New insights into host factors in HIV-1 pathogenesis

Drug Repurposing Approaches to Combating Viral Infections

Development of novel antiviral molecules from the beginning costs an average of $350 million to $2 billion per drug, and the journey from the laboratory to the clinic takes about 10–15 years. Utilization of drug repurposing approaches has generated substantial interest in order to overcome these drawbacks. A drastic reduction in the failure rate, which otherwise is ~92%, is achieved with the drug repurposing approach. The recent exploration of the drug repurposing approach to combat the COVID-19 pandemic has further validated the fact that it is more beneficial to reinvestigate the in-practice drugs for a new application instead of designing novel drugs. The first successful example of drug repurposing is zidovudine (AZT), which was developed as an anti-cancer agent in the 1960s and was later approved by the US FDA as an anti-HIV therapeutic drug in the late 1980s after fast track clinical trials. Since that time, the drug repurposing approach has been successfully utilized to develop effective therapeutic strategies against a plethora of diseases. Hence, an extensive application of the drug repurposing approach will not only help to fight the current pandemics more efficiently but also predict and prepare for newly emerging viral infections. In this review, we discuss in detail the drug repurposing approach and its advancements related to viral infections such as Human Immunodeficiency Virus (HIV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

Transmission routes of human immunodeficiency virus and affecting factors

Acquired immunodeficiency syndrome (AIDS) was first reported more than 30 years ago among homosexuals in the United States. The epidemiology of this disease indicates that there are three modes of transmission: Blood, mother-to-child, and sexual contact transmission. The pathogen of AIDS is human immunodeficiency virus (HIV), primarily HIV-1. HIV-1 could not break through the structurally and functionally integral skin, and primarily invades the human body through the mucosa irrespective of their integrity. Therefore, the mucosae are the natural transmission routes for HIV-1. The mucosae involved in HIV-1 transmission include the mucosae of the gastrointestinal tract and the urogenital tract. The risks of HIV-1 transmission vary significantly between mucosal sites and individuals, and are associated with mucosal integrity, abundance of target cells, immune status of the host, commensal microbes, and host genetic background. Many factors are closely related to the barrier function of the mucosa, and studies on their roles in HIV-1 invasion could promote the prevention and control of mucosal transmission of HIV-1.

The mutable vaccine for mutable viruses

Mutable viruses, such as HIV, pose difficult obstacles to prevention and/or control by vaccination. Mutable viruses rapidly diversify in populations and in individuals, impeding development of effective vaccines. We devised the 'mutable vaccine' to appropriate the properties of mutable viruses that undermine conventional strategies. The vaccine consists of a DNA construct encoding viral antigen and regulatory sequences that upon delivery to B cells target the enzymatic apparatus of 'somatic hypermutation' causing the construct to mutate one million-times baseline rates and allowing production and presentation of antigen variants. We postulate the mutable vaccine might thus anticipate diversification of mutable viruses, allowing direct control or slowing of evolution. Initial work presented here should encourage consideration of this novel approach.

Identifying factors associated with changes in CD4(+) count in HIV-infected adults in Saskatoon, Saskatchewan

More than doubling the national mean, Saskatchewan has the highest incidence of HIV in Canada. The progression of HIV is characterized by the decline in CD4⁺ T cells over time and can lead to immunological AIDS. Clinicians in Saskatoon, Saskatchewan, have observed a more rapid progression to AIDS in the recent years. The goal of this retrospective longitudinal cohort study was to investigate the rate of CD4⁺ cell depletion, as well as to determine the effects of multiple clinical and social factors that may contribute to an accelerated progression of HIV to AIDS in this population.

OBJECTIVE:

To assess the impact of clinical and social factors unique to HIV-infected adults in Saskatoon, Saskatchewan, regarding the rate of CD4⁺ count change, and to identify factors associated with a risk of CD4⁺ count decline.

METHODS:

A retrospective longitudinal cohort study from medical chart reviews at two clinics was conducted in Saskatoon. Univariate and multivariate linear mixed effects models were used to assess the impact of selected factors on CD4⁺ count change.

RESULTS:

Four hundred eleven HIV-infected patients were identified from January 1, 2003 to November 30, 2011. Two hundred eighteen (53%) were male, mean (± SD) age was 35.6 ±10.1 years, 257 (70.8%) were First Nations or Métis, 312 (80.2%) were hepatitis C virus (HCV) coinfected and 300 (73.3%) had a history of injection drug use (IDU). In univariate models, age, ethnicity, HCV, IDU, antiretroviral therapy and social assistance were significant. Using ethnicity, HCV and IDU, three multivariate models (models 1, 2, 3) were built due to high correlation. First Nations or Métis ethnicity, HCV coinfection and a history of IDU were associated with significantly lower CD4⁺ counts in multivariate models. Older age and social assistance were associated with significantly lower CD4⁺ counts in models 1 and 3. Age was marginally significant in model 2 (P=0.055). Not prescribed antiretroviral therapy was associated with a significantly negative CD4⁺ count slope in all multivariate models.

CONCLUSION:

The unique epidemiology of this HIV-infected population may be contributing to CD4⁺ count change. Increased attention and resources focused on this high-risk population are needed to prevent disease progression and to improve overall health and quality of life.

Nonhuman primate models for HIV/AIDS vaccine development

The development of HIV vaccines has been hampered by the lack of an animal model that can accurately predict vaccine efficacy. Chimpanzees can be infected with HIV-1 but are not practical for research. However, several species of macaques are susceptible to the simian immunodeficiency viruses (SIVs) that cause disease in macaques, which also closely mimic HIV in humans. Thus, macaque-SIV models of HIV infection have become a critical foundation for AIDS vaccine development. Here we examine the multiple variables and considerations that must be taken into account in order to use this nonhuman primate (NHP) model effectively. These include the species and subspecies of macaques, virus strain, dose and route of administration, and macaque genetics, including the major histocompatibility complex molecules that affect immune responses, and other virus restriction factors. We illustrate how these NHP models can be used to carry out studies of immune responses in mucosal and other tissues that could not easily be performed on human volunteers. Furthermore, macaques are an ideal model system to optimize adjuvants, test vaccine platforms, and identify correlates of protection that can advance the HIV vaccine field. We also illustrate techniques used to identify different macaque lymphocyte populations and review some poxvirus vaccine candidates that are in various stages of clinical trials. Understanding how to effectively use this valuable model will greatly increase the likelihood of finding a successful vaccine for HIV.

Kruppel-like factor 2 modulates CCR5 expression and susceptibility to HIV-1 infection

CCR5, a cell surface molecule critical for the transmission and spread of HIV-1, is dynamically regulated during T cell activation and differentiation. The molecular mechanism linking T cell activation to modulation of CCR5 expression remains undefined. Kruppel-like factor 2 (KLF2) is a transcription factor that promotes quiescence, survival, and in part by modulating chemokine receptor levels, induces homing to secondary lymphoid organs. Given the relationship between T cell activation and chemokine receptor expression, we tested whether the abundance of KLF2 after T cell activation regulates CCR5 expression and, thus, susceptibility of a T cell to CCR5-dependent HIV-1 strains (R5). We observed a strong correlation between T cell activation, expression of KLF2 and CCR5, and susceptibility to infection. To directly measure how KLF2 affects CCR5 regulation, we introduced small interfering RNA targeting KLF2 expression and demonstrated that reduced KLF2 expression also resulted in less CCR5. Chromatin immunoprecipitation assays identified KLF2 bound to the CCR5 promoter in resting but not CD3/28 activated T cells, suggesting that KLF2 directly regulates CCR5 expression. Introduction of KLF2 under control of a heterologous promoter could restore CCR5 expression and R5 susceptibility to CD3/28 costimulated T cells and some transformed cell lines. Thus, KLF2 is a host factor that modulates CCR5 expression in CD4 T cells and influences susceptibility to R5 infection.

Viral tropism, fitness and pathogenicity of HIV-1 subtype C

The majority of studies on HIV-1 pathogenesis have been conducted on subtype B HIV-1 (B-HIV) strains. However, B-HIV strains constitute the minority of HIV-1 cases worldwide, and are not common in regions that stand to benefit the most from advances in HIV-1 research such as southern Africa and Asia, where the HIV-1 pandemic is at its worst. The majority of individuals with HIV-1 are infected with subtype C HIV-1 (C-HIV) and reside in Southern Africa and Central Asia. Relatively little is known about C-HIV, but current evidence suggests the pathogenesis of C-HIV is distinct from B-HIV and other HIV-1 subtypes. This article summarizes what is currently known about the viral tropism, fitness and pathogenicity of C-HIV, and compares and contrasts these features to B-HIV. A thorough understanding of the molecular pathogenesis of C-HIV is important for a targeted approach to developing vaccines and novel drugs optimized for effectiveness in populations that are most in need.

Association between HIV-1 RNA level and CD4 cell count among untreated HIV-infected individuals

OBJECTIVES

We examined the significance of plasma HIV-1 RNA levels (or viral load alone) in predicting CD4 cell decline in untreated HIV-infected individuals.

METHODS

Data were obtained from the British Columbia Centre for Excellence in HIV/AIDS. Participants included all residents who ever had a viral load determination in the province and who had never taken antiretroviral drugs (N = 890). We analyzed a total of 2074 viral load measurements and 2332 CD4 cell counts. Linear mixed-effects models were used to predict CD4 cell decline over time.

RESULTS

Longitudinal viral load was strongly associated with CD4 cell decline over time; an average of 1 log(10) increase in viral load was associated with a 55-cell/mm(3) decrease in CD4 cell count.

CONCLUSIONS

Our results support the combined use of CD4 cell count and viral load as prognostic markers in HIV-infected individuals before the introduction of antiretroviral therapy.

Patterns of diversity in HIV-related loci among subspecies of chimpanzee: concordance at CCR5 and differences at CXCR4 and CX3CR1

Human immunodeficiency virus type 1 (HIV-1) arose in humans via zoonotic transmissions of simian immunodeficiency viruses (SIV(cpz)) from common chimpanzees, Pan troglodytes. Despite the close relatedness of the two viruses and their hosts, we do not yet understand what causes SIV(cpz) to be nonpathogenic in chimpanzees, and HIV/AIDS to be one of the most devastating infectious diseases to have emerged in humans. There have been a number of genes identified in humans that confer disease resistance/susceptibility toward HIV-1, but little is known about the evolution and diversity of most of these chemokine receptor genes in chimpanzees. Here we show that genetic variation in chimpanzees differs across the various loci related to HIV-1, and that the pattern of variation differs among the chimpanzee subspecies. For all three subspecies, low diversity at CCR5 is confined to a small area of chromosome 3, suggesting that a selective sweep at this locus may have predated subspeciation. In contrast, diversity and neutrality tests suggest differing evolutionary forces among subspecies at CXCR4 and CX(3)CR1, with directional selection (in Pan troglodytes vellerosus) and demographic expansion (Pan troglodytes troglodytes) offering the most likely scenarios. These are some of the first data demonstrating differentiation in functional loci among chimpanzee subspecies.

Significance of variation within HIV, EBV, and KSHV subtypes

Since their initial transmission to humans, viruses have diversified extensively through recombination and mutation. The presence of intra- and inter-individual viral diversity influences disease progression, drug resistance, and therapy and presumably explains the conflicting results in many studies, including the failure of peptide-based vaccination strategies. Although HIV is a small RNA virus, coinfection with large DNA viruses, notably the oncogenic gamma-herpesviridae human herpesvirus-8 and Epstein Barr virus, is common. This coinfection occurs secondary to immunosuppression and shared transmission routes with high-risk predisposing behavior. In addition, all 3 of these viruses can lead to chronic infections, long periods of latency, and reactivation characterized by pain and suffering. The efficient targeting of their genetic diversity represents one of the major challenges in their control, both in prophylactic and therapeutic strategies. An understanding of diversity will help delineate whether population-specific vaccine strategies are necessary.

Polymorphisms in tumor necrosis factor and other cytokines as risks for infectious diseases and the septic syndrome

An increasing number of genetic association studies have implicated polymorphisms of cytokine genes as host genetic factors influencing susceptibility to infectious disease, primarily using a candidate gene approach based on knowledge of disease pathogenesis. The application and limitations of association studies are reviewed together with the impact of recent advances in single nucleotide polymorphism mapping on strategic approaches to defining genetic susceptibility loci. It often remains unclear whether associated genetic polymorphisms are themselves functionally relevant or acting only as markers within an extended haplotype, and experimental approaches to investigating the functional impact of polymorphisms in noncoding regulatory DNA sequences are discussed. An overview of genetic associations of cytokine genes with infectious disease is presented, together with discussion of recent studies in a number of infectious diseases including hepatitis, HIV, malaria, and sepsis.

HIV-1 replication in cell lines harboring INI1/hSNF5 mutations

Background

INI1/hSNF5 is a cellular protein that directly interacts with HIV-1 integrase (IN). It is specifically incorporated into HIV-1 virions. A dominant negative mutant derived from INI1 inhibits HIV-1 replication. Recent studies indicate that INI1 is associated with pre-integration and reverse transcription complexes that are formed upon viral entry into the target cells. INI1 also is a tumor suppressor, biallelically deleted/mutated in malignant rhabdoid tumors. We have utilized cell lines derived from the rhabdoid tumors, MON and STA-WT1, that harbor either null or truncating mutations of INI1 respectively, to assess the effect of INI1 on HIV-1 replication.

Results

We found that while HIV-1 virions produced in 293T cells efficiently transduced MON and STA-WT1 cells, HIV-1 particle production was severely reduced in both of these cells. Reintroduction of INI1 into MON and STA-WT1 significantly enhanced the particle production in both cell lines. HIV-1 particles produced in MON cells were reduced for infectivity, while those produced in STA-WT1 were not. Further analysis indicated the presence of INI1 in those virions produced from STA-WT1 but not from those produced from MON cells. HIV-1 produced in MON cells were defective for synthesis of early and late reverse transcription products in the target cells. Furthermore, virions produced in MON cells were defective for exogenous reverse transcriptase activity carried out using exogenous template, primer and substrate.

Conclusion

Our results suggest that INI1-deficient cells exhibit reduced particle production that can be partly enhanced by re-introduction of INI1. Infectivity of HIV-1 produced in some but not all INI1 defective cells, is affected and this defect may correlate to the lack of INI1 and/or some other proteins in these virions. The block in early events of virion produced from MON cells appears to be at the stage of reverse transcription. These studies suggest that presence of INI1 or some other host factor in virions and reverse transcription complexes may be important for early events of HIV-1 replication.

Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals

Evolution of the HIV-1 V3 loop was monitored in 15 subjects over a period of 5 years at approximately 6-month intervals. Putative recombination was detected in many of the sequences. Evolutionary trees were estimated from the nonrecombinant viral sequences found in each individual. Selection and altered demographic regimes were detected with logit and other contingency analyses in a highly context-dependent fashion. Mutations leading to amino acid substitutions are subject to positive selection over a broad range of clinical conditions in the nonsyncytium-inducing (NSI) form, and the growth rates of the NSI strains and their level of genetic subdivision change little in going from a healthy immune system to a severely compromised immune system. In contrast, the SI form has a significant increase in growth rate as the immune system goes from healthy to compromised, particularly in those subjects who did not receive any antiviral drug therapy. This increase in SI growth rate results in a significant growth advantage of SI over NSI when the immune system is compromised. The SI strains also show more demographic subdivision when the immune system is healthy than when the immune system is compromised, and the SI form has greater demographic subdivision than NSI in subjects with healthy immune systems who also are not receiving antiviral drug therapy. Positive selection on amino-acid-changing mutations weakens and then intensifies again in the SI strains in going from healthy to compromised immune systems. These patterns are consistent with other studies that suggest that NSI strains inhibit replication of SI strains, that the V3 loop is more hidden from the immune system in the NSI form, that evolution in the V3 loop influences cell tropism and coreceptor usage, that substrate for replication of SI forms increases as the disease progresses, and that death of CD8 cells is influenced by the type of coreceptor usage typically found in SI but not in NSI strains. Finally, the transition between NSI and SI forms is associated with a burst of evolutionary change due to strong positive selection at sites other than those that define the NSI/SI phenotypes.

HIV-1 and the hijacking of dendritic cells: a tug of war

Dendritic cells are critical for host immunity and are involved both in the innate and adaptive immune responses. They are among the first cells targeted by HIV-1 in vivo at mucosal sites. Dendritic cells can sequester HIV-1 in endosomal compartments for several days and transmit infectious HIV-1 to interacting T cells in the lymph node, which is the most important site for viral replication and spread. Initially, the cellular immune response developed against HIV-1 is strong, but eventually it fails to control and resolve the infection. The most dramatic effect seen on the immune system during untreated HIV-1 infection is the destruction of helper CD4(+) T cells, which leads to subsequent immune deficiency. However, the immunomodulatory effects of HIV-1 on different dendritic cell subpopulations may also play an important role in the pathogenesis of HIV-1. This review discusses the effects HIV-1 exerts on dendritic cells in vivo and in vitro, including the binding and uptake of HIV by dendritic cells, the formation of infectious synapses, infection, and the role of dendritic cells in HIV-1 pathogenesis.

Possession of human leucocyte antigen DQ6 alleles and the rate of CD4 T-cell decline in human immunodeficiency virus-1 infection

Polymorphism amongst the human leucocyte antigen (HLA) class II genes could influence antigen presentation and the ability to control human immunodeficiency virus (HIV)-1 by modulating the virus specific CD4 immune response. To examine the effect of such polymorphisms on disease progression, we studied a cohort of 46 HIV-1 infected long-term non-progressors (LTNPs), 87 intermediate progressors (IPs) and 26 rapid progressors. Kaplan-Meier survival analysis of all patients in the cohort on time to a CD4 count less than 350 cells/ micro l, showed a trend for a slower rate of CD4 decline in patients with, compared to those without, the DRB1*15-DQB1*06 haplotype (hazard ratio (HR) 0.69, 95% CI 0.46-1.01, P = 0.06). A similar effect was not observed with the DRB1*13-DQB1*06 haplotype (HR 1.18, 95% CI 0.75-1.88, P = 0.46), but was observed when DQB1*06 alleles were considered irrespective of their DR association (HR 0.74, 95% CI 0.52-1.05, P = 0.06). Major HLA-DQ6 alleles encode aspartate (Asp) at position 57 on the DQbeta chain, a phenotype associated with protection from other immune disorders. We therefore examined the frequency of all DQbeta57 Asp+ alleles, but could not detect a significant effect on the rate of CD4 decline. To examine whether the genotype associated with slower CD4 decline was over-represented in patients with a slow rate of disease progression, we conducted a categorical analysis of a subset of patients with an extended follow-up of 14+years. We found a higher proportion of LTNPs at 14+ years possessed the DRB1*15-DQB1*06 haplotype compared to IPs at 14+ years (38.46 versus 18.18%), though this difference did not reach statistical significance. When DQB1*06 alleles irrespective of their DR association were considered, the protective effect was greater (76.9% LTNPs versus 18.18% IPs, P = 0.04). Our results highlight the potential protective effect of HLA DQB1*06 alleles on the course of HIV disease.

Differential gene expression during HIV-1 infection analyzed by suppression subtractive hybridization

OBJECTIVE

Characterization of the effects of HIV-1 infection and apoptosis on cellular and viral gene expression.

METHODS

Flow cytometry was used to analyze infection and apoptosis concurrently in HIV-1IIIB-infected CEM-SS T cells. Suppression subtractive hybridization (SSH) was applied to cells from different time points of infection to construct subtracted complementary DNA (cDNA) libraries. Differential screening and Northern blots confirmed differential gene expression and these genes were sequenced and compared with database.

RESULTS

T cells undergo apoptosis at early stages of HIV-1IIIB infection (days 5-7 post-infection). Surprisingly, cells begin to recover after day 9 and by day 18 almost all infected cells are viable, even though they maintain the same level of infection. By SSH, differential gene expression profiles between day 7 and day 18 after HIV-1IIIB infection were characterized. SSH yielded two subtracted cDNA libraries; differential screening of the subtracted cDNA libraries suggested that 200 out of 864 colonies were highly expressed at their respective time points. DNA sequence analysis identified specific apoptosis-related genes, HIV-1 viral genes, and other candidate genes of interest. Northern blot analysis confirmed that some of these genes were expressed predominantly at the 'apoptotic' or 'non-apoptotic' time points.

CONCLUSIONS

Known and novel cellular gene products have been identified that are directly (or inversely) correlated with apoptosis and may regulate cell death in HIV-1 infection. These results provide a framework for functional studies on the differentially expressed genes and may suggest novel therapeutic approaches for treatment of HIV-1-infected individuals.

Human immunodeficiency virus type 1 fitness is a determining factor in viral rebound and set point in chronic infection

Human immunodeficiency virus type 1 (HIV-1) isolates from 20 chronically infected patients who participated in a structured treatment interruption (STI) trial were studied to determine whether viral fitness influences reestablishment of viremia. Viruses derived from individuals who spontaneously controlled viremia had significantly lower in vitro replication capacities than viruses derived from individuals that did not control viremia after interruption of antiretroviral therapy (ART), and replication capacities correlated with pre-ART and post-STI viral set points. Of note, no clinically relevant improvement of viral loads upon STI occurred. Virus isolates from controlling and noncontrolling patients were indistinguishable in terms of coreceptor usage, genetic subtype, and sensitivity to neutralizing antibodies. In contrast, viruses from controlling patients exhibited increased sensitivity to inhibition by chemokines. Sensitivity to inhibition by RANTES correlated strongly with slower replication kinetics of the virus isolates, suggesting a marked dependency of these virus isolates on high coreceptor densities on the target cells. In summary, our data indicate that viral fitness is a driving factor in determining the magnitude of viral rebound and viral set point in chronic HIV-1 infection, and thus fitness should be considered as a parameter influencing the outcome of therapeutic intervention in chronic infection.

Evidence for Gag p24-specific CD4 T cells with reduced susceptibility to R5 HIV-1 infection in a UK cohort of HIV-exposed-seronegative subjects

AIM

To characterize HIV-1 Gag p24-specific CD4 cell responses in HIV-exposed-seronegative (ES) individuals.

METHODOLOGY

Twelve ES individuals, of diverse ethnicity and wild type for the CCR5 Delta-32 mutation, were identified. Controls were HIV-negative blood donors. Gag p24-specific and total Vbeta+ CD4 cells that expressed MIP-1beta, IFN-gamma and IL-2 were enumerated by intracytoplasmic cytokine staining. beta-Chemokine expression was correlated with susceptibility to R5 HIV-1 infection, as measured by polymerase chain reaction for integrated HIV-1 and by p24 enzyme-linked immunosorbent assay.

RESULTS

Similar numbers of mitogen-stimulated and Vbeta+ MIP-1beta+, IFN-gamma+ and IL-2+ T cells were found in ES and HIV-negative control subjects. However, all ES subjects tested had an HIV Gag p24-specific MIP-1beta+, IFN-gamma+ and IL-2+ CD4 T-cell response that was rare in controls. p24-Specific cells of all ES but no control subjects could be expanded by in-vitro Ag/IL-2 stimulation, and when re-stimulated with an overlapping peptide series showed evidence of a broad CD4 cell memory response directed against multiple regions of Gag p24. Mitogen-stimulated ES CD4 cells were as susceptible to HIV infection as those from control subjects, but p24-specific IFN-gamma+ CD4 cells of six out of seven ES subjects tested were less susceptible to R5 HIV-1 infection than the counterpart fraction depleted of p24-specific IFN-gamma+ cells. The addition of blocking anti-beta-chemokine antibodies did not promote R5 HIV-1 infection of p24-specific IFN-gamma+ cells.

CONCLUSION

Specific CD4 cell immunity, characterized by a broadly directed memory Gag-p24 CD4 cell response and reduced susceptibility of specific CD4 cells to R5 HIV-1 infection, is a likely correlate of non-transmission.

HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation

Worldwide, 90% of HIV-1 infections are transmitted heterosexually. Because the genital mucosa are the sites of initial contact with HIV-1 for most exposed individuals, study of the virus from the genital tract is critical for the development of vaccines and therapeutics. Previous analyses of HIV-1 in various tissues have documented compartmentalization of viral genomes. Whether compartmentalization was associated with viral phenotypic differences or immune status, however, was not well understood. We compared HIV-1 gp120 env sequences from the genital tract and plasma of 12 women. Eight women displayed compartmentalized HIV-1 RNA genomes, with viral sequences from each site that were clearly discrete, yet phylogenetically related. The remaining four exhibited env sequences that were intermingled between the two sites. Women with compartmentalized HIV-1 genomes had higher CD4+ cell counts than those displaying intermingled strains (P = 0.02). Intrapatient HIV-1 recombinants comprising sequences that were characteristic of both sites were identified. We next compared viral phenotypes in each compartment. HIV-1 coreceptor usage was often compartmentalized (P 0.01). The number of N-linked glycosylation sites, associated with neutralization resistance, also differed between compartments (P < 0.01). Furthermore, disparities between the density of gp120 glycosylations in each compartment correlated with higher CD4+ counts (P = 0.03). These data demonstrate that the genital tract and plasma can harbor populations of replicating HIV-1 with different phenotypes. The association of higher CD4+ cell counts with compartmentalization of viral genomes and density of gp120 glycosylations suggests that the immune response influences the development of viral genotypes in each compartment. These findings are relevant to the prevention and control of HIV-1 infection.

Psycho-Endocrine-Immune Response to Mindfulness-Based Stress Reduction in Individuals Infected with the Human Immunodeficiency Virus: A Quasiexperimental Study

OBJECTIVES

The purpose of this study was to examine the effects of a structured, 8-week, Mindfulness-Based Stress Reduction (MBSR) program on perceived stress, mood, endocrine function, immunity, and functional health outcomes in individuals infected with the human immunodeficiency virus (HIV).

DESIGN

This study used a quasiexperimental, nonrandomized design.

METHODS

Subjects were specifically recruited (nonrandom) for intervention (MBSR) or comparison group. Data were collected at pretest and post-test in the MBSR group and at matched times in the comparison group. t Tests where performed to determine within-group changes and between-group differences.

RESULTS

Natural killer cell activity and number increased significantly in the MBSR group compared to the comparison group. No significant changes or differences were found for psychological, endocrine, or functional health variables.

CONCLUSIONS

These results provide tentative evidence that MBSR may assist in improving immunity in individuals infected with HIV.

Polymorphism of human and primate RANTES, CX3CR1, CCR2 and CXCR4 genes with regard to HIV/SIV infection

Among genes that influence human susceptibility to HIV (human immunodeficiency virus) infection or AIDS (acquired immunodeficiency syndrome) progression, chemokine-receptor and chemokine genes were extensively studied because of their role as HIV co-receptors or co-receptor competitors, respectively. We have studied in non-human primates (chimpanzee, gorilla, gibbon, orang-utan, crab-eating and rhesus macaque, baboon and marmoset) the RANTES, CCR2 and CX3CR1 gene sequences in regions surrounding human mutations that were associated with susceptibility to HIV or AIDS progression: RANTES G-403A and C-28G, CCR2 V64I, CX3CR1 V249I and CX3CR1 T280M. Among these five dimorphisms, only RANTES G-403A is observed in one of the eight primate species studied here (gibbon). This suggests that these mutations appeared recently in humans and probably do not account for variable HIV/SIV disease progression in primates. It is noteworthy that chimpanzees, which are naturally resistant to HIV-1- and HIV-2-induced AIDS, do not have the human mutations associated with delayed disease progression. Inter-species and intra-species polymorphic positions are observed in primates and we discuss the potential impact of these mutations on HIV/SIV disease progression. Particularly, we identified polymorphisms in old-world monkey (OWM) genes, and it could be of great importance to analyse the possible association between these polymorphisms and disease progression in OWM species that are currently used in research for HIV vaccine and therapy.

The race between initial T-helper expansion and virus growth upon HIV infection influences polyclonality of the response and viral set-point

Infection with HIV is characterized by very diverse disease-progression patterns across patients, associated with a wide variation in viral set-points. Progression is a multifactorial process, but an important role has been attributed to the HIV-specific T-cell response. To explore the conditions under which different set-points may be explained by differences in initial CD4 and CD8 T-cell responses and virus inoculum, we have formulated a model assuming that HIV-specific CD4 cells are both targets for infection and mediators of a monoclonal or polyclonal immune response. Clones differ in functional avidity for HIV epitopes. Importantly, in contrast to previous models, in this model we obtained coexistence of multiple clones at steady-state viral set-point, as seen in HIV infection. We found that, for certain parameter conditions, multiple steady states are possible: with few initial CD4 helper cells and high virus inoculum, no immune response is established and target-cell-limited infection follows, with associated high viral load; when CD4 clones are initially large and virus inoculum is low, infection can be controlled by several clones. The conditions for the dependence of viral set-point on initial inoculum and CD4 T-helper clone availability are investigated in terms of the effector mechanism of the clones involved.

The role of dendritic cells in the pathogenesis of HIV-1 infection

Dendritic cells are professional antigen-presenting cells required for generation of adaptive immunity. These cells are one of the initial target cells for HIV-1 infection or capture of virions at site of transmission in the mucosa. DCs carrying HIV-1 will migrate to the lymphoid tissue where they can contribute to the dissemination of the virus to adjacent CD4+ T cells. In addition, HIV-1-exposed DCs may have impaired antigen-presenting capacity resulting in inadequate expansion of HIV-1-specific T cell responses. Here, we review the infection of different subtypes of DCs by HIV-1 and the relevance of these cells in the transmission and establishment of HIV-1 disease. In addition, we discuss the mechanisms through which HIV-1-DC interactions could be exploited to optimise the generation and maintenance of HIV-1-specific T cell immunity.

New insights into the immunology and evolution of HIV

Fewer than one million HIV infected individuals are currently receiving anti-retroviral therapy. The limitations of such treatment have underscored the need to develop more effective strategies to control the spread and pathogenesis of HIV. Typically, naturally occurring protective immune responses provide the for such development. It is now clear however that HIV can utilise the milieu of an activated immune system to its own replicative advantage. Mobilisation of the immune response, intended to thwart the virus, may instead fuel its dissemination, 'immune escape' and spread. The immense genetic variation of HIV contributes to lack of immune control and the development of progressive disease in the majority of infected, untreated individuals. Further delineation of the intimate interactions between the HIV and the immune system will be critical and recent advances in this direction are discussed.

Mamu-A*01 allele-mediated attenuation of disease progression in simian-human immunodeficiency virus infection

Expression of several major histocompatibility complex (MHC) class I alleles is associated with a protective effect against disease progression in both human immunodeficiency virus type 1 and simian immunodeficiency virus infection. To understand the mechanism underlying this effect, we investigated the expression of the MHC class I allele Mamu-A*01 in simian-human immunodeficiency virus (SHIV) infection, one of the major models for evaluation of AIDS vaccine candidates. We found that disease progression was significantly delayed in Mamu-A*01-positive rhesus monkeys infected with the highly pathogenic SHIV 89.6P. The delay corresponded not only to a noted Mamu-A*01-restricted dominant cytotoxic T-lymphocyte (CTL) response but also to a lower viral load in lymph nodes (LN) and, importantly, to minimal destruction of LN structure during early infection. In contrast, Mamu-A*01-negative monkeys exhibited massive destruction of LN structure with accompanying rapid disease progression. These data indicate that MHC class I allele-restricted CTL responses may play an important role in preservation of lymphoid tissue structure, thereby resulting in attenuation of disease progression in immunodeficiency virus infection.

Consistent patterns in the development and immunodominance of human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses following acute HIV-1 infection

Human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T-cell responses generated during acute infection play a critical role in the initial control of viremia. However, little is known about the viral T-cell epitopes targeted during acute infection or about their hierarchy in appearance and relative immunodominance over time. In this study, HIV-1-specific CD8+ T-cell responses in 18 acutely infected individuals expressing HLA-A3 and/or -B7 were characterized. Detailed analysis of CD8 responses in one such person who underwent treatment of acute infection followed by reexposure to HIV-1 through supervised treatment interruptions (STI) revealed recognition of only two cytotoxic T-lymphocyte (CTL) epitopes during symptomatic acute infection. HIV-1-specific CD8+ T-cell responses broadened significantly during subsequent exposure to the virus, ultimately targeting 27 distinct CTL epitopes, including 15 different CTL epitopes restricted by a single HLA class I allele (HLA-A3). The same few peptides were consistently targeted in an additional 17 persons expressing HLA-A3 and/or -B7 during acute infection. These studies demonstrate a consistent pattern in the development of epitope-specific responses restricted by a single HLA allele during acute HIV-1 infection, as well as persistence of the initial pattern of immunodominance during subsequent STI. In addition, they demonstrate that HIV-1-specific CD8+ T-cell responses can ultimately target a previously unexpected and unprecedented number of epitopes in a single infected individual, even though these are not detectable during the initial exposure to virus. These studies have important implications for vaccine design and evaluation.

Coreceptor phenotype of natural human immunodeficiency virus with nef deleted evolves in vivo, leading to increased virulence

The Sydney Blood Bank Cohort is a group of patients with slowly progressive infection by a human immunodeficiency virus strain containing spontaneous deletions within the nef long terminal repeat region. In 1999, 18 years after the initial infection, one of the members (D36) developed AIDS. In this work, we used an ex vivo human lymphoid cell culture system to analyze two viral isolates obtained from this patient, one prior to the onset of AIDS in 1995 and one after disease progression in 1999. Both D36 isolates were less potent in depleting CD4(+) T cells than a reference dualtropic, nef-bearing viral isolate. However, the 1999 isolate was measurably more cytotoxic to CD4(+) T cells than the 1995 isolate. Interestingly, although both isolates were nearly equally potent in depleting CCR5(+) CD4(+) T cells, the cytotoxic effect of the 1999 isolate toward CCR5(-) CD4(+) T cells was significantly higher. Furthermore, GHOST cell infection assays and blocking experiments with the CXCR4 inhibitor AMD3100 showed that the later D36 1999 isolate could infect both CCR5(+) and CCR5(-) CXCR4(+) cells efficiently, while infection by the 1995 isolate was nearly completely restricted to CCR5(+) cells. Sequence analysis of the V1/V2 and V3 regions of the viral envelope protein gp120 revealed that the more efficient CXCR4 usage of the later isolate might be caused by an additional potential N-glycosylation site in the V1/V2 loop. In conclusion, these data show that an in vivo evolution of the tropism of this nef-deleted strain toward an X4 phenotype was associated with a higher cytopathic potential and progression to AIDS.

Recovery of replication-competent HIV type 1-infected circulating monocytes from individuals receiving antiretroviral therapy

The affect of antiretroviral therapy (ART) on HIV-1 recovery from blood monocytes was determined in purified peripheral blood monocyte-derived macrophage (MDM) cultures from HIV-1-infected subjects with undetectable plasma viremia or active viral replication. Additionally, the association between replication-competent HIV-1-infected MDM and neurocognitive status was examined. Fifty-two individual with previous AIDS-defining illnesses receiving nucleoside analogues with and without protease inhibitors or no ART were followed for up to 1.5 years. Detection of plasma viremia significantly correlated with the occurrence of infected monocytes. Viral replication was detected in less than 10% of the MDM cultures from 23 individuals receiving effective antiretroviral therapy. In contrast, approximately 50% of the MDM cultures from 29 individuals with active viral replication and evidence of decreased immune function, including all individuals with neurocognitive impairment, produced detectable virus indicating that a lack of adequate ART results in increased abundance of replication-competent blood monocytes. Proviral DNA levels were a minimum of 13-fold higher in MDM from subjects with active viral replication. The infrequent detection of viral DNA in cultures from individuals receiving effective ART suggested low levels of circulating monocytes harboring replication-incompetent virus. These studies demonstrate that HIV-infected individuals on ART with breakthrough viremia have significantly higher levels of circulating infected monocytes, the precursors of tissue macrophages.

Important contribution of p15 Gag-specific responses to the total Gag-specific CTL responses

OBJECTIVES

HIV-1 p15 Gag and its protease cleavage products, NCp7 and p6, are believed to play a major role in viral infectivity and assembly during the early and late stages of the retroviral life cycle. However, the extent to which p15 Gag is targeted by the host immune system in natural infection as well as precise cytotoxic T lymphocyte (CTL) epitopes within this protein remains to be defined.

METHODS

In this study, 57 HIV-1 infected individuals and 10 HIV-1 negative controls were screened for CD8 and CD4 T-cell responses using overlapping peptides spanning the entire p15 Gag protein as well as the p17 Gag and p24 Gag proteins. Peptide-specific interferon-gamma production was measured by Elispot assay and flow-based intracellular cytokine quantification, and cytotoxic activity was confirmed after isolation of peptide-specific CD8 T-cell lines.

RESULTS

CD8 T lymphocytes specific to p15 Gag were found in 46% (26/57) of HIV-1 infected individuals studied and contributed on average 17% (range, 0-100%) to the total Gag-specific T-cell responses. Responses were clustered within three immunodominant regions of p15 Gag, mapping to important functional sites. These studies also include the description of the first three optimally defined CTL epitopes within p15 Gag.

CONCLUSIONS

These results indicate that p15 Gag is frequently recognized by HIV-1-specific CD8 T cells in HIV-1 infection and will be important in the comprehensive assessments of CTL responses in infected persons, as well as the design and testing of future HIV-1 vaccines and immunotherapeutic interventions.