HIV Mutation and Its Consequence

Wayne T. Calumag

1B1 Medicine Dept. of Biochemistry FEU-NRMF

I.                  INTRODUCTION

A.  Nature of HIV

B.   Transmisson of HIV

C.   Life Cycle of HIV

II.             BODY

A.  Entry of HIV into target cells

B.   HIV Replication

C.  Causes of HIV infection

           III.       CONCLUSION





















AIDS is a human viral disease that ravages the immune system, undermining the body’s capacity to defend itself against certain microbial organisms. It usually lead to death from multiple infections or  other disturbances of an individuals natural defenses.          AIDS is the end stage of a chronic infection with human immunodeficiency virus type I (HIV I) one of the lentivirus subgroup of retroviruses. The retroviruses which make up a large family (Retroviridae) infect mainly vertebrates. They have a unique replication cycle whereby their genetic information is encoded by RNA rather than DNA. Retroviruses contain an RNA-dependent DNA polymerase (a reverse transcriptase) that directs the synthesis of a DNA form of the viral genome after infection of a host cell. The designation retroviruses denotes that information in the form of RNA is transcribed into DNA in the host cell a sequence the overturned a central dogma of molecular biology that information passes unidirectional from DNA to RNA to protein. The family Retroviridae includes three subfamilies Oncoviridae of which human T cell lymphotrophic virus (HTLV) type I is the most important in humans, Lentiviridae of which  human immunodeficiency virus (HIV) is the most important in humans and Spurnaviridae, the foamy viruses named for the pathologic appearance of infected cells. 

 The HIV retrovirus enters certain white blood cells of the immune system of its human host, particularly the T (for thymus-derived) lymphocytes, or T cells.  Specialized ‘helper’ T cells, also called CD4 cells is the chief target of HIV. An important feature of HIV-I is its ability to mutate rapidly.  The reverse transcriptase enzyme, in creating viral DNA from RNA, makes errors in the genetic material that is not corrected.  There errors lead in many cases to inactive viruses, but some mutations enable the virus to change enough to avoid attack by the immune system of the person it infects.  Over time, the original infecting virus becomes diversified in its human host whose immune system becomes damaged progressively during this process.  When the immune system has been substantially compromised, symptoms of secondary diseases emerge.  Thus, the “incubation period” of  AIDS, from the time of initial infection until symptoms develop, is very variable, with an average of about ten years.

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HIV-I is transmitted only through intimate contact between people or through blood transfer.  The virus is spread from infected to uninfected persons through sexual intercourse, the sharing of needles and syringes, or transfusion of blood products.  Transfusion of blood from an HIV-infected person is almost certain to result in infection of the recipient.  AIDS has afflicted many hemophiliacs who received clotting factor derived from pooled blood of many donors, before the danger was recognized and blood products cleanses of the virus.  Needle sharing involves transfusion of smaller amounts of blood but still a means of spreading the virus.  Other forms of sexual activity can also transmit the organism form person to person, but kissing on the lips which to carry relatively little, if any risk of spreading HIV.  Medical personnel are at some risk if injured with   blood tainted sharp objects form a carrier.  However, the usual types of nonsexual contact among people in household or at work do not involve any significant risk.  The AIDS virus can be spread during pregnancy from mother to fetus, or to the newborn infant at the time of birth, or by breast feeding.

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HIV is an RNA virus whose whole mark is the reverse transcription of its genomic RNA to DNA by the enzyme reverse transcriptase.  The life cycle of HIV begins with the high affinity of the gp120 protein via apportion of its VI region near the N terminus to its receptor on the host cells surface.  The CD4 molecule is a 55 kDa protein found predominantly on a subset of T-lymphocytes that are responsible for helper or inducer function of the immune system.  It is also express on the surface of monocytes/macrophages and dendritic/Langerhans cell.  It has recently been demonstrated that the co-receptor that must be present together with the CD4 molecule for fusion and entry of T cell tropic strains of HIV is a molecule termed CXCR4, while the co-receptor for tropic strains of HIV is a B-chemokine receptor CCR5.  Both receptors belong to the family of 7 transmembrane domain G protein-coupled cellular receptors.  Following binding fusion with host cell membrane.  RNA is encoded and internalized in the target cell.  The reverse transcriptase which is contained in the infecting virion, then catalyzes the reverse transcription of the genomic RNA into double stranded DNA translocated to the nucleus where it is integrated randomly in to the host cell chromosomes through the action of another virally encoded enzyme, integrase.  This provirus may remain transcriptionally inactive (latent), or it may manifest driving levels of gene expression, up to active transduction of virus. Cellular activation place an important role in the life cycle of HIV and is critical to the pathogenesis of HIV disease.  Following initial binding and internalization of virions in the target cells, incompletely reverse-transcribed the DNA intermediates labile in quiescent cells will not integrate efficiently into the host cell genome unless cellular activation occurs shortly after infection.  Furthermore, activation of the host cell is required for the initiation of transcription of the integrated proviral DNA into either genomic RNA or mRNA.  In this regard, activation of HIV expression from the latent state depends on the interaction of a number of cellular and viral factor.  Following transcription, HIV mRNA is translated into proteins that undergo modification through glycolization, phosphorylation and cleavage.  The viral core is formed by the assembly of HIV proteins, enzymes and genomic RNA at the plasma membrane of the cells.  Binding of property virions occurs through the host cell membrane where the core acquires it external envelope.  Each point on the life cycle of HIV is a real and potential for therapeutic intervention.  Thus far, the reverse transcriptase and protease enzyme have proven to be susceptible to pharmacologic disruption.   

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The nature of the pathogen-host relationship is recognized as being a dynamic coevolutionary process where the immune system has required ongoing adaptation and improvement to combat infection. Under survival pressure from sophisticated immune responses, adaptive processes for microbes, including viruses, have manifested as immune evasion strategies. This proposes a theory that virus immune evasion can be broadly classified into 'acquisition' or 'erroneous replication' strategies. Acquisition strategies are characteristic of large genome dsDNA viruses, which (i) replicate in the cell nucleus; (ii) have acquired host genes that can be used to directly manipulate responses to infection; (iii) are often latent for the lifetime of the host; and (iv) have little or no serious impact on health. Alternatively, erroneous replication strategies are characteristic of small genome RNA viruses, which are recognized as being the cause of many serious diseases in humans. It is proposed that this propensity for disease is due to the cytoplasmic site of replication and truncated temporal relationship with the host, which has limited or removed the evolutionary opportunity for RNA viruses to have acquired host genes. This has resulted in RNA viruses relying on error-prone replication strategies which, while allowing survival and persistence, are more likely to lead to disease due to the lack of direct viral control over potentially host-deleterious inflammatory and immune responses to infection. Entry of human immunodeficiency virus type 1 (HIV-1) into target cells requires both CD4 (ref. 1, 2) and one of a growing number of G-protein-coupled seven-transmembrane receptors. Viruses predominantly use one, or occasionally both, of the major co-receptors CCR5 or CXCR4, although other receptors, including CCR2B and CCR3, function as minor co-receptors. CCR3 appears critical in central nervous system infection. A 32-base pair inactivating deletion in CCR5 (delta 32) common to Northern European populations has been associated with reduced, but not absolute, HIV-1 transmission risk and delayed disease progression. A more commonly distributed transition causing a valine to isoleucine switch in transmembrane domain I of CCR2B (64I) with unknown functional consequences was recently shown to delay disease progression but not reduce infection risk.  The genome of human immunodeficiency virus type 1 (HIV-1) contains two direct repeats (R) of 97 nucleotides at each end. These elements are of critical importance during the first-strand transfer of reverse transcription, during which the minus-strand strong-stop DNA (-sssDNA) is transferred from the 5' end to the 3' end of the genomic RNA. This transfer is critical for the synthesis of the full-length minus-strand cDNA. These repeats also contain a variety of other functional domains involved in many aspects of the viral life cycle. In this study, they have introduced a series of mutations into the 5', the 3', or both R sequences designed to avoid these other functional domains. Using a single-round infectivity assay, they determined the ability of these mutants to undergo the various steps of reverse transcription utilizing a semiquantitative PCR analysis. They found out that mutations within the first 10 nucleotides of either the 5' or the 3' R sequence resulted in virions that were markedly defective for reverse transcription in infected cells. These mutations potentially introduce mismatches between the full-length -sssDNA and 3' acceptor R. Even mutationss that would create relatively small mismatches, as little as 3 bp, resulted in inefficient reverse transcription. In contrast, virions containing identically mutated R elements were not defective for reverse transcription or infectivity. Using an endogenous reverse transcription assay with disrupted virus, they show that virions harboring the 5' or the 3' R mutations were not intrinsically defective for DNA synthesis. Similarly sized mismatches slightly further downstream in either the 5', the 3', or both R sequences were not detrimental to continued reverse transcription in infected cells. These data are consistent with the idea that certain mismatches within 10 nucleotides downstream of the U3-R junction in HIV-1 cause defects in the stability of the cDNA before or during the first-strand transfer of reverse transcription leading to the rapid disappearance of the -sssDNA in infected cells. These data also suggest that the great majority of first-strand transfers in HIV-1 occur after the copying of virtually the entire 5' R.  The human immunodeficiency virus type 1 (HIV-1) Vif protein plays a critical role in the production of infectious virions. They reported that packaging of Vif is dependent on the packaging of viral genomic RNA in both permissive and restrictive HIV-1 target cells. Mutations in the nucleocapsid zinc finger domains that abrogate packaging of viral genomic RNA abolished packaging of Vif. Additionally, an RNA packaging-defective virus exhibited significantly reduced packaging of Vif. Finally, deletion of a putative RNA-interacting domain in Vif abolished packaging of Vif into virions. Virion-associated Vif was resistant to detergent extraction and copurified with components of the viral nucleoprotein complex and functional reverse transcription complexes. Thus, Vif is specifically packaged into virions as a component of the viral nucleoprotein complex. Our data suggest that the specific association of Vif with the viral nucleoprotein complex might be functionally significant and could be a critical requirement for infectivity of viruses produced from restrictive host cells. The human immunodeficiency virus (HIV) gag polyprotein is processed by the viral protease to yield the structural proteins of the virus. One of these structural proteins, p15, and its protease cleavage products, p7 and p6, are believed to be responsible for the viral RNA binding which is prerequisite for assembly of infectious virions. To better understand potential interactions between viral RNA, p15, and the HIV protease, they have synthesized p15 in an in vitro system and studied its processing by the viral protease. Using this system, they demonstrate that p15 synthesized in vitro is properly cleaved by the HIV protease in an RNA-dependent reaction. Mutation of cysteine residues in either zinc-binding domain of the p7 portion of p15 does not alter the RNA-dependent cleavage, but mutation of three basic residues located between the zinc-binding domains blocks HIV protease susceptibility. The results support a previously unrecognized role for the interaction of RNA and nucleocapsid-containing gag precursors that may have important consequences for virus assembly

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Retroviral replication is highly dependent on post-transcriptional regulation because a single primary transcript directs synthesis of many viral proteins. The identification and characterization of two post-transcriptional regulatory systems (Rev/RRE and CTE) revealed the efficient use of cellular transport pathways by retroviruses to achieve production of infectious progeny virus. The Rev/RRE system of HIV-1 consists of the viral Rev protein which binds to its target sequence on incompletely spliced RNAs and channels these into the CRM1-dependent export pathway, which is normally used for export of cellular proteins and RNAs (U snRNAs and 5 S rRNA). The CTE, on the other hand, directly recruits the cellular mRNA export receptor TAP to the viral RNA. Both systems have in common that they recruit a key player of a specific cellular export pathway and this recruitment appears to out-compete the respective cellular target molecules. The fact that CTE can functionally substitute for Rev/RRE, yielding a replication-competent virus, indicates that very short sequence elements are sufficient for post-transcriptional control. The presence of short dominant export signals could relieve the selective pressure on the remainder of the genome to maintain a sequence that is easily exported. The resultant increase in permitted sequence space may increase the potential for immune escape, thereby providing a selective advantage for the virus. Replication of the CTE-dependent HIV-1 variant is significantly impaired compared with the wild-type virus. Considering that post-transcriptional control in the case of HIV is also used to provide a temporal switch from the early phase of regulatory protein expression to the late phase of virion production, one may suggest that the CRM1 export pathway is advantageous for the rapid delivery of large amounts of cargo (i.e. HIV RNA). This would be in accordance with its normal function because CRM1 has been shown to direct the nuclear export of cellular regulatory proteins which must be accomplished rapidly as well. In summary, retroviruses have evolved fascinating ways to deal with their cellular environment and to make use of cellular transport pathways, allowing nuclear export of intron-containing RNAs which are normally restricted to the nucleus. Specific signals on the viral RNAs recruit key factors of cellular export, thus bypassing these restrictions and ensuring efficient viral replication.            During studies examining the rate of human immunodeficiency virus type 1 (HIV-1) mutation in a single cycle of replication, the 5' long terminal repeat of one progeny provirus was found to contain an insertion of 147 bp including an entire tRNA sequence as well as an additional 66 bp insertion of nonviral origin. Database searches revealed that 65 of 66 bp aligned with the human CpG island sequence found on chromosomes 6, 14, and 17. Therefore it seems probable that it is of human cellular sequence origin and was transduced by HIV-1. This is the first demonstration that HIV-1 can capture a cellular sequence. The site of integration of the parental provirus was mapped to chromosome 1p32.1. Sequence with homology to the transduced CpG island was not found on chromosome 1, suggesting that the transduced cellular sequence was not linked to the site of viral integration.

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            Initial infection with an attenuated form of human immunodeficiency virus type 1 (HIV-1) may give rise to some of the rare asymptomatic infections that have been observed. Recently, data have been presented suggesting that a persistent mutation in the essential activation domain of the HIV-1 Rev regulatory protein might have contributed to the maintenance of the asymptomatic state in one individual. Here, we have used a range of assays for in vivo Rev function to examine whether natural sequence variation in the normally highly conserved Rev activation domain can indeed affect Rev function. Analysis of five distinct natural sequence variants of the Rev domain demonstrated that each produced a two- to fourfold drop in Rev function when compared to the consensus activation domain sequence A sixth sequence, reported for the MN isolate of HIV-1, proved entirely inactive. However, resequencing of this region of the MN genome revealed that this isolate actually encodes a consensus Rev activation domain. Overall, these data reveal that even natural sequence variation in the essential Rev activation domain can result in significantly reduced Rev function and suggest that isolates containing such sequence variation are likely to replicate less effectively. Some of the major features of the acquired immune deficiency syndrome may be understood in terms of the characteristics of the virus. Life-long infection is a consequence of the life cycle of retroviruses, the formation of stably integrated viral genetic information into host-cell DNA. The silent infection, controlled replication, and profile replication may be understood in terms of the interactions of the positive and negative regulatory genes that control virus growth. Selective infectivity and selective cytotoxicity of HIV-1 are primarily the consequences of the properties of the envelope glycoprotein and its interactions with the surface CD4 molecule. The ability of HIV-1 to enter a state of prolific replication in the presence of an antiviral immune response is largely attributed to the design of the outside of the virus. The functional domains of the envelope glycoprotein are not accessible to the immune system and other regions appear to be covered by a dense cloud of sugar molecules. Concealment of the virus by regulated growth, by budding to the interior surfaces of macrophages as well as concealment by a sugar coating, may help to explain the failure to protect chimpanzees from infection by candidate vaccines. Rapid medical prophylaxis is required in populations that currently experience high incidence of HIV-1 infection. Chemoprevention, the use of chemicals to prevent establishment of viral infection, in addition to vaccination should be investigated as means to control the AIDS epidemic.

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 The central dogma of molecular biology is that DNA replicate starting from DNA to RNA and then finally to synthesis of proteins.  Human immunodeficiency virus acts differently and it defies that central dogma in which their genetic information is encoded by RNA rather than DNA.  Retroviruses (HIV) contain in RNA dependent polymerase (reverse transcriptase) that diverts the synthesis of a DNA form of the viral genome of the infected host cells.  It is very important to understand how viral components collaborate to convert the human immunodeficiency virus type1 genome from single-stranded RNA into double-stranded DNA because it is in this process where scientist is focusing on to find a cure for this kind of disease.  Human immunodeficiency virus attacks the immune system and it is the weakening of the immune system that is devastating to the patient, examples are life-long infections and other illnesses as a consequence of ineffective functioning of a person.  It is concluded, that life-long infection is a consequence of the life-cycle of retroviruses (HIV) and the formation of stably integrated viral genetic information into the host cell DNA.


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