Vanessa And Jeffrey Rough Draft

Each year, about 500 million people become infected with Acquired Immunodeficiency Syndrome (AIDS). AIDS is most prevalent in sub-Saharan Africa and has quickly made its way to the Indian sub-continent (Letvin 930). Worldwide, an estimated 70 million people have AIDS, and 15,000 new cases occur daily. Seventy-five percent of the world’s infections occur in the less developed countries of sub-Saharan Africa (Kegley 274). Unfortunately, there is no cure for AIDS despite the vast number of antiretroviral therapies available. In 2005, the United Nations’ Human Development Report stated “the HIV/AIDS pandemic has inflicted the single greatest reversal in human development” (Piot 526). The search for an HIV vaccine has increasingly become an issue with scientists worldwide, who have taken several approaches to enhance the human body’s immune system in attempt to ward off this detrimental disease. Because of the high infection rate of HIV-1 throughout the world, the development of a vaccine has become the focus of researchers and scientists.
Human Immunodeficiency Virus (HIV) is a versatile retrovirus of the genus lentivirus, which mutates rapidly to escape the body’s immune system (Butler 23). Since the virus has extreme diversity, it was grouped into several categories. Due to the discovery of many new isolates, the current HIV classification was developed. I'm confused. Are the "several categories" that you talked about the same as the current classification? The two major virus strains that cause AIDS are HIV-1 and HIV-2. HIV-1 was the first documented isolated strain and is now the most prevalent form. HIV-2 was isolated from patients in West Africa three years after HIV-1 was documented. HIV-2 is morphologically and biologically consistent with HIV-1 but differs in antigenic epitopes and envelope glycoproteins (fig 1). HIV-1 is furthered divided into three groups: M (main), O (outlier), and N (non-M, non-O) Could you further describe what these strains are. These strains show similarity to HIV-1 with a 65-70% sequence homology than HIV-2 with a 56% homology rate. sequence of what, the viral genome? As noted from the numerous classes and groupings, HIV-1 has a high mutation rate. Circulating strains can differ by as much as 35% of what? AAsequence? in envelope proteins and up to 20% in conserved proteins. The process for finding a vaccine has been complicated due to its rapid mutation rate which allows its escape from the human immune system.

Fig. 1: The molecular structure of the HIV viron including its associated proteins (Huckaby).
Viral Transmission

To understand the strategies for finding a vaccine, it is crucial to first understand the immune response of the human body to HIV infection. HIV-1 can be transmitted as cell-associated viruses (infected cells) or cell-free viruses. Viral transmission can occur through the exchange of body fluids, either through sexual contact or hematogenously (i.e. sharing contaminated needles, blood transfusions) (Letvin 930). The spread of HIV-1 through sexual intercourse has been the leading form of transmission. Sexual intercourse is capable of producing microvascular tears which are, and where do they occur; therefore, people with breeched mucosal epithelial tissue (i.e. genital ulcers) are at higher risk of transmission because HIV-1 has easier access into the epithelial tissues to initiate infection (Letvin 935). Intact genital epithelium may be a formidable obstacle to preventing HIV-1 transmission; however, it is still not proven if HIV-1 can cross intact epithelium to initiate infection (Kaizu 915, Letvin 935).
Viral Replication

Once HIV-1 has been introduced into a host, a burst of viral replication occurs within the first few weeks. Cell-free viruses must insert its single-stranded RNA into a host cell in order to increase its progeny. increase progeny or have progeny at all? HIV-1 specifically targets CD4+ T-cells by recognizing surface-expressed CD4 and CC-chemokine receptor 5 (CCR5) on host membrane host T-cell membranes?, or all membranes(Liang 259). Once the RNA genome has been inserted into the host cell, it undergoes reverse transcription to copy transcribe itself into double-stranded DNA which is capable of being inserted into the host’s genome. Every time the virus creates progeny, it uses an inherently inaccurate process. The mechanism of reverse transcription lacks proofreading abilities; consequently, the newly infected cell contains a proviral genome which differs by roughly one nucleotide from the parent strand due to the inaccurate replication (Letvin 931).
After the initial burst of HIV replication, HIV-1 establishes a latent infection at a very early stage, and CD4+ T-cell memory is rapidly destroyed (Gudmunsdotter 221). CD4+ T-cells are vital to the immune response for determining B- cell antibody production against a pathogen as well as activation and growth of CD8+ cytotoxic T lymphocytes (CTL) through the release of cytokines such as Il-2 (Makedonas 213). CD4+ and CD8+ T-cells are essential for controlling HIV viremia, but once CD4+ T-cells are destroyed, the body can no longer ward off viremia efficiently (Gudmunsdotter 221). Peak viremia occurs around three weeks after initial infection, which is why administering an HIV vaccine in the early stages of infectionis crucial because there is still adequate CD4+ count (Oliveira). do you really need the part of the sentence after because, you basically said the same thing in the first part of the sentence Since no significant or obvious symptoms are apparent within two to ten years after infection, it is difficult to administer a vaccine within a time period which would benefit the patient (Butler 26).
Mucosal Immune Response

Tight junctions of epithelial tissue of the human body i don't know if "of the human body is nessisary, i think it's kinda implied are the first innate barrier from infections (Neutra 148). Scientists are unsure if HIV-1 is able to cross an intact epithelial barrier, which means this might be a formidable obstacle defense instead of obsticale maybe? (Kaizu 915). Epithelial cells detect conserved microbial units through the use of Toll-like receptors (TLR). Theyuse the antecedent respond by producing mucus and cytokines. Mucus produced by the epithelial cells is a thick layer, making it harder for the bacteria and viruses to cross the cell membranes. Released cytokines signal to underlying mucosal cells such as dendritic cells (DCs) and macrophages to trigger innate, non-specific defenses. are dendridic cells and marophages mucosal cell? Part of the adaptive immune response occurs through local production and secretion of immunoglobulin A (IgA), which promotes entrapment of antigens in mucous and if it has the right specificity, could block microbial attachment to epithelial surfaces (Neutra 149). Immunoglobulin G (IgG) synthesis occurs after antigen recognition which can potentially neutralize pathogens that enter mucosal tissues (Neutra 150). Female genital tracts contain large numbers of these IgG-secreting plasma cells. Together, IgA and IgG concentrations may play a role in preventing the spread of sexually transmitted pathogens from entering the body and may be a significant factor in producing an effective mucosal vaccine (Neutra 149-150).
Humoral Immune Response

Evidence suggests that CD8+ CTLs may be involved in clearing the HIV-1 infection of the first organism that was infected the organism of the first cells that have been infected with HIV-1 (Pinto 867). HIV-specific CD8+ T cells are capable of directly killing HIV-1 infected CD4+ T cells (Makedonas 210). These CTLs specifically target cells expressing HIV-1 gag, pol, and env (What do these stand for?), which shows these cells play an important role in the clearance of viremia and are responsible for the initial control of viral replication (Pinto 867). The immunological pressure mediated by CD8+ T-cell recognition aids in the expansion of viral mutants (Makedonas 210). This signifies the effectiveness of CTL changes throughout the course of a humoral immune response because the rates of escape and reversion occur across different epitopes of HIV-1 (Loh 27). The escape rates of HIV-1 from the immune system are directly related to the positive selection sites on the virus where mutation causes genetic diversity (Oliveira). The HIV-1 antigens contain thousands of epitopes that could potentially be presented to CD8+ T-cells, yet only a relatively small fraction can induce an immune response—this is the basis of immunodominance. There are nine positively selected protein sites on HIV-1, which can present many different epitopes; however, fewer than three epitopes are targeted during a primary infection (Li 97, Oliveira). Human CTLs have polymorphic human leukocyte antigen (HLA) class I molecules, which recognize and bind to CTL epitopes on viral proteins. Due to the polymorphism of these sites, CTL response is unsuccessful in completely controlling the infection allowing the virus to further escape the immune response (Poon1 409). Vaccine researchers are trying to enhance the immune response of CTLs by increasing more epitope binding of CTLs to HIV-1 (Li 103). If CTL responses can be elicited with a high magnitude to a series of viral epitopes which exhibit high escape, then optimal control of virus replication can be achieved (Deresinski 1).
Dendritic cells (DCs) in the body phagocytose foreign particles and digest them with various enzymes, antimicrobial peptides, and proteases isn't a protease an enzyme?. The digested pathogen is then presented to lymphocytes such as B-cells and T-cells. HIV-1 activates the rho-GTPases so the DCs will phagocytose it. The exposure of gp120 from the envelope glycoprotein can lead to impaired maturation of DCs, triggering the secretion of IL-10, a cytokine which is associated with immunosuppressive responses (Shan 1638). IL-10 works as an anti-inflammatory cytokine by stopping the production of tumor necrosis factor (TNF), which decreases vascular permeability and catabolism. The exposure of gp120 (Explain what gp stands for) also inhibits IL-12, which is associated with the recruitment of natural killer cells, which are specifically designed to kill virally infected cells. One feature which distinguishes gp120 from many other vaccine immunogens is its biological activity; gp120 can bind to several cell surface receptors: CD4, CCR5, CXCR4, and several mannose C-type lectin receptors (MCLR). When gp120 binds to a receptor, signal transduction occurs causing adverse effects in the cell (Shan 1638). Researchers probed the IL-10 response to gp120 using blocking ligands but found this to be ineffective. However, ligands such as CV-N and 2G12 mAB will bind to gp120 mannoses and inhibit the production of IL-10 (Shan 1645).
Antiretroviral Therapies

When the AIDS/HIV epidemic first began, people who contracted the disease had a short life expectancy after contractionwere not expected to live very long after contraction. Since then, safe and effective drugs have been developed to slow the progression of HIV, so the infected person can live a longer, healthier life. Currently, 30 different drugs have been developed that will slow the onset of AIDS. These drugs fall into four major groups: reverse transcriptase (RT) inhibitors, protease inhibitors, entry and fusion inhibitors, and integrase inhibitors (NIAID 1). The recommended treatment consists of a multi-drug combination of three or more different classes and is called highly active antiretroviral therapy (HAART) (U.S department 7). HAART regimens are often unable to clear HIV-1 out of the body because the HIV-1 strains often become resistant to these drugs due to their rapid mutation rate (Secasan).
The four types of drugs which are generally prescribed in HAART work in different ways. RT occurs when the HIV RNA is converted into HIV DNA. Consequently, the RT inhibitor can either incorporate faulty DNA building blocks into the HIV DNA so the chain cannot be completed, or it can bind to RT in this paragraph you have used RT to mean reverase transcription, and here you are using it mean reverse transcriptase, i believe, double check this , interfering with the ability to make HIV DNA from HIV RNA. Protease inhibitors block the protease enzyme that HIV uses to produce infectious particles while entry and fusion inhibitors block HIV from entering the host cell by interfering with the ability of HIV to attach to the cell membrane (NIAID 1). Two different classes of integrase inhibitors exist; older classes block the virus from replicating once inside the T-cell, whereas newer classes stop the enzyme which allows the virus into the DNA (Kuhr). These methods of antiretroviral therapy are helpful in suppressing the virus, even at undetectable levels; however, they are not able to completely eliminate HIV from the body. Since HIV cannot be completely eliminated, infected people must receive therapy for life (NIAID 1).
Simulating a Human Model with Test Subjects

When testing possible vaccines, it is crucial to simulate (as closely as possible ) to a human model. Two of the most common test subjects that are typically used are macaques and humanized mice. Macaques (Macaca fascicularis) provide a nonhuman primate model (Kaizu 912)I think this doesn't need to be stated since a maquace by definintion isn't a human and is a primate. Often they can be inoculated with Simian Immunodefieciency Virus (SIV), which is similar to HIV, but is only found in monkeys. SIV-infected monkeys do recapitulate nice big word!!! many aspects of human HIV infection but not HIV-1 replication; therefore, this model cannot entirely support a HIV vaccine model (Denton 80). However, since humans and primates are reproductively similar, female cycling macaques have shown to be practical for a model of intravaginal HIV transmission (Kaizu 912).
Although mice are drastically different than humans, researchers have found a way to humanize them and produce a viable alternative to testing vaccines. There are various models for humanizing mice, but the common theme is to transplant human hematopoietic stem cells (HSC) into an immunodeficient mouse. These HSCs engraft the mouse bone marrow and then are capable of producing human immune cells such as T-cells, B-cells, and dendritic cells. Another advanced model is humanized bone marrow-liver-thymus (BLT) mice. These are developed by implanting human fetal thymus and liver tissue under the kidney capsule of immunodeficient mice and then transplanting human fetal liver CD34+ cells. These mice have shown to be an excellent model for simulating human immune responses (Denton 80).
Vaccines based on inactivated viruses and proteins

Viruses and humans have many different structures. One of these consists of the envelope surrounding the virus and its components.kind of an awkward sentence One main component of the envelope is the glycoproteins: glycoprotein 160, which is broken into two different parts, glycoprotein 120 (the surface subunit), and glycoprotein 41 (the transmembrane subunit). I would move this part of you paper ealrier since you talk about glycoproteins and stuff in earlier sections The glycoprotein extensions in the envelope help the virus attach to the host’s cell membrane so the virus can be inserted into the host cell. One hypothesis for an HIV-1 vaccine is not to allow the virus to attach to the cell; hence the virus cannot enter the host. One study found injecting recombinant glycoprotein (rgp) 160 into volunteers caused the subjects to constitute antibodies against the rgp 160. They found that the higher the dose of rgp 160 given, the stronger the antibody response was. Booster shots were given to several people to determine whether one dose was sufficient. The researchers found that booster shots were needed in order to for the body to keep producing antibodies against the rgp 160 (Kovacs 921). Researchers also found that immunized volunteers had antibody responses to epitopes found on HIV. Compared to an HIV-1 infected person, similar epitopes were targeted in the immunized patients and in higher percentages (Kovacs 922).
Researchers found injecting subjects with rgp 160 had little to no adverse side effects and would be an immunogenic vaccine which is capable of inducing neutralizing antibodies with a greater frequency than is seen in naturally acquired infection. ** I would break this last sentence up** However, the problem with this vaccine is it must be administered before the subject is infected with HIV-1 and given regimens every 6 months for best results. awkward sentence This vaccine would not eliminate the virus completely, but it would only make it harder for the virus to enter the host cell.
Other research has proposed engineering vaccine antigens to cope with the HIV-1 diversity. The Nef protein and Gag protein are found at high frequencies in natural viral populations. Using these antigens present in viral populations and targeting them with CD8+ CTL responses could be critical in controlling viremia during infection (Nickle 754-755). could you exlpain nef and Gag more, i'm kinda confused at their significance
Liang, et al. identified positive selection sites which are likely to be restricted by host immune responses. They found that C3, C4, and C5 regions were most targeted positive selection sites across the virus’s envelope while C1 and C2 had very little positive selection sites. However, this study supports the hypothesis stating positive selection site frequency has increased over time across the conserved regions of HIV-1 envelope. If the frequencies of the positive selection sites increase through the years, the CD8+ CTLs may be able to destroy HIV-1 without vaccines (Liang 143).

Neutralization of HIV-1 with antibodies

The generation of broadly neutralizing antibodies is a high priority in the development of a vaccine against HIV-1. However, most antibodies against HIV-1 have narrow specificity; consequently, designing methods to target these conserved regions of HIV-1 epitopes may allow for a neutralization of the virus (Blish 90). Not only is there narrow specificity but also six major globally prevalent strains of HIV-1 exist, and a vaccine must be found for each (Brown 6089).
HIV-1 has evolved a number of mechanisms in order to shield itself from neutralizing antibody responses against conserved regions of the envelope proteins. The gp160 that is cleaved into gp120 and gp41shield these conserved regions with both variable loops and with the addition of potential N-linked glycosylstaion sites. However, two amino acid mutations within the gp41 complex were identified, which expose multiple neutralization epitopes on the HIV-1 envelope proteins (Blish 90). The neutralizing antibodies are directed against the envelope spike, which consists of a trimer of gp120 bound to a trimer of membrane-spanning gp41. what is a trimer…did I miss this earlier? This structure may provide resistance against neutralization for HIV-1, however, the presences of five variable loop regions (V1-V5) are altered under selection pressure and may mutate rapidly to evade immune detection (Brown 6090).
Neutralization of HIV-1 with mutations

HIV-1 must maintain a functional envelope while accumulating enough mutations to escape the immune response. A place for such mutations is within the variable loop regions of the envelope. The third variable loop (V3) is a disulphide-linked amino acid sequence located at positions 301-336 on HIV-1 (Fenouillet 419) which is characterized by major sequence variation and is important for phenotypes in HIV-1, such as co-receptor usage and cell tropism. Therefore, researchers target this area of the virus for neutralization (Poon2). All neutralization attempts at the V3 loop have failed because this area allows the virus to shift between residues to escape the immune system while retaining its structure and function. The key question, however, is whether or not the early selection pressure imposed by neutralizing antibodies in this region will have a long term impact on HIV disease progression. Researchers predict that the virus will be able to rapidly escape; however, this may reduce the peak in virema at the time of primary infection (Mosier). Other researchers suggest that a successful vaccine must elicit responses against conserved regions where mutations would severely compromise the viability of the virus. This research suggests areas such as V3 are mutable segments which act as decoys, subverting responses away from conserved regions such as Pol and Gag (Rolland 1551).
Vaccines based on vectors

Effective vaccines need to stimulate vast amounts of neutralizing antibodies as well as a robust cellular-mediated immune response. One current strategy to achieve this has been through genetic immunization with DNA. The confidence in this method lays in the fact stating memory, effector, and humoral immune responses are induced. One study done by Locher et al. evaluated various adjuvants and their efficiency in distribution of a recombinant vector. This possible vaccine was designed by synthesizing the gp140 gene from HIV-2 by use of mammalian codons and cloning it into a plasmid vector. This vector was able to express eukaryotic genes at high levels and, therefore, elicit a gp140-specific systemic antibody response. One issue with genetic immunization is DNA rapidly degrades once injected into the body, making it unable to elicit a strong systemic response. Researchers have investigated various adjuvants for a reliable delivery method of recombinant DNA plasmids throughout the body and determined that cationic liposome formulation is effective in helping elicit a response (Locher 107).
Another HIV-1 vaccine study employed the use of viral vectors as a means of eliciting a CTL response What is a CTL response. The specific virus used in this study was the Canarypox virus because of its approved safety for humans. This virus is unable to replicate in humans and does not produce any infectious virus which could potentially harm the test subjects. The benefit to using this particular virus is that it is large and able to encode a vast majority of the genes 2 spacesfor HIV-1 specific proteins in hopes of eliciting a more robust CTL response. Using a prime-boost regimen, previous studies with recombinant Carnarypox vectors have induced HIV-1 CTL responses in up to 35% of uninfected healthy human test subjects. In this particular study, the recombinant vector encoded 2 vaccinia-virus genes, which inhibit apoptosis of the infected cells and thus allowing for a greater chance at a systemic immune response (Goepfert 1249). Between this study and previous ones, there have been no determined tolerable doses, however, interestingly enough, increasing the doses of the recombinant vector by 6-fold did not elicit a stronger CTL response. Although the test subjects in this study did generate neutralizing antibodies against HIV-1, they were of such a low tite r that there is still much needed work on this strategy for an effective HIV-1 vaccine (Goepfert 1255).
Stopping HIV-1 at the mucosal surfaces

HIV-1 transmission occurs most often through exposure of HIV-1 infected cells and cell-free virus to mucosal surfaces such as vaginal epithelium. Research done on non-human primates has shown HIV-1 can be transmitted even when the vaginal epithelium is completely intact. didn't you say earlier in your paper that it was not known if the virus could cross intact epithelium? Once the virus has crossed the epithelial barrier, mucosal antigen-presenting cells interact with the local CD4+ T cells, rendering them susceptible to viral infection. These CD4+ T cells are now unable to initiate the appropriate immune response, and HIV-1 can replicate and circulate throughout the body and inhabit lymphatic tissues (Neutra154). The goal of mucosal vaccines is centered on neutralizing the virus just as it enters the body and preventing any replication and spread. Injection of a vaccine directly at the epithelial barrier could offer an additional layer of protection. The HIV-specific antibodies could neutralize the virus and block the virus from attaching or entering their target cells. does nuetralize mean inhibit it, cuz if it does you can cut out the last half of this sentence One study on macaques has shown large doses of vaginally administered gp120-specific monoclonal antibodies prevented SHIV (chimeric SIV containing the HIV envelope glycoprotein) transmission. Mucosal vaccines would be administered through a prime-boost strategy to elicit a mucosal and humoral response. Much research still must be done in this area of HIV-1 vaccine development; however, mucosal vaccines have extreme potential (Neutra 156).
Another strategy to stop HIV-1 transmission being studied currently is microbicides. These ideally would be used as topical agents for the vaginal surface. As an alternative to a preventative HIV-1 vaccine, these agents are still being evaluated. The goal of microbicides is to prevent HIV-1 transmission through targeting the virus while in the lumen of the vagina or by preventing the virus from adhering and/or entering the host cell. Early research focused on N-9, which is a surfactant which is able tocapable of disturbing the cell and viral membranes. Studies found it did have anti-HIV activity, however, its ability to disrupt cell membranes often led to genital ulcers. I think you could combine this sentence as well as the sentence before it. Compromising the mucosal epithelium actually led to an increase in HIV transmission rates. The World Health Organization stated that N-9 should not be administered but microbicides have potential to be a safe and effective alternative to a vaccine. Current models of low efficacy have shown to be 60% effective in preventing transmission, and it has been estimated they can avert 2.5 million new HIV infections over 3 years (Wilkinson 1563).

HIV-1 has several mechanisms to escape the immune system, thus rendering it difficult for researchers to develop a vaccine. However, several different strategies have been tested which have targeted HIV during different stages of infection. Each strategy has advantages as well as disadvantages to being a potential vaccine candidate. These include vaccines that hinder the effectiveness of the glycoproteins on the viral envelope from attaching to the host cell membrane, vaccines that neutralize HIV-1 with antibodies, and vaccines that employ vectors recombined with genes specifically designed to elicit a CTL response against HIV-1. One way in which vaccines can be administered to induce a systemic response against HIV-1 is injecting the vaccine at mucosal surfaces where viral transmission is most likely to occur (Neutra 156).
With all the studies done on developing a successful vaccine for HIV-1, there lies great potential in what has been discovered; however, the structure and defense mechanisms integrated into the HIV-1 virion have created many obstacles for a successful vaccine. Those obstacles include finding a highly conserved region of the virus which, if potentially mutated, would compromise the viability of the virus, avoiding decoys such as the highly mutable V3 loop, and finding an antibody that has a greater range of neutralizing the HIV-1 virion (Rolland 1551, Poon2).
Despite the efforts in developing a vaccine against HIV-1, there has yet to be a breakthrough which would prevent an HIV-1 infection. However, many therapies exist for HIV-1 infected persons, which can drastically reduce viral loads and sometimes nearly eliminate HIV-1 from the body. Until an effective vaccine is discovered, it is vital that research is conducted which would look into new treatment options (Kuhr).

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