology Course 37 28 Institute of Biotechnology Research and Development . Particularly. in particular. This is in part due to human trafficking and exploitation. 25% of male IDU in Hanoi is reported to buy sex and do not use condoms.

The diameter of the HIV virion measured in negatively stained preparations is in the range 80–110 nm.Virology Report Can Tho University 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. HIV VIRION The virion has the general characteristics of retroviruses but. pol. migrant husbands who. rev. tat.000 in 2007. Men having pre-marital or extra-marital sexual relationships with female sex workers inevitably expose their wives to HIV/AIDS risk. In addition to the standard gag. It is reported that more than 1% of pregnant women in some provinces are found HIV positive. vpu. perinatal transmission presents another channel of HIV transmission. and nef (Figure 18 and Figure 19. Table 4 and Table 5). Particularly in provinces with mobile populations. Women may contract HIV/AIDS through partners who are undisclosed IDU. being away from home. the capsid is cone shape with a diameter of 40–60 nm at the wide end and about 20 nm at the narrow end. in contrast to most retroviruses. Generally. vpr. are likely buy sex and use drugs may contract HIV and transmit to their wives. there is one capsid per virion.000 in 2000 to 90. though virions with two or more capsids have been reported. and env genes. Sequence analysis of the genome of HIV-1 revealed it to be considerably more complex than many other retroviruses. Advanced Biotechnology Course 37 29 Institute of Biotechnology Research and Development . IV. six additional reading frames were identified: vif. With potentially high HIV prevalence among women. only one of the two RNA molecules is shown covered by NC proteins microscopy are at the upper end of this range or greater. while results from cryo-electron Figure 18 Diagram of an HIV-1 virion For clarity. The number of women with HIV infection is estimated to increase from less than 30.

which encode Tat. which make only two mRNAs (unspliced and singly spliced). or Nef In each class of spliced RNA there are multiple species. Figure 19 Genome structure and RNA splicing pattern of HIV-1 Advanced Biotechnology Course 37 30 Institute of Biotechnology Research and Development . The unspliced 9-kb full-length RNA.Virology Report Can Tho University In contrast to simpler retroviruses. The singly spliced 4-kb class of RNAs. or Env 3. The doubly spliced 2-kb class of RNAs. Rev. generated by the presence of several different 3 and 5 splice sites. used to produce Gag and Gag-Pol proteins 2. which encode Vif. Vpr. Vpu. splicing of the HIV-1 primary transcript generates more than 25 mRNAs that fall into three size classes (Figure 19): 1.

Wt.Virology Report Can Tho University 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. 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. Advanced Biotechnology Course 37 31 Institute of Biotechnology Research and Development . in KDa) p23 p16 p15 p19 p27 V.

whereas those using CCR5 are termed R5 (or macrophage-tropic) viruses. and Rantes CXCR4) for to CCR5. particularly in a region that undergoes a high rate of evolution. primary receptors and chemokine receptors which vary from different host cells. Viruses using CXCR4 are Figure 20 Model of HIV-1 entry designated X4 (or T cell-tropic) viruses. only the R5 strain is sexually transmitted.1 Receptors of HIV-1 There are two types of receptors for HIV-1 virus. Mip1ß. Beside the presence of CD4 alone on the cell surface. Primary receptor for HIV-1 is the CD4 antigen. The ability of ligands for these receptors (Mip1α. designated variable domain 3. as both CD4positive T cells and macrophages are vital for development of both humoral antibody and cell-mediated immunity. block SDF-1 virus for entry demonstrates their significant role in the infection process. infection also requires the presence of either the CCR5 or CXCR4 chemokine receptor. Thus HIV-1 attacks at the very heart of the immune system. These strain differences depend on variations in the SU protein (gp 120). Although both forms of HIV-1 may be present in an inoculum.Virology Report Can Tho University V. Natural resistance to HIV-1 infection is associated with a mutation in CCR5 that results in a loss of cell surface expression of the Advanced Biotechnology Course 37 32 Institute of Biotechnology Research and Development . found on the surface of both and helper T lymphocytes macrophages.

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). In contrast to CD4+ T cells. In contrast. Binding to CD4 (Figure 20a) induces a conformational change in gp120 that exposes regions that interact with the chemokine receptor. HIV-1 infection of macrophages results in a low level of virus replication. Advanced Biotechnology Course 37 33 Institute of Biotechnology Research and Development . Old world monkeys experimentally infected with HIV-1 express Trim5. allowing release of the nucleocapsid into the cytoplasm (Figure 20c). 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. a protein that promotes rapid degradation of the capsid before reverse transcription can occur. they either accelerate capsid breakdown or block transport of the viral preintegration complex into the nucleus. Vpr. The viral capsid associates with cellular microfilaments and reverse transcription of the viral genome begins. and IN. Designated ―restriction factors‖. MA encodes a classical nuclear import signal that interacts with the importin family of proteins. In contrast. Lv1) that can block this stage of the infection. Release of the virus occurs upon fusion of the vacuoles with the plasma membrane. with the bulk of the virus accumulating in intracellular vacuoles.2 Special feature of HIV-1 Most retroviruses cannot productively infect non-dividing cells because the preintegration complex. both Vpr and IN interact directly with components of the nuclear pore. Experiments in several species have identified host proteins (Ref1. is unable to enter the intact nucleus. Unfortunately. the human Trim 5 homolog fails to recognize HIV-1. containing proviral DNA. Once released into the cytoplasm. Integration of proviral DNA must therefore await the disintegration of the nuclear membrane when the cell divides. Three virus-encoded proteins in the preintegration complex facilitate this transport: MA. the viral nucleocapsid partially breaks down to permit access to nucleotide pools within the cell.Virology Report Can Tho University protein. V.

Tat The Tat protein increases HIV-1 transcription by stimulating elongation by RNA polymerase II. The function of Tat is achieved by its binding to Tat-responsive element (TAR) on nascent RNAs. which is localized in the cell nucleus. thus its name.a. Tat.3. Increasing the extent of phosphorylation of CTD promote the movement of the polymerase away from the point of initiation and facilitate the elongation stage.Virology Report Can Tho University V. which located just downstream the transcription start site.3 Functions of HIV additional proteins V. and (2) the nucleotide sequence within the loop. which forms the recognition element for Tat binding. abbreviated from ―transactivator of transcription‖. Figure 21 Mechanism of Tat function Advanced Biotechnology Course 37 34 Institute of Biotechnology Research and Development . Expression of this protein dramatically increases the amount of viral RNA. TAR forms a stem-loop structure with two regions essential for its function: (1) a bulge in the stem. The form of RNA polymerase II that participates in initiation contains few phosphate groups within its carboxy-terminal domain (CTD). Tat increases phosphorylation of CTD by recruitment of cyclin-dependent kinase (cdk)9/cyclin T to the transcription complex (Figure 21b). so it has low efficiency in elongation (Figure 21a). is a highly basic 86-amino acid protein produced by doubly spliced mRNA. Tat increases viral RNA abundance by increasing the elongation efficiency of RNA polymerase molecules.

only the doubly spliced 2kb RNAs are transported to the cytoplasm. Rev. Transport of Rev back into the nucleus requires dissociation of the Rev/RNA complex. A 240-nucleotide sequence within env.Virology Report Can Tho University V. and Nef. is required for the transport of unspliced and 4-kb (singly spliced) class of viral RNAs from the nucleus to the cytoplasm. termed the Rev response element (RRE). the export of Rev results in the export of the mRNA. which mediates the docking of Rev to the nuclear pore. However. Rev is returned to the nucleus. Together. Tat and Rev are essential for virus replication because they regulate HIV-1 transcription and transport of mRNAs that code for viral structural proteins. Following integration of proviral DNA and its transcription at a basal level. Subsequently. export and translation of the 2-kb (doubly spliced) one is not dependent on Rev. the Tat and Rev proteins strongly upregulate viral protein expression. Their action results in the expression of viral proteins in two stages. This permits the synthesis of Tat. The 116-amino acid Rev protein contains both a nuclear localization signal and a nuclear export signal. 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 Advanced Biotechnology Course 37 35 Institute of Biotechnology Research and Development . where Rev binds is required for Rev action (Figure 22). Transport to the cytoplasm involves binding of the nuclear export signal on Rev to the cellular protein exportin 1. which docks Rev to the cytoplasmic face of the nuclear pore.b. where the cycle is repeated. Rev binds to importin . Rev The Rev protein mediates cytoplasmic transport of viral RNA that code for HIV-1 structural proteins. If Rev is simultaneously bound to an mRNA via its RRE. abbreviated from regulator of expression of virion proteins.3. Rev.

This prevents its incorporation into virions. and can induce deamination of multiple deoxycytidine residues in the DNA product of reverse transcription made during a subsequent infection.3.viral defense mechanism. APOBEC3G. Recent studies have shown that APOBEC3G also directly impairs the reverse transcription reaction. mutants of APOBEC3G that lack deoxycytidine deaminase activity retain some antiviral activity. allowing two proteins to be made from the same gene using either the native or edited messenger RNA. significantly reducing the yield of proviral DNA. APOBEC3G therefore functions to defend the cell against infection by mutating the DNA copy of the HIV-1 genome. and therefore counteracts this cellular anti.c. Env. V. However. Vpr. Advanced Biotechnology Course 37 36 Institute of Biotechnology Research and Development . The original member of this family. APOBEC3G is a member of a family of cellular proteins that deaminate cytidines (in RNA) or deoxycytidines (in DNA) to either uridine or deoxyuridine. This leads to mutations in viral structural and regulatory proteins. APOBEC3G is incorporated into virions during assembly.d. Virus lacking Vif enters cells normally but generates a lower level of proviral DNA than wild-type virus. Deletion of the Vif gene reduces infectivity of HIV-1 in cell cultures and in animal models used to test pathogenicity. allowing the expression of proteins encoded by the 9-kb and 4-kb classes of mRNAs (Gag. V. 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. Vif. and Vpu). with a corresponding reduction in infectivity. Vpr Vpr (virion protein R) is a 100-amino acid protein that is recruited into virions (10–100 molecules per virion) by virtue of its interaction with the carboxy-terminal region of Gag. Gag/pol. was so named because it deaminates a specific cytidine residue in the mRNA coding for Apolipoprotein B. Vif is required to overcome the action of a host cell protein. APOBEC1. The absence of Vif within infecting virions cannot be compensated by expressing it in the cells being infected. Vif acts by binding to APOBEC3G and inducing ubiquitination and degradation of this protein by proteasomes.3. Vif Vif increases virion infectivity by counteracting a cellular deoxcytidine deaminase.Virology Report Can Tho University (Rev).

2). Vpu acts by binding to CD4 and to the cellular protein ß-TrCP. Vpr also facilitates packaging within the virion of the cellular enzyme uracil DNA glycoslase.e. This enzyme can remove deoxyuridine residues incorporated into viral DNA during reverse transcription because of high levels of dUTP in the cell. In the absence of Vpu. Recent work has determined that Vpu Advanced Biotechnology Course 37 37 Institute of Biotechnology Research and Development . which may be beneficial for virus replication since HIV-1 transcription by is the most active at this stage of the cell cycle. Vpu has two known activities within the cell. Enhancement of virus release from the plasma membrane: This activity is dependent upon the transmembrane portion of Vpu. Vpu also enhances the release of other.3. This protein accumulates in the Golgi apparatus and the endosome compartment of the cell. V. which makes it unavailable for the synthesis of viral DNA. both CD4 and gp160. Expression of Vpu results in enhanced release of virus from the cell surface. and they can bind to each other at that intracellular site. Vpu (virion protein unique to HIV-1) is an 81-amino acid protein that is inserted into membranes via its amino-terminal domain.Virology Report Can Tho University 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. Degradation of CD4: The cellular CD4 protein is a receptor for HIV that interacts with gp120 at the cell surface. This induces the ubiquitination of CD4 and its subsequent degradation by proteasomes. are made in the endoplasmic reticulum. However. Vpr may do this by targeting for degradation cellular proteins that are needed to pass from the G2 phase to mitosis. the precursor of gp120. unrelated viruses. gp 41 and gp 120. No homologs have been identified in related lentiviruses such as HIV-2 and simian immunodeficiency virus. this effect is not restricted to HIV-1. thus releasing gp160 and increasing surface expression of its cleavage products. The aggregate that forms retains gp160 inside the cell and therefore reduces gp120 incorporation into the virions released (Figure 23a). Vpr can also arrest and delay infected cells in the G2 stage of the cell cycle. Remarkably. virions accumulate on the cell surface in a partially budded state. Vpu Vpu protein enhances release of progeny virions from infected cells.

This activity of Nef requires its interaction with another adaptor protein. their absence can be important in disease progression. Virions produced in the absence of Nef appear to have a Advanced Biotechnology Course 37 38 Institute of Biotechnology Research and Development . The loss of surface CD4 is caused by an increase in the cycling of CD4 between the cell surface and the endosome compartment. 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.Virology Report Can Tho University induces degradation of tetherin. Infection of monkeys with simian immunodeficiency virus containing point mutations in the Nef gene resulted in the rapid generation of revertant viruses with a functional Nef gene. but it is unclear which of these activities is important for disease. Nef binds to CD4 and to the adaptor protein AP2 on the plasma membrane. V. Expression of Nef in mouse T cells and macrophages causes a disease that resembles the late stages of AIDS.f. no difference in the structure of virions produced in the presence or absence of Nef has been detected. Enhancement of virus infectivity: HIV Nef mutants make virus particles that have reduced capacity to infect cells. showing that there is considerable selection pressure for an active Nef protein. Nef may enhance infectivity by modification of virion structure. This effect cannot be reversed by expression of Nef in cells infected with Nef-minus virus. The loss of cell surface MHC 1 means that the cell cannot present viral antigens to circulating cytotoxic T lymphocytes. AP1. however. Simian immunodeficiency virus mutants with deletions of the Nef gene are viable. a host cell protein located on the plasma membrane that is believed to interact with budding virions and promote their endocytosis. Because these are important mediators of immune responses. Three activities have been attributed to Nef. but have lower titers and fail to induce disease in infected monkeys. Nef-induced loss of MHC 1 from the cell surface is due to a block in trafficking of MHC 1 from the Golgi apparatus to the plasma membrane. These findings implicate Nef as an important determinant of disease in infected animals. Nef Nef protein is an important mediator of pathogenesis. thus masking the infection from the immune system. 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. and this complex is recruited into clathrin-coated pits and endosomes (Figure 23b). In contrast.3.

unlike T cells activated by antigens. thus making them susceptible to productive infection by HIV-1. all activators of HIV-1replication. Nef acts to kill cells that could otherwise help to clear the infection. At present.Virology Report Can Tho University reduced ability to complete proviral DNA synthesis upon infection of target cells. Nef also prevents apoptosis of the infected cell by inhibition of Ask-1. prolonging the lifetime of the infected cell and maximizing production of new virus. This also results in increased release of chemokines from infected cells. Nef also inactivates Bad. and interleukin-1. Activation of the kinase Hck results in increased expression of interleukin-6. a pro-apoptotic factor. it is unclear which of the multiple activities of Nef are directly involved in pathogenesis in infected animals. where nucleocapsids are released after fusion. Initial studies yielded promising results in adult monkeys. However. However. 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. known to be involved in stimulation of cell growth and inhibition of apoptosis. inducing apoptosis of surrounding uninfected CD8-positive and CD4positive T cells by interaction between FasL and Fas. By stimulating PI-3 kinase. Expression of FasL on the surface of the infected cell is also increased by Nef. a kinase that links death receptors with cellular caspases involved in initiating apoptosis. 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. Nef also interacts via its proline-rich domain with members of the Src family of tyrosine protein kinases and alters their activity. T cells activated by Nef cannot effectively mount an immune response. resulting in general activation of the cell and promoting virus replication. In so doing. recruiting uninfected T cells to the sites of virus infection and activating them. tumor necrosis factor-. Modification of cell signaling: Nef has been implicated in alterations of signaling in T cells. Activation of T cells by Nef is caused by modulation of the activity of a number of cellular protein kinases involved in signaling pathways. vaccinated animals displayed resistance to subsequent challenge with wild- Advanced Biotechnology Course 37 39 Institute of Biotechnology Research and Development . 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. One such target is the host serine/threonine protein kinase Pak2.

a. targeting virus entry. Figure 23 Down-regulation of CD4 expression VI.1. infection of young animals with virus lacking Nef induced disease.1 Treatment VI. and adults experienced complications over a prolonged period of time.Virology Report Can Tho University type virus. integration and protein cleavage. reverse transcription. Chemotherapy Five classes of antiretrovirals are currently available in clinical practice (Table 6). TREATMENT AND PREVENTION OF AIDS VI. However. Advanced Biotechnology Course 37 40 Institute of Biotechnology Research and Development .

current therapy requires the simultaneous use of multiple drugs to generate a higher barrier for the virus to overcome. and lipodystrophy) Because each class of drug only targets one step of HIV replication and each has its own disadvantages. Examples .Production costs are high .Side-effects of the drugs such as insomnia. insulin resistance.Lamivudine (3TC) Drawbacks Able to inhibit cellular DNA polymerase γ responsible for synthesis of mitochondrial DNA.Virology Report Can Tho University 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. pancreatitis…) Non-nucleoside RT inhibitors (NNRTIs) Bind tightly to viral RT close to the polymerase active site. 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. neuropathy.Fusion inhibitors: enfuvirtide (ENF) . Intergrase inhibitors Inhibit strand transfer . and cause allosteric inhibition Nevirapine (NVP). vivid dreams. 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. such as AZT and 3TC) and a PI (Highly active antiretroviral therapy – HAART) 41 Advanced Biotechnology Course 37 Institute of Biotechnology Research and Development . and prevent the cleavage of Gag/Pol protein. efavirenz (EFV) .Zidovudine or azidothymidine (AZT) . leading to adverse sideeffects (as lactic acidosis.Vulnerable to loss of activity through the rapid emergence of resistance Ritonavir Frequent and severe sideeffects (hyperlipidaemia. The most effective combination involves three drugs: two NRTIs (usually two nucleoside analogs.CCR5 inhibitors: maraviroc. vicriviroc RAL Exhibit a low barrier to the emergence of resistance and viruses with mutation at intergrase gene .

Nonetheless. efficacious vaccine that prevented HIV infection would provide the most important means of limiting the AIDS pandemic. there is no imminent prospect of developing a prophylactic vaccine. In the absence of such vaccine. Immunotherapy A safe. VI. there is some optimism that HIV may be held in check by such complex drug treatments. many AIDS patients have benefited from the effects of these new combinations of drugs and can even return to work. Although immunotherapy for chronic. 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.Virology Report Can Tho University It is now possible to quantify effects of drug treatment by assaying the amount of viral genome in the plasma of the patient. Although it is still too early to tell whether eradication can be achieved. Many approaches to developing vaccines have been attempted. Drug combinations can reduce the load to undetectable levels and therefore. 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.1. a combination of conventional drugs and immunotherapy may be better than either alone. 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). The first target of the RNAi was Advanced Biotechnology Course 37 42 Institute of Biotechnology Research and Development . persistent infections is more problematic.1. 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. Much effort will continue to be placed on vaccine discovery and development. experimental protection of macaques against challenge by the same virus strain as the immunogen has been achieved. SHIV may be useful in testing future envelope-based vaccine candidates. For patients whom antiretroviral treatment has failed.b. 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. VI. For example. and recombine with incoming viruses.c. but unfortunately. passive transfer of neutralizing antibody in sufficient concentration can block infection if administered at the time of challenge. effort has been turned towards immunotherapy. because HIV may repair its fitness.

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. complementary approach of targeting on cellular transcripts that encode for Advanced Biotechnology Course 37 43 Institute of Biotechnology Research and Development . 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.Virology Report Can Tho University HIV infection may be due to extensive research in this area leading to accumulation of knowledge regarding the life cycle of the virus. Thus. 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. Figure 24 A model for the mechanism of RNA interference Although the inhibition of HIV-encoded RNAs by RNAi has been made possible. RNases within the cell then remove these fragments. 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. the RNAi mechanism proceeds via the following steps (Figure 24): 1. However. Hence. 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. RNAi has been illustrated in the prevention of HIV infection in cells. 2. in cases where the cells are infected by the HIV retrovirus.

Some miRNAs function to regulate developmental timing. 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. For instance. Another significant progress in this area is the use of the hematopoietic progenitor stem cells. which are isolated. Although similar to siRNA. miR-122 is specifically expressed in liver cells and was found to be required for efficient Hepatitis C virus (HCV) replication in hepatocytes. cell proliferation and tumorigenesis. and the co-receptors CCR5 and CXCR4 have proved successful in the inhibition of viral replication as well as its cell entry. which is becoming an active area of research. it can be noted that compared to the ribozymes or the antisense approaches. However. since HIV-1 switches to CXCR4 tropism during the course of AIDS. However. apoptosis.Virology Report Can Tho University functions has been carried out. signal transduction. followed by re-infusion into the patient‘s blood stream. the human miRNA. The introduction of the siRNAs has posed great challenge as the vectors used for the delivery initiated immunological reactions within the body. transduced with the vector carrying the therapeutic genes. Experiments to investigate the ability of miRNA inhibiting the infection of HIV have been carried out and obtained some different results. followed by reinfusion. Therefore. The pre-clinical study of this approach Advanced Biotechnology Course 37 44 Institute of Biotechnology Research and Development . NFκB. its transduction with lentiviral vector carrying the anti-HIV antisense RNAs and expansion. It was overcome partly by an approach involving the isolation of the T-cells of patients. miRNAs are derived from endogenous RNAs that contain stem-loop structures. Targeting only the CCR5 co-receptor may also present problems. viral targets became essential for the successful study of RNAi based therapy for HIV. in a different. 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. Down-regulation of various cellular cofactors such as the HIV receptor CD4. The mixture of shRNAs with several antiviral genes has become a potent alternative anti-HIV approach. 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. the RNAi based therapy is more potent. creating a more virulent infection. the down-regulation of the various cofactors present within the cell by RNAi necessary for the progress of HIV infection was studied.

Sexually Transmitted Infections Sexually transmitted infections are a risk factor for acquisition of HIV. such as cellulose sulfate and PRO-2000. further work is being undertaken.000 copies ml-1) or have drug resistance. including the topical use of antiretroviral drugs.2. since recent research indicated that microbicides may cause inflammatory effect on genital epithelium.2. VI. These are thought to act by disrupting the virus—cell interaction. have a high viral load (>10. progress in the field was slowed. who otherwise may not be able to convince sexual partners to adopt safer sex practices.b. It follows that control of sexually transmitted infections may be an important and cost-effective method for reducing transmission of HIV.Virology Report Can Tho University on the human trials in near future will mark a revolution in the therapeutics for the HIV based infection. Microbicides Topical administration of microbicides to vagina and/or rectum has been proposed as appropriate for women in particular. With these combined strategies. Advanced Biotechnology Course 37 45 Institute of Biotechnology Research and Development . In addition. but should also be given to infants born to untreated mothers. who has a low viral load. Treatment of the mother. safe sex messages remain the cornerstone of any prevention campaign. Compounds in development include polyanions.2 Prevention VI. and non-ionic surfactants such as nonoxynol-9. with AZT during the last trimester of pregnancy and the infant for the first six weeks of life reduces 60–70% in vertical transmission. alterations to epithelial permeability and/or alterations to natural genital microbial flora. within the microbicides programme. Exclusive formula-feeding is also recommended to all HIV-positive mothers. VI. Therefore. vertical transmission of HIV can be reduced to negligible levels. Nevertheless. VI.a. local genital tract inflammation increases HIV infecting.2. Mother-to-Child Transmission There is a linear correlation between maternal viral load and risk of transmission. HAART is not only recommended in pregnant women who require treatment for their own health. However.c.

VI. compared with a rate of 18. to be taken over four weeks. Current guidance suggests truvada (TDF and FTC) and kaletra (LPV/r) as the PEP of choice.d. and also the potential increase in risky behavior consequent on the reassurance given by use of this approach. Four factors were associated with increased risk of occupationally acquired HIV infection: (i) deep injury. Post-exposure Prophylaxis (PEP) Post-exposure prophylaxis (PEP) was initially addressed in the context of occupational exposure to HIV-1. Antenatal treatment of the pregnant woman with ZDV was omitted (through choice or limited clinical care).2. such as needle stick injuries. SIV/macaque animal models demonstrated a protective effect of TDF when administered within 72 hours of inoculation. (iii) injury with a needle which had been placed in a source patient‘s artery or vein and (iv) terminal HIV-related illness in the source patient (now explained through a high viral load). attention has turned to post-exposure prophylaxis following sexual exposure (PEPSE). neonatal ZDV started within 48 hours of birth was associated with an HIV transmission rate of 9. It has been considered that there is no risk of HIV transmission where intact skin is exposed to HIV-infected blood. the average risk is estimated at less than 1 in 1000. or indeed. rapid development of resistance in cases of transmission.4% when ZDV was started at a later time. (ii) visible blood on the needle. are ongoing. where the risk of acquisition is increased in the passive partner in anal intercourse. with or without FTC. More recently. After a mucocutaneous exposure. Trials of TDF. 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.Virology Report Can Tho University VI. for example.3%.2. and such protection was enhanced by treatment for more than 10 days.e. 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. Such an approach is relevant for. Advanced Biotechnology Course 37 46 Institute of Biotechnology Research and Development . Concerns with this approach include the risk of resistance in cases where the recipient is already HIV infected. Pre-exposure Prophylaxis (PREP) There is increasing interest in the use of antiretroviral drugs with low toxicity prior to possible exposure. sex workers.

so treatment for HIV-1 must be continued for life. T cells are activated by the presence of antigen fragments during contact with dendritic cells. because they do not express viral proteins. Besides. To generate an immune response. 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. About 1% of infected cells remained latent. Reverse transcriptases do not have highly efficient proofreading mechanisms. although it appears promising for treating HIV-1 infections. will be of little use in the developing countries. Consequently. resulting in about 1 – 10 mutations per one proviral DNA molecule. the kinds of HIV-1 drug therapies are both too complex and too expensive for use where the need is the greatest. part of the difficulty is also associated with an attempt to develop inhibitors that are both potent and safe. has complicated HIV treatment.Virology Report Can Tho University Remained problems in treatment of HIV/AIDS Successful long-term treatment of HIV-1 infection remains an unrealized goal for many reasons. and thus render HIV-1 a difficult target for both the immunotherapy and drug treatment strategies. Another difficulty is the ability of HIV-1 to direct the transport of proviral DNA into the cell nucleus. both within one individual and within a population. Besides. which presents a problem for the immune system. and thus cannot be readily distinguished from uninfected cells by the immune system. Latent infection complicates the elimination of HIV-1. and eventually lead to infection and death of the T cells. The first reason is due in part to the high degree of variation in the virus. In fact. because of errors generated during reverse transcription. the rapid emergence of drug-resistant strains. which currently represent approximately 10% of new infections in develop countries. where the majority of AIDS cases exist. which viral RNA is not expressed. dendritic cells collect HIV-1 virions on their surface. However. They represent a substantial obstacle to treatment and a cure. The third problem is that chemotherapy. T cells that would support an immune response against HIV-1 are exposed to virus while interacting with dendritic cells. Removal of patients from chemotherapy invariably results in reemergence of the infection. facilitating entry of proviral DNA into the nucleus. after HIV-1 proviral DNA integrates into the host cell genome. Advanced Biotechnology Course 37 47 Institute of Biotechnology Research and Development .

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.Virology Report Can Tho University 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. and the late phase consisting of all steps for the synthesis of viral proteins and eventually the assembly of virions. rendering it perhaps the most intensively studied disease agent of our time. and integration of proviral DNA to the host genome. is a characteristic member of retroviruses. reverse transcription to make the proviral DNA. considerable resources have been committed to understanding HIV-1biology and pathology. HIV-1 has caused major global pandemic. intergrase. Its life cycle can be conveniently divided into two phases: The early phase comprising of entry of virus into the host cell. HIV-1 possesses 6 additional proteins. Retroviruses pack two identical copies of positive-strand RNA along with three important common retroviral enzymes: reverse transcriptase. The poor efficiency of reverse transcriptase cause a high degree of mutation in the virus. In response to health crisis. and protease in a 100 nm spherical enveloped virion. Advanced Biotechnology Course 37 48 Institute of Biotechnology Research and Development . termed acquired immunodeficiency syndrome (AIDS) that affects males and females equally. rendering it some special features that benefit their replication in the host cell. HIV-1. which belongs to the sub-family lentiviruses.

miRNA and HIV: promises and challenges. Paul D.  Carter. John J. and Harold E Varmus." Cell Research 15.  Rossi. Cold Spring Harbor Laboratory Press. 2011. 5th. John R.. Nicholas H. Joint United Nations Programme on HIV/AIDS (UNAIDS)." BioTechniques 40. 4 (2006): 25-29. and Venetia Saunders. Retroviruses. no. John. Yamina Bennasser. Principles and Practice of Clinical Virology. John M. 1997. Wiley.  UNAIDS World AIDS Day Report 2011. Banatvala. Wiley.. 2011.Virology Report Can Tho University REFERENCES  Acheson. and Kuan Teh Jeang. "siRNA. 2007. Virology: Principles and Applications. 11 (2005): 935946. Jangu E. and Barry D. John Wiley & Sons Ltd. Man Lung. Advanced Biotechnology Course 37 49 Institute of Biotechnology Research and Development . no. "RNAi as a treatment for HIV-1 infection. Pattison.  Coffin.  Zuckerman.  Yeung. Arie J. 2nd. Stephen H Hughes. 2004. Shu Yun Le. Griffiths. Fundamentals of Molecular Virology. Schoub.