Pathogenesis Of HIV Infection Research Articles

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

We have developed a full genome virus detection process that combines sensitive nucleic acid preparation optimised for virus identification in fecal material with Illumina MiSeq sequencing and a novel post-sequencing virus identification algorithm. Enriched viral nucleic acid was converted to double-stranded DNA and subjected to Illumina MiSeq sequencing. The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. De novo assembly was then used to generate full viral genomes. The sensitivity of this process was demonstrated with a set of fecal samples from HIV-1 infected patients. A quantitative assessment of the mammalian, plant, and bacterial virus content of this compartment was generated and the deep sequencing data were sufficient to assembly 12 complete viral genomes from 6 virus families. The method detected high levels of enteropathic viruses that are normally controlled in healthy adults, but may be involved in the pathogenesis of HIV-1 infection and will provide a powerful tool for virus detection and for analyzing changes in the fecal virome associated with HIV-1 progression and pathogenesis.

Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective

Why some individuals develop AIDS rapidly whereas others remain healthy without treatment for many years remains a central question of HIV research. An evolutionary perspective reveals an apparent conflict between two levels of selection on the virus. On the one hand, there is rapid evolution of the virus in the host, and on the other, new observations indicate the existence of virus factors that affect the virulence of infection whose influence persists over years in infected individuals and across transmission events. Here, we review recent evidence that shows that viral genetic factors play a larger role in modulating disease severity than anticipated. We propose conceptual models that reconcile adaptive evolution at both levels of selection. Evolutionary analysis provides new insight into HIV pathogenesis.

Complement and HIV-I infection/HIV-associated neurocognitive disorders

The various neurological complications associated with HIV-1 infection, specifically HIV-associated neurocognitive disorders (HAND) persist as a major public health burden worldwide. Despite the widespread use of anti-retroviral therapy, the prevalence of HAND is significantly high. HAND results from the direct effects of an HIV-1 infection as well as secondary effects of HIV-1-induced immune reaction and inflammatory response. Complement, a critical mediator of innate and acquired immunity, plays important roles in defeating many viral infections by the formation of a lytic pore or indirectly by opsonization and recruitment of phagocytes. While the role of complement in the pathogenesis of HIV-1 infection and HAND has been previously recognized for over 15years, it has been largely underestimated thus far. Complement can be activated through HIV-1 envelope proteins, mannose-binding lectins (MBL), and anti-HIV-1 antibodies. Complement not only fights against HIV-1 infection but also enhances HIV-1 infection. In addition, HIV-1 can hijack complement regulators such as CD59 and CD55 and can utilize these regulators and factor H to escape from complement attack. Normally, complement levels in brain are much lower than plasma levels and there is no or little complement deposition in brain cells. Interestingly, local production and deposition of complement are dramatically increased in HIV-1-infected brain, indicating that complement may contribute to the pathogenesis of HAND. Here, we review the current understanding of the role of complement in HIV-1 infection and HAND, as well as potential therapeutic approaches targeting the complement system for the treatment and eradications of HIV-1 infection.

Multiparametric Bioinformatics Distinguish the CD4/CD8 Ratio as a Suitable Laboratory Predictor of Combined T Cell Pathogenesis in HIV Infection

HIV disease progression is characterized by numerous pathological changes of the cellular immune system. Still, the CD4 cell count and viral load represent the laboratory parameters that are most commonly used in the clinic to determine the disease progression. In this study, we conducted an interdisciplinary investigation to determine which laboratory parameters (viral load, CD4 count, CD8 count, CD4 %, CD8 %, CD4/CD8) are most strongly associated with pathological changes of the immune system. Multiparametric flow cytometry was used to assess markers of CD4(+) and CD8(+) T cell activation (CD38, HLA-DR), exhaustion (PD-1, Tim-3), senescence (CD28, CD57), and memory differentiation (CD45RO, CD27) in a cohort of 47 untreated HIV-infected individuals. Using bioinformatical methods, we identified 139 unique populations, representing the "combined T cell pathogenesis," which significantly differed between the HIV-infected individuals and healthy control subjects. CD38, HLA-DR, and PD-1 were particularly expressed within these unique T cell populations. The CD4/CD8 ratio was correlated with more pathological T cell populations (n = 10) and had a significantly higher average correlation coefficient than any other laboratory parameters. We also reduced the dimensionalities of the 139-unique populations by Z-transformations and principal component analysis, which still identified the CD4/CD8 ratio as the preeminent surrogate of combined T cell pathogenesis. Importantly, the CD4/CD8 ratio at baseline was shown to be significantly associated with CD4 recovery 2 y after therapy initiation. These results indicate that the CD4/CD8 ratio would be a suitable laboratory predictor in future clinical and therapeutic settings to monitor pathological T cell events in HIV infection.

Differential Blood and Mucosal Immune Responses against an HIV-1 Vaccine Administered via Inguinal or Deltoid Injection

Mucosal immunity is central to sexual transmission and overall pathogenesis of HIV-1 infection, but the ability of vaccines to induce immune responses in mucosal tissue compartments is poorly defined. Because macaque vaccine studies suggest that inguinal (versus limb) vaccination may better target sexually-exposed mucosa, we performed a randomized, double-blinded, placebo-controlled Phase I trial in HIV-1-uninfected volunteers, using the recombinant Canarypox (CP) vaccine vCP205 delivered by different routes. 12 persons received vaccine and 6 received placebo, divided evenly between deltoid-intramuscular (deltoid-IM) or inguinal-subcutaneous (inguinal-SC) injection routes. The most significant safety events were injection site reactions (Grade 3) in one inguinal vaccinee. CP-specific antibodies were detected in the blood of all 12 vaccinees by Day 24, while HIV-1-specific antibodies were observed in the blood and gut mucosa of 1/9 and 4/9 evaluated vaccinees respectively, with gut antibodies appearing earlier in inguinal vaccinees (24–180 versus 180–365 days). HIV-1-specific CD8+ T lymphocytes (CTLs) were observed in 7/12 vaccinees, and blood and gut targeting were distinct. Within blood, both deltoid and inguinal responders had detectable CTL responses by 17–24 days; inguinal responders had early responses (within 10 days) while deltoid responders had later responses (24–180 days) in gut mucosa. Our results demonstrate relative safety of inguinal vaccination and qualitative or quantitative compartmentalization of immune responses between blood and gut mucosa, and highlight the importance of not only evaluating early blood responses to HIV-1 vaccines but also mucosal responses over time.Trial RegistrationClinicalTrials.gov NCT00076817

A refined parameter estimating approach for HIV dynamic model

HIV dynamic models, a set of ordinary differential equations (ODEs), have provided new understanding of the pathogenesis of HIV infection and the treatment effects of antiviral therapies. However, to estimate parameters for ODEs is very challenging due to the complexity of this nonlinear system. In this article, we propose a comprehensive procedure to deal with this issue. In the proposed procedure, a series of cutting-edge statistical methods and techniques are employed, including nonparametric mixed-effects smoothing-based methods for ODE models and stochastic approximation expectation–maximization (EM) approach for mixed-effects ODE models. A simulation study is performed to validate the proposed approach. An application example from a real HIV clinical trial study is used to illustrate the usefulness of the proposed method.

Immune Activation and the Role of TLRs and TLR Agonists in the Pathogenesis of HIV-1 Infection in the Humanized Mouse Model

Immune activation plays a critical role in HIV-1 pathogenesis, but the pathways that are responsible for HIV-1-associated immune activation are not well understood. Recent advances in the development of a humanized mouse model for HIV-1 infection might provide new approaches to study the mechanisms of HIV-1 associated immune activation, and to test interventions aimed at reducing HIV-1 pathogenesis.

Hybrid Bayesian inference on HIV viral dynamic models

Modelling of HIV dynamics in AIDS research has greatly improved our understanding of the pathogenesis of HIV-1 infection and guided for the treatment of AIDS patients and evaluation of antiretroviral therapies. Some of the model parameters may have practical meanings with prior knowledge available, but others might not have prior knowledge. Incorporating priors can improve the statistical inference. Although there have been extensive Bayesian and frequentist estimation methods for the viral dynamic models, little work has been done on making simultaneous inference about the Bayesian and frequentist parameters. In this article, we propose a hybrid Bayesian inference approach for viral dynamic nonlinear mixed-effects models using the Bayesian frequentist hybrid theory developed in Yuan [Bayesian frequentist hybrid inference, Ann. Statist. 37 (2009), pp. 2458–2501]. Compared with frequentist inference in a real example and two simulation examples, the hybrid Bayesian approach is able to improve the inference accuracy without compromising the computational load.

Avances recientes en HIV/SIDA: Patogénesis, historia natural y carga viral.

Results of recent investigations have given us a new understanding of the pathogenesis of HIV infection. This findings provide us with a kinetic model of pathogenesis in which continuous, high-grade viral replication. This findings provide us with a kinetic model of pathogenesis in which continuous, high-grade viral replication is the principal force driving the destruction of CD4 lymphocytes. This knowledge will lead us to design better treatment strategies directed to curtail viral replication and prevent the emergence of viral resistance, and the use of combination antiretroviral therapy is a first example of these new strategies. The concept of viral load is introduced, and we discuss the usefulness of viral load in the clinical prognosis of this disease, and its use as an aid in the decision-making process when starling or mordifyng antiretroviral therapy in our patients.

Variants in ZNRD1 Gene Predict HIV-1/AIDS Disease Progression in a Han Chinese Population in Taiwan

Patients demonstrate notable variations in disease progression following human immunodeficiency virus (HIV) infection. We aimed to identify ZNRD1 and RNF39 genetic variants linked to AIDS progression. We conducted a genetic association study in HIV-1-infected Han Chinese patients residing in Taiwan. The clinical characteristics of 143 HIV-1-infected patients were measured, and patients were split into 2 groups: AIDS progression and AIDS non-progression. Genotyping of ZNRD1 and RNF39 was performed in all participants. We found that patients in the AIDS progression group had higher HIV-1 viral loads and lower CD4 cell counts than did patients in the AIDS non-progression group. The frequency of the AA genotype of ZNRD1 (rs16896970) was lower in the AIDS progression group than in the AIDS non-progression group. Patients with AA genotypes had lower levels of HIV-1 viral loads and higher levels of CD4 cell counts than did patients with AG+GG genotypes. AIDS progression in patients with the AA group is significantly different from that in patients with the AG and GG groups by using Kaplan-Meier survival analysis. The hazard ratio for progression was lower in the AA group than in the AG and GG groups. We identified a SNP that contributes to AIDS progression in HIV-1-infected patients in this population. This SNP had a significant protective influence on AIDS progression, and polymorphisms of the ZNRD1 gene may play a role in the pathogenesis of HIV-1 infection.

Pathogenesis of HIV infection

Over the past three decades of intense research on the contribution of viral and host factors determining the variability in HIV-1 infection outcome, HIV pathogenesis is still a fascinating topic that requires further study. An understanding of the exact mechanism of how these factors influencing HIV pathogenesis is critical to the development of effective strategies to prevent infection. Significant progress has been made in identifying the role of CCR5 (R5) and CXCR4 (X4) HIV strains in disease progression, particularly with the persistence of R5 HIV-1 strains at the AIDS stage. This indicates that R5 strains are as fit as X4 in causing CD4+ T cell depletion and in contribution to disease outcome, and so questions the prerequisite of the shift from R5 to X4 for disease progression. In contrast, the ability of certain HIV strains to readily use CXCR4 for infection or entry into macrophages, as the case with viruses are homozygous for tropism by CCR5delta32. This raises another major paradox in HIV pathogenesis about the source of X4 variants and how do they emerge from a relatively homogeneous R5 viral population after transmission. The interactions between viral phenotypes, tropism and co-receptor usage and how they influence HIV pathogenesis are the main themes addressed in this review. A better understanding of the viral and host genetic factors involved in the fitness of X4 and R5 strains of HIV-1 may facilitate development of specific inhibitors against these viral populations to at least reduce the risk of disease progression.

The p38 MAPK NF-κB pathway, not the ERK pathway, is involved in exogenous HIV-1 Tat-induced apoptotic cell death in retinal pigment epithelial cells

The mechanism through which human immunodeficiency virus (HIV) infection causes retinal disease and the loss of vision in AIDS patients remains unknown. The HIV-1 transactivator protein Tat (HIV-1 Tat) plays a pivotal role in the pathogenesis of HIV-1 infection and is often described as pleiotropic at different concentrations. In a previous study, we demonstrated that the HIV-1 Tat protein can disrupt the barrier function of retinal pigment epithelium (RPE) at 100nM without affecting cell viability. The present study was undertaken to determine if HIV-1 Tat can induce RPE cell death at different concentrations and to determine the mechanism of any observed cell death. The results demonstrated that two RPE cell lines (ARPE-19 and D407) treated with Tat at concentrations of 200nM and above exhibited reduced growth and apoptosis in a dose- and time-dependent manner. The disruption of mitochondrial outer membrane permeabilisation, the activation of caspase-3/7 and 9, the downregulation of Bcl-2, the upregulation of Bax, and the activation of p38 MAPK, ERK and NF-κB were all observed in HIV-1 Tat-treated RPE cells. When exposed to an inhibitor or transfected with siRNA of p38 MAPK and NF-κB, the level of cell death and deregulation of the expression of the apoptotic protein were attenuated. These effects were not observed with an ERK inhibitor or siRNA. Based on these results, we suggest that the induction of apoptosis by HIV-1 Tat in RPE cells may be mediated by p38 MAPK and NF-κB activation and involve the mitochondrial pathway. Therefore, these pathways may provide clues leading to novel therapeutic approaches for the retinopathy induced by HIV infection.

Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics

Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS) were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.

Longitudinal Changes of Peripheral Blood DC Subsets and Regulatory T Cells in Chinese Chronic HIV-1-Infected Patients during Antiretroviral Therapy

It has been emphasized that chronic generalized immune dysfunction is the leading event in the pathogenesis of HIV infection, in which the contribution of dendritic cells (DCs) and regulatory T cells (Tregs) should not be underestimated. In current study, we assessed the longitudinal changes of peripheral blood DC subsets and Tregs in chronically asymptomatic treatment-naive HIV-1-infected patients during 60 weeks of antiretroviral therapy (ART), and compared with those in healthy controls and long term non-progressors (LTNPs). Blood samples were collected at week 0, 4, 12, 24, 48 and 60 of treatment to measure the counts of DC subsets and Tregs by flow cytometry and IFN-a plasma levels by ELISA. The counts of myeloid dendritic cells (mDCs) increased during ART, reaching similar levels to healthy controls at week 60 post ART but still lower than those of LTNPs. In HIV-1-infected patients, the mDCs counts were directly correlated with CD4 counts during ART. Changes in mDCs at week 8 were positively correlated with the changes in CD4 counts at week 60 post ART. However, the counts and function of plasmacytoid dendritic cells (pDCs) remained relatively stable during ART, and similar to those in healthy controls and LTNPs. The percentage of Tregs increased before ART and normalized after ART. Importantly, we found pDCs counts were associated with percentage of Tregs during ART, which may help in understanding of the role of these cells in HIV infection.

The properties and role of tumor necrosis factor alpha in the pathogenesis of HIV infection

This review presents the current understanding regarding the tumor necrosis factor alpha: its origin, receptors, main properties and its role in the pathogenesis of HIV infection (the infection, caused by the Human Immunodeficiency Virus). Tumor necrosis factor alpha induces viral replication in CD4+ T lymphocytes, monocytes and macrophages, promotes death of uninfected CD4+ T lymphocytes as well as CD8+ by the mechanism of apoptosis, allowing the progression of immunodeficiency. Tumor necrosis factor alpha maintains the viability of infected CD4+ T lymphocytes, contributing to the formation of the viral reservoir in the patient. Elevated levels of the tumor necrosis factor alpha in the blood plasma of HIV-infected individuals should be regarded as a marker of disease progression.

Genomic HIV RNA Induces Innate Immune Responses through RIG-I-Dependent Sensing of Secondary-Structured RNA

BackgroundInnate immune responses have recently been appreciated to play an important role in the pathogenesis of HIV infection. Whereas inadequate innate immune sensing of HIV during acute infection may contribute to failure to control and eradicate infection, persistent inflammatory responses later during infection contribute in driving chronic immune activation and development of immunodeficiency. However, knowledge on specific HIV PAMPs and cellular PRRs responsible for inducing innate immune responses remains sparse.Methods/Principal FindingsHere we demonstrate a major role for RIG-I and the adaptor protein MAVS in induction of innate immune responses to HIV genomic RNA. We found that secondary structured HIV-derived RNAs induced a response similar to genomic RNA. In primary human peripheral blood mononuclear cells and primary human macrophages, HIV RNA induced expression of IFN-stimulated genes, whereas only low levels of type I IFN and tumor necrosis factor α were produced. Furthermore, secondary structured HIV-derived RNA activated pathways to NF-κB, MAP kinases, and IRF3 and co-localized with peroxisomes, suggesting a role for this organelle in RIG-I-mediated innate immune sensing of HIV RNA.Conclusions/SignificanceThese results establish RIG-I as an innate immune sensor of cytosolic HIV genomic RNA with secondary structure, thereby expanding current knowledge on HIV molecules capable of stimulating the innate immune system.

Role of G protein-Coupled Vasoactive Intestinal Peptide Receptors in HIV Integration

The pathogenesis of HIV infection is closely linked to the replication of the virus in vivo. Even though the progress in anti-HIV-1 chemotherapy in the past several years has been dramatic, the efficient protection against HIV-1 infection still remains one of the most important global challenges. The complete blockage of AIDS progression appears to be difficult with current treatment due to the rapid occurrence of viral drug-resistance, increasing cost and the likelihood of adverse side effects. Furthermore, although originally regarded with high hope, development of a suitable vaccine appears to be years away. The purpose of this article is to describe previous findings regarding a potentially important role of the vasoactive intestinal peptide/pituitary adenylate cyclase-activating polypeptide (VPAC) family of G protein-coupled receptors in HIV-1 infection, to provide evidence for the involvement of these receptors in providing signals that can control the integration of the virus into the host DNA and to report new findings that support a role for VPAC receptors in the facilitation of HIV integration.

CD8-EOMEShigh T cells define a subpopulation of CD8 memory cells that restore CD127high expression after cART treatment in HIV infected patients. (105.27)

Abstract After acute viral infection a small population of effector CD8 T cells upregulate CD127 expression and develop into long lived resting memory T cells. During chronic infections, such as HIV, there is an accumulation of CD8 T cells with effector/memory-like phenotype. These observations led to the hypothesis that there is a developmental impairment in the long lived resting memory T cells within that setting. The transcription factors RUNX3 and Eomesodermin (EOMES) are important in the development of long lived memory CD8 T cells. We studied the dynamics of CD127 expression, RUNX3 and EOMES in patients with HIV infection and different levels of viremia. Consistent with other reports, CD127 expression was decreased in the memory CD8 T cell subset. The CD8 memory CD127low T cells showed increased expression of RUNX3 and EOMES mRNA, as well as effector molecules perforin and granzyme B. In patients with suppressed viremia, we could identify two populations of CD8 T cells expressing EOMEShigh and EOMESint. The EOMESint cells showed a short-lived effector phenotype (perforin+, granzyme B+, CD127low) and the EOMEShigh cells showed a memory-like phenotype (perforin-, CD127high). These results suggest that in human CD8 T cells, EOMES is necessary for the maintenance of long lived memory CD8 T cells and its expression was influenced by HIV-RNA levels and the associated inflammatory environment (R=0.4, p=0.01). These findings provide new insights into the pathogenesis of HIV infection.

Characterization of HIV Type 1 env Gene in Cerebrospinal Fluid and Blood of Infected Chinese Patients

HIV infection in the central nervous system (CNS) can progress to AIDS dementia complex; currently, little information on the characterization of the HIV-1 env gene from the CNS is available in infected Chinese patients. In the study, the C2-V5 regions of the HIV envelope gene were cloned and sequenced from both cerebrospinal fluid (CSF) and blood samples of five infected Chinese patients. Sequence analysis revealed that the sequences from Yunan province clustered closely with subtypes CRF07_BC, CRF08_BC, and C, and the sequences from blood showed a significantly higher divergence from those from the CSF. In addition, as predicted by the 11/25 charge rule and geno2pheno program, most of the HIV viral quasispecies from both CSF and blood use CCR5 as coreceptor. These data provide valuable information on a detailed evaluation of the pathogenesis of HIV infection in different tissues of Chinese HIV-infected patients, and our findings would be helpful for the design of vaccines and therapy strategies.

Morphine Potentiates Neuropathogenesis of SIV Infection in Rhesus Macaques

Despite the advent of antiretroviral therapy, complications of HIV-1 infection with concurrent drug abuse are an emerging problem. Opiates are well known to modulate immune responses by preventing the development of cell-mediated immune responses. Their effect on the pathogenesis of HIV-1 infection however remains controversial. Using the simian immunodeficiency virus/macaque model of HIV pathogenesis, we sought to explore the impact of morphine on disease progression and pathogenesis. Sixteen rhesus macaques were divided into two groups; four were administered saline and 12 others morphine routinely. Both groups of animals were then inoculated with SIVmacR71/17E and followed longitudinally for disease pathogenesis. The morphine group (M+V) exhibited a trend towards higher mortality rates and retardation in weight gain compared to the virus-alone group. Interestingly, a subset of M+V animals succumbed to disease within weeks post-infection. These rapid progressors also exhibited a higher incidence of other end-organ pathologies. Despite the higher numbers of circulating CD4+ and CD8+ T cells in the M+V group, CD4/CD8 ratios between the groups remained unchanged. Plasma and CSF viral load in the M+V group was at least a log higher than the control group. Similarly, there was a trend toward increased virus build-up in the brains of M+V animals compared with controls. A novel finding of this study was the increased influx of infected monocyte/macrophages in the brains of M+V animals.