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1.  Exercise Training Reduces Central Adiposity and Improves Metabolic Indices in HAART-Treated HIV-Positive Subjects in Rwanda: A Randomized Controlled Trial 
As HAART becomes more accessible in sub-Saharan Africa, metabolic syndromes, body fat redistribution (BFR), and cardiovascular disease may become more prevalent. We conducted a 6-month, randomized controlled trial to test whether cardiorespiratory exercise training (CET), improves metabolic, body composition and cardiorespiratory fitness parameters in HAART-treated HIV+ African subjects with BFR. Six months of CET reduced waist circumference (−7.13 ± 4.4 cm, p < 0.0001), WHR (−0.10 ± 0.1, p < 0.0001), sum skinfold thickness (−6.15 ± 8.2 mm, p < 0.0001) and % body fat mass (−1.5 ± 3.3, p < 0.0001) in HIV+BFR+EXS. Hip circumference was unchanged in non-exercise control groups. CET reduced fasting total cholesterol (−0.03 ± 1.11 mM, p < 0.05), triglycerides (−0.22 ± 0.48 mM, p < 0.05) and glucose levels (−0.21 ± 0.71 mM, p < 0.05) (p < 0.0001). HDL-, LDL-cholesterol and HOMA values were unchanged after CET. Interestingly, HIV+ subjects randomized to non-exercising groups experienced increases in fasting plasma glucose levels, whereas HIV seronegative controls did not (p < 0.001). Predicted VO2 peak increased more in the HIV+BFR+EXS than in all other groups (4.7 ± 3.9 ml/kg/min, p < 0.0001). Exercise training positively modulated body composition and metabolic profiles, and improved cardiorespiratory fitness in HAART-treated HIV+ Africans. These beneficial adaptations imply that exercise training is a safe, inexpensive, practical, and effective treatment for evolving metabolic and cardiovascular syndromes associated with HIV and HAART exposure in resource-limited sub-Saharan countries, where treatment is improving, morbidity and mortality rates are declining, but where minimal resources are available to manage HIV- and HAART-associated cardiovascular and metabolic syndromes.
doi:10.1089/aid.2007.0023
PMCID: PMC3936606  PMID: 18275343
2.  Factors Associated with Poor Immunologic Response to Virologic Suppression by Highly Active Antiretroviral Therapy in HIV-Infected Women 
Virologic response to highly active antiretroviral therapy (HAART) typically results in a substantial rise in CD4 cell counts. We investigated factors associated with poor CD4 response among HIV-infected women followed at 6-monthly intervals in the Women’s Interagency HIV Study. Women with nadir CD4 counts <350 cells/mm3 who achieved at least 6 months of plasma HIV RNA < 400 copies/ml were studied. Demographic, clinical, and treatment factors were compared between immunologic nonresponders, defined as the lower quartile of CD4 count change after two visits with virologic suppression (<56 cell/mm3; n = 38), and the remaining group of responders (n = 115). Immunologic nonresponders had lower baseline HIV RNA levels and higher CD4 counts, more frequently used HAART 6 months prior to achieving consistent viral suppression, and more commonly had HIV RNA levels >80 but <400 copies/mL at both suppressive visits (21 vs. 7.8%, p = 0.024). In multivariate analysis, higher CD4 count and lower HIV RNA level at the last presuppressive visit were associated with immune nonresponse. We conclude that higher baseline CD4 count and lower HIV RNA level were associated with poor immunologic response to HAART in women with virologic suppression for at least 6 months. Persistent low level viremia may also contribute.
doi:10.1089/aid.2006.22.222
PMCID: PMC3126664  PMID: 16545008
3.  HSV-2 infection increases HIV DNA detection in vaginal tissue of mice expressing human CD4 and CCR5 
AIDS research and human retroviruses  2009;25(11):1157-1164.
The goal of this study was to develop an in vivo murine model that can be used to study the influence of HSV-2 on HIV infection. Mice expressing transgenes for human CD4, CCR5 and Cyclin T1 were infected intra-vaginally with HSV-2 and 3-7 days later infected with HIV. HIV DNA was detected by real time PCR. The frequency of detection of HIV DNA was significantly higher (65%) in vaginal tissue of HSV-2-infected mice compared to mock-infected mice (35%) when HIV was given 3 days after HSV-2. HSV-2 infected mice also had significantly higher levels of HIV DNA in vaginal tissue. HIV DNA was not detected in vaginal tissue of mice lacking human CD4. Longer periods (5 or 7 days) between infection with HSV-2 and HIV did not increase the frequency of detection or the amount of HIV DNA detected. HIV DNA was also detected in lymph nodes from some of the mice that were infected intra-vaginally with HSV-2 and HIV. Flow cytometric and mRNA analysis of human CD4 in vaginal tissue suggested that HSV-2 infection increased the number of T cells expressing human CD4 in vaginal tissue. This study provides evidence that HIV infection of cells occurs in the vagina of mice expressing human CD4, CCR5 and Cyclin T1 and that HSV-2 infection increases HIV infection. These findings demonstrate that this model can be used to study the mechanisms responsible for increased susceptibility to HIV in HSV-2-infected persons and for testing preventative treatments.
doi:10.1089/aid.2009.0035
PMCID: PMC2826840  PMID: 19886831
4.  The Dead Cell: A Potent Escort for HIV-1 Trans-Infection 
AIDS research and human retroviruses  2009;25(11):1123-1128.
HIV-1 trans-infection is a process by which one cell acts as an HIV-1 “escort” to enhance infection of another. There has recently been much debate concerning (i) the types of cells that may act as escorts, (ii) requirements for virus internalization by the escort, and (iii) the sensitivity of trans-infection to inhibition by neutralizing antibodies. To address these questions, trans-infection was monitored by incubating target cells with HIV-1 in the presence or absence of mouse or human cells as candidate escorts in vitro. After a two day culture, target cells were tested for levels of HIV-1 infection. Results showed that a variety of murine and human cells were capable escorts for HIV-1 trans-infection. Cell integrity was not required, as escorts could be freeze/thawed (or fractionated to yield purified membranes/microsomes) prior to their incubation with HIV-1. In fact, the freeze/thawed or fractionated cells were often superior to their viable counterparts as mediators of trans-infection. The process was sensitive to antibody neutralization. Confirmatory experiments were conducted with more than one target cell and more than one source of HIV-1. Results demonstrated that there may be multiple cell types and mechanisms with which trans-infection can be accomplished. Apparently the simple binding of fragmented escort membranes to HIV-1 may be sufficient to enhance virus fusion or endocytosis at the target cell surface. The fact that dead cells or membranes can support this activity may explain, at least in part, the high frequency of human HIV-1 infections at sites of tissue damage.
doi:10.1089/aid.2009.0021
PMCID: PMC2787888  PMID: 19886832
HIV-1 Trans-infection; membranes; microsomes; neutralizing antibodies
5.  Amplification of Simian Retroviral Sequences from Human Recipients of Baboon Liver Transplants 
Investigations into the use of baboons as organ donors for human transplant recipients, a procedure called xenotransplantation, have raised the specter of transmitting baboon viruses to humans and possibly establishing new human infectious diseases. Retrospective analysis of tissues from two human transplant recipients with end-stage hepatic disease who died 70 and 27 days after the transplantation of baboon livers revealed the presence of two simian retroviruses of baboon origin, simian foamy virus (SFV) and baboon endogenous virus (BaEV), in multiple tissue compartments. The presence of baboon mitochondrial DNA was also detected in these same tissues, suggesting that xenogeneic “passenger leukocytes” harboring latent or active viral infections had migrated from the xenografts to distant sites within the human recipients. The persistence of SFV and BaEV in human recipients throughout the posttransplant period underscores the potential infectious risks associated with xenotransplantation.
PMCID: PMC2963433  PMID: 9671210
6.  Genotypic Susceptibility Scores and HIV Type 1 RNA Responses in Treatment-Experienced Subjects with HIV Type 1 Infection 
This study compared the role of genotypic susceptibility scores (GSS) as a predictor of virologic response in a group (n = 234) of HIV-infected, protease inhibitor (PI)-experienced subjects. Two scoring methods [discrete genotypic susceptibility score (dGSS) and continuous genotypic susceptibility score (cGSS)] were developed. Each drug in the subject's regimen was given a binary susceptibility score using Stanford inferred drug resistance scores to calculate the dGSS. In contrast to the dGSS, the cGSS model was designed to reflect partial susceptibility to a drug. Both GSS were independent predictors of week 16 virologic response. We also compared the GSS to a phenotypic susceptibility score (PSS) model on a subset of subjects that had both GSS and PSS performed, and found that both models were predictive of virologic response. Genotypic analyses at enrollment showed that subjects who were virologic nonresponders at week 16 revealed enrichment of several mutated codons associated with nucleoside reverse transcriptase inhibitors (NRTI) (codons 67, 69, 70, 118, 215, and 219) or PI resistance (codons 10, 24, 71, 73, and 88) compared to subjects who were virologic responders. Regression analyses revealed that protease mutations at codons 24 and 90 were most predictive of poor virologic response, whereas mutations at 82 were associated with enhanced virologic response. Certain NNRTI-associated mutations, such as K103N, were rapidly selected in the absence of NRTIs. These data indicate that GSS may be a useful tool in selecting drug regimens in HIV-1-infected subjects to maximize virologic response and improve treatment outcomes.
doi:10.1089/aid.2007.0127
PMCID: PMC2928289  PMID: 18462083
7.  Genomic Analysis of HIV Type 1 Strains Derived from a Mother and Child Pair of Long-Term Nonprogressors 
To investigate the viral features of long-term nonprogressive HIV-1 infection and the selection of viral genomes, we studied serial complete HIV-1 sequences obtained from a mother–child pair, both long-term nonprogressors. Analysis of four genomic sequences demonstrated that all viral genes were intact, lacking major deletions or premature stop codons to easily explain the slow disease progression. These data suggest that viral attenuation, if present, was caused by subtle sequence variations or virus–host interactions. Serial sequences from an HIV-1-infected mother–child pair afforded us the opportunity to examine the immune selection of HIV-1 sequences years after transmission between individuals. We demonstrated that the daughter's strains were most likely subjected to immunoselection or immunoediting according to the presence of novel MHC class I alleles that differed between mother and daughter. An analysis of nef-specific cytotoxic T-lymphocyte responses in the child, whose HIV-1 nef sequence differed from the maternal nef, supported this interpretation. This study highlights the potential of full genome analysis in the investigation of pathogenesis and immune selection during HIV-1 evolution.
doi:10.1089/aid.2006.0180
PMCID: PMC2925658  PMID: 17331038
8.  Altered bystander apoptosis induction and pathogenesis of Enfuvirtide resistant HIV-1 Env mutants 
In previous studies on mechanisms of HIV-1 mediated pathogenesis we showed that bystander apoptosis mediated by cell surface expressed HIV-1 Env correlated with the fusogenic properties of the gp41 subunit of Env. A crucial step in HIV gp41-mediated fusion is the re-folding of the protein into a six helix bundle along the N- and C-terminal coiled coil domains. These domains have been targeted by peptide inhibitors that inhibit gp41 mediated fusion. One of these inhibitors, Enfuvirtide, is the first such drug approved for therapy. More recently, clinical data suggests that the beneficial effects of Enfuvirtide extend beyond virus suppression and are associated with certain resistance mutations in gp41. In this study we characterized the bystander apoptosis inducing potential of mutants associated with increased CD4 counts that arise during Enfuvirtide therapy. While all mutant clones were reduced in both cell to cell fusion activity and apoptosis induction there was limited effect on virus infection or replication. The viruses found to have apoptosis inducing activity in the order WT>V38M>V38A>G36D>V38E which correlated with cell to cell fusion but not infection. Interestingly, the level of resistance as determined by IC50 of Enfuvirtide also correlated inversely with both cell fusion and apoptosis in that the most resistant Envs were least fusogenic and pathogenic. This suggests the beneficial effects of Enfuvirtide therapy beyond virus suppression maybe mediated by selecting less pathogenic HIV isolates over time.
doi:10.1089/aid.2009.0010
PMCID: PMC2791676  PMID: 19619009
9.  Analysis of HIV Type 1 gp41 and Enfuvirtide Susceptibility among Men in the United States Who Were HIV Infected Prior to Availability of HIV Entry Inhibitors 
We analyzed HIV gp41 from 195 men in the United States who were HIV-1 infected between 1999 and 2002, before enfuvirtide (ENF) was approved for clinical use in the United States. gp41 genotyping results were obtained for 175 samples. None of the samples had major ENF resistance mutations. Six (3.4%) samples had minor ENF resistance mutations in the HR1 region (V38G, N43K, L44M, L45M). Twenty-eight (16%) samples had the N42S polymorphism, which is associated with ENF hypersusceptibility. Accessory mutations in the HR2 region were identified in some samples (E137K, S138A). Five of the six samples with HR1 resistance mutations were analyzed with a phenotypic assay; one sample had reduced ENF susceptibility (a sample with N42S + L44M + E137K). Prior to the availability of ENF, some men in the United States were infected with HIV that contained mutations associated with ENF resistance or hypersusceptibility. However, most of the mutations were not associated with phenotypic ENF resistance.
doi:10.1089/aid.2009.0014
PMCID: PMC2746939  PMID: 19552592
10.  Short Communication: In Utero HIV Infection Is Associated with an Increased Risk of Nevirapine Resistance in Ugandan Infants Who Were Exposed to Perinatal Single Dose Nevirapine 
Use of single dose nevirapine (sdNVP) to prevent HIV mother-to-child transmission is associated with the emergence of NVP resistance in many infants who are HIV infected despite prophylaxis. We combined results from four clinical trials to analyze predictors of NVP resistance in sdNVP-exposed Ugandan infants. Samples were tested with the ViroSeq HIV Genotyping System and a sensitive point mutation assay (LigAmp, for detection of K103N, Y181C, and G190A). NVP resistance was detected at 6–8 weeks in 36 (45.0%) of 80 infants using ViroSeq and 33 (45.8%) of 72 infants using LigAmp. NVP resistance was more frequent among infants who were infected in utero than among infants who were diagnosed with HIV infection after birth by 6–8 weeks of age. Detection of NVP resistance at 6–8 weeks was not associated with HIV subtype (A vs. D), pre-NVP maternal viral load or CD4 cell count, infant viral load at 6–8 weeks, or infant sex. NVP resistance was still detected in some infants 6–12 months after sdNVP exposure. In this study, in utero HIV infection was the only factor associated with detection of NVP resistance in infants 6–8 weeks after sdNVP exposure.
doi:10.1089/aid.2009.0003
PMCID: PMC2752753  PMID: 19552593
11.  Use of Tissue Culture Cell Lines to Evaluate HIV Antiviral Resistance 
Most current assays of HIV antiviral resistance are based on either sequencing of viral genes (genotypic assays) or amplification and insertion of these genes into standardized virus backbones and culture. These latter are called phenotypic assays. But the only generally accepted phenotypic assay is based upon culture of intact patient virus, performed in phytohemagglutinin-activated peripheral blood mononuclear cells (PHA blasts) in the presence of differing drug concentrations. However, PHA blast culture is difficult and not always reproducible. Therefore we have sought cell lines that may produce more predictable results, yet faithfully mirror results in PHA blasts. We have compared 10 different cell lines for receptor and coreceptor expression, growth of laboratory-adapted strains of HIV, growth by direct inoculation of PBMC from infected patients, and in assays of antiviral drug effects. One of these cell lines, C8166-R5, is statistically not inferior to CD8-depleted PHA blasts for culturing HIV from the peripheral blood cells of patients. The effective concentrations of antiviral drugs of all classes were similar when assayed in C8166-R5 or PHA blasts. Known drug-resistant isolates grown in C8166-R5 demonstrated the predicted effects. We followed a patient longitudinally and demonstrated that resistance testing in C8166-R5 was predictive of clinical outcome. These experiments represent the first steps in developing a clinically useful phenotypic drug resistance assay based upon culturing the patient’s own virus.
doi:10.1089/aid.2007.0242
PMCID: PMC2895164  PMID: 18671478
12.  Hepatitis B Virus Genotype Distribution and Its Lamivudine-Resistant Mutants in HIV-Coinfected Patients with Chronic and Occult Hepatitis B 
Hepatitis B virus (HBV) genotypes were examined in HIV-infected patients with chronic and occult HBV infection. From a total population of 593 HIV-infected patients, 22 individuals (prevalence 3.7%) were found to be HBsAg while 72 (12.1%) were found to be anti-HBc alone. From them, 20 and 4 were HBV DNA positive, respectively. These last four patients are therefore considered to be HBV infected in an occult form. The genotypes could be determined in all 24 HBV-infected patients. HBV-A was the most common (20/24; 83.3%), followed by HBV-D (2/24; 8.3%) and HBV-F (1/24; 4.2%). The remaining sample exhibited mixed infection involving genotypes A and D as pure ones, thus also forming part of three intergenotypic recombinant forms exhibiting different mosaic S gene patterns. The sexual route of transmission was predominant among HBV genotype A-infected patients. Among the 24 HBV DNA-positive patients, point mutations related to lamivudine resistance were found in four strains. These viral strains showed a methionine-to-valine substitution at codon 204 (rtM204V) in association with an upstream B-domain change at rtL180M. Additionally, two of them exhibited the additional rtV173L mutation. The value of HBV molecular monitoring including both HBV viral genomic characterization and genotypic resistance profile in HIV-HBV-coinfected individuals is discussed.
doi:10.1089/aid.2006.0172
PMCID: PMC2894418  PMID: 17506609
13.  Design and Characterization of an HIV-Specific Ribonuclease Zymogen 
AIDS research and human retroviruses  2008;24(11):1357-1363.
Ribonucleases are evoking medical interest because of their intrinsic cytotoxic activity. Most notably, ranpirnase, which is an amphibian ribonuclease, is in advanced clinical trials as a chemotherapeutic agent for the treatment of cancer. Here, we describe a strategy to create a novel antiviral agent based on bovine pancreatic ribonuclease (RNase A), a mammalian homologue of ranpirnase. Specifically, we have linked the N- and C-termini of RNase A with an amino-acid sequence that is recognized and cleaved by human immunodeficiency virus (HIV) protease. This linkage obstructs the active site, forming an HIV-specific RNase A zymogen. Cleavage by HIV-1 protease increases ribonucleolytic activity by 50-fold. By relying on the proper function of HIV-1 protease, rather than its inhibition, our approach will not engender known mechanisms of resistance. Thus, we report an initial step towards a new class of agents for the treatment of HIV/AIDS.
doi:10.1089/aid.2008.0146
PMCID: PMC2888699  PMID: 19025416
14.  Increased Mortality in Rural Patients with HIV in New England 
Although patients with human immunodeficiency virus (HIV) infection who live in the rural United States receive less expert care and less antiretroviral treatment, the impact of living in rural areas on mortality from HIV infection is unstudied. We compared mortality rates in 327 rural and 317 urban patients with HIV infection in a retrospective cohort study using a multivariate logistic regression model. Rural patients with HIV infection were older at the end of follow-up (43.4 vs. 41.4 years, p = 0.002), and more likely white (93.0% vs. 77.9%, p < 0.001), and a greater proportion were men who have sex with men (55.5% vs. 36.1%, p < 0.001). While the mean year of diagnosis was 1994 in rural patients and 1995 in urban patients (p < 0.001), the mean CD4+ T cell count at presentation was similar in the two groups: 376 vs. 351 cells/μl (p = 0.298). Rural patients in our cohort were more likely to receive antiretroviral medications at any CD4 count (73.7 vs. 62.1%, p = 0.0016), and received PCP prophylaxis at comparable rates (23.5% vs. 25.6%, p = 0.555). Mortality was higher in rural patients (10.4% vs. 6.0%, p = 0.028). The risk of mortality remained higher in rural patients when adjusting for age, sex, race, HIV risk factors, year of diagnosis, travel time, lack of insurance, and receipt of antiretroviral treatment or PCP prophylaxis in a logistic regression model (OR 2.11, 1.064 to 4.218, p = 0.047). Patients with HIV who live in rural areas have higher mortality rates than urban patients with HIV.
doi:10.1089/aid.2006.0206
PMCID: PMC2872149  PMID: 17530995
15.  The Association of HIV Infection with Left Ventricular Mass/Hypertrophy 
Left ventricular hypertrophy (LVH) is an independent predictor of major cardiovascular events. Cardiovascular risk is increased among human immunodeficiency virus (HIV)-infected patients. To assess LV mass/hypertrophy in HIV infection, 654 women enrolled in the Women's Interagency HIV Study underwent transthoracic echocardiography. There were 454 HIV-infected and 200 uninfected women, mean age 40.8 ± 9.3 years. LV mass/height2.7 was similar between the HIV-infected and the HIV-uninfected groups (41.4 ± 11.1 vs. 39.9 ± 10.3 g/h2.7; p = 0.37). The prevalence of LVH was similar between the two groups (LVH by LV mass/height2.7 criteria 15.0% vs. 13.0%, p = 0.29). Relative wall thickness (RWT), defined as the ratio of LV wall thickness to cavity diameter, was also similar between the HIV-infected and HIV-uninfected groups (0.36 ± 0.05 vs. 0.37 ± 0.06, p = 0.16). On multiple linear regression analysis adjusting for age, W/H ratio, triceps skinfold thickness, systolic/diastolic BP, diabetes, hypertension and dyslipidemia; HIV status (b = 2.08, p = 0.02, CI 0.27–3.88); weight (b per kg = 0.15, p<0.01, CI 0.08–0.22); and smoking duration (b per one-year increase = 0.08, p = 0.03, CI 0.01–0.16) were independent correlates of LV mass/height2.7 (Model R2 = 0.20, p<0.001). Weight (aOR = 1.04, CI 1.01–1.06) and smoking duration (aOR = 1.03, CI 1.01–1.06) were independent correlates of LVH. Being HIV negative, increased age, increased triceps skinfold thickness, and higher W/H ratio were independent correlates of higher RWT. Among HIV-infected women, higher LV mass was not associated with a history of AIDS-defining illness, nadir CD4+ count <200 cells/μl, or with the duration of highly active antiretroviral therapy (HAART). Women taking NRTIs had higher LV mass. Higher RWT was associated with current CD4+ count. In conclusion, HIV infection is associated with greater LV mass but not with a higher prevalence of LVH. Among HIV-infected women, RWT, but not LV mass, is associated with the degree of immunosuppression.
doi:10.1089/aid.2008.0170
PMCID: PMC2801578  PMID: 19397399
16.  A Novel Codon Insert in Protease of Clade B HIV-1 
A novel combination of three codon inserts in the pol coding region of HIV-1 RNA was identified in a highly antiretroviral experienced study subject with HIV-1 infection. A one codon insert was observed in the protease region between codon 40 and 41 simultaneously with a two codon insert present in the reverse transcriptase region at codon 69.
doi:10.1089/aid.2008.0310
PMCID: PMC2749665  PMID: 19397401
17.  Delaying a Treatment Switch in Antiretroviral-Treated HIV Type 1-Infected Patients with Detectable Drug-Resistant Viremia Does Not Have a Profound Effect on Immune Parameters: AIDS Clinical Trials Group Study A5115 
Some patients are unable to achieve and maintain an undetectable plasma HIV-1 RNA level with combination antiretroviral therapy (ART) and are therefore maintained on a partially suppressive regimen. To determine the immune consequences of continuing ART despite persistent viremia, we randomized 47 ART-treated individuals with low to moderate plasma HIV-1 RNA levels (200–9999 copies/ml) to either an immediate switch in therapy or a delayed switch (when plasma HIV-1 RNA became ≥10,000 copies/ml). After 48 weeks of follow-up, naive and memory CD4+ T cell percents were comparable in the two groups. The proportion of subjects with a lymphocyte proliferative response to Candida, Mycobacterium avium- intracellulare complex, or HIV-gag was also not significantly different at week 48. Delaying a treatment switch in patients with partial virologic suppression and stable CD4+ T cells does not have profound effects on immune parameters.
doi:10.1089/aid.2008.0200
PMCID: PMC2755543  PMID: 19239354
18.  Bioinformatic Prediction Programs Underestimate the Frequency of CXCR4 Usage by R5X4 HIV Type 1 in Brain and Other Tissues 
AIDS research and human retroviruses  2008;24(9):1215-1220.
Human immunodeficiency virus (HIV-1) variants in brain primarily use CCR5 for entry into macrophages and microglia, but dual-tropic (R5X4) HIV-1 has been detected in brain and cerebral spinal fluid (CSF) of some patients with HIV-associated dementia (HAD). Here, we sequenced the gp120 coding region of nine full-length dual-tropic (R5X4) env genes cloned directly from autopsy brain and spleen tissue from an AIDS patient with severe HAD. We then compiled a dataset of 30 unique clade B R5X4 Env V3 sequences from this subject and 16 additional patients (n = 4 brain and 26 lymphoid/blood) and used it to compare the ability of six bioinformatic algorithms to correctly predict CXCR4 usage in R5X4 Envs. Only one program (SVMgeno2pheno) correctly predicted the ability of R5X4 Envs in this dataset to use CXCR4 with 90% accuracy (n = 27/30 predicted to use CXCR4). The PSSMSINSI, Random Forest, and SVMgenomiac programs and the commonly used charge rule correctly predicted CXCR4 usage with >50% accuracy (22/30, 16/30, 19/30, and 25/30, respectively), while the PSSMX4R5 matrix and “11/25” rule correctly predicted CXCR4 usage in <50% of the R5X4 Envs (10/30 and 13/30, respectively). Two positions in the V3 loop (19 and 32) influenced coreceptor usage predictions of nine R5X4 Envs from patient MACS1 and a total of 12 Envs from the dataset (40% of unique V3 sequences). These results demonstrate that most predictive algorithms underestimate the frequency of R5X4 HIV-1 in brain and other tissues. SVMgeno2pheno is the most accurate predictor of CXCR4 usage by R5X4 HIV-1.
doi:10.1089/aid.2008.0009
PMCID: PMC2801411  PMID: 18788913
19.  Positive association between HIV RNA and IL-6 in the genital tract of Rwandan Women 
Infections and inflammation in the genital tract can influence HIV expression or HIV susceptibility. The goal of this study was to determine if significant relationships exist between cytokines and HIV in genital tract secretions from 57 HIV-seropositive Rwandan women. Genital tract secretions were obtained by cervicovaginal lavage (CVL). Ten different cytokines in CVL were measured by multiplex Cytometric Bead Arrays. HIV RNA in CVL and plasma were measured by quantitative PCR. In univariate analysis, genital tract HIV RNA was significantly associated with plasma HIV RNA and several of the cytokines, while in multivariate analysis, genital tract HIV RNA was only significantly associated with plasma HIV RNA and IL-6. This association of IL-6 with HIV RNA levels suggests that IL-6 is an indicator for conditions that induce HIV expression and that IL-6 may contribute to induction of HIV expression in the genital tract.
doi:10.1089/aid.2008.0004
PMCID: PMC2792594  PMID: 18671479
20.  Elevated NT-pro-BNP Levels Are Associated with Comorbidities among HIV-Infected Women 
AIDS research and human retroviruses  2009;25(10):997-1004.
HIV infection is associated with left ventricular (LV) dysfunction and accelerated atherosclerosis. These conditions result in elevation of plasma natriuretic peptide (NP) levels. The present study compares N-terminal-pro-BNP (NT-pro-BNP) levels in HIV-infected and -uninfected women and identifies factors influencing NT-pro-BNP levels in HIV-infected women. A total of 454 HIV-infected and 200 HIV-uninfected participants from the Women’s Interagency HIV Study (WIHS) had NT-pro-BNP determination. Elevated NT-pro-BNP level was defined using previously determined age stratified cut-off values of >164 ng/liter (age <60 years) and >225 (age ≥60 years). HIV-infected women were older (41.6 ± 8.9 vs. 38.9 ± 10.5 years, p <0.01) and were more likely to have anemia, hepatitis C virus (HCV) antibodies, and kidney dysfunction than HIV-uninfected women. HIV-infected women had significantly higher NT-pro-BNP levels (142.4 ± 524.8 vs. 73.6 ± 115.1 ng/liter, p = 0.01) and a higher prevalence of elevated NT-pro-BNP (12.1% vs. 7.5%; p = 0.08). In univariate analyses, elevated NT-pro-BNP was significantly associated with age, systolic BP, hypertension, anemia, triglyceride levels, kidney disease, and HCV seropositivity, but not HIV infection. In multivariate analysis, elevated NT-pro-BNP levels were significantly associated with anemia and kidney function, and had a borderline association with the presence of HCV antibodies. Among HIV-infected women, NT-pro-BNP levels were not independently associated with measures of severity of infection or with HAART use. Although HIV-infected women have higher NT-pro-BNP levels than HIV-uninfected women, the differences are due to non-HIV factors such as anemia, kidney disease, and HCV coinfection. These findings suggest that natriuretic peptide levels are a global marker of comorbidity in the setting of HIV infection.
doi:10.1089/aid.2009.0038
PMCID: PMC2791362  PMID: 19803714
21.  Cellulose Acetate 1,2-Benzenedicarboxylate Inhibits Infection by Cell-Free and Cell-Associated Primary HIV-1 Isolates 
Cellulose acetate 1,2-benzenedicarboxylate (CAP), a pharmaceutical excipient used for enteric film coating of capsules and tablets, was previously shown to have potent inhibitory activity against infection by human immunodeficiency virus type 1 (HIV-1) T cell line-adapted (TCLA) strains. In the present study, we determined the inhibitory activity of CAP against infection by cell-free and cell-associated primary HIV-1 isolates with distinct genotypes and biotypes in cervical explants, peripheral blood mononuclear cells (PBMCs), monocyte-derived macrophages (MDMs), and CEMx174 5.25M7 cells. CAP blocked infection by cell-free and cell-associated HIV-1 in cervical explants. It inhibited infection by cell-free primary HIV-1 isolates (clades A to G and group O) in PBMCs, MDMs, and CEMx174 5.25M7 cells and blocked transmissions of the cell-associated primary HIV-1 isolates from dendritic cells (DCs) to PBMCs, from MDMs to PBMCs, and from PBMCs to CEMx174 5.25M7 cells. The inhibitory activity of CAP on infection by the cell-free and cell-associated primary HIV-1 isolates is independent of viral subtypes and coreceptor usage. These data suggest that CAP is a good microbicide candidate that can be further developed for preventing sexual transmission of HIV-1.
doi:10.1089/aid.2006.22.411
PMCID: PMC2788998  PMID: 16706617
22.  Geographic HIV Type 1 Subtype Distribution in Rakai District, Uganda 
AIDS research and human retroviruses  2009;25(10):1045-1048.
To analyze HIV-1 subtype distribution, sequence analysis was performed on serum specimens obtained in 1994 from the Rakai Health Sciences community cohort in Uganda. Portions of gag-p24 and env-gp41 were sequenced and HIV subtype was determined for 773 subjects residing in 10 community clusters in rural Uganda. Subtypes A (17%) and D (70%) were the most common strains in the population. Subtype distribution varied by geographic region with significantly more subtype A in northern community clusters compared with southern clusters (21% vs. 8%, p < 0.001) and more subtype D in southern clusters compared with northern clusters (78% vs. 65%, p < 0.008). These data illustrate the geographic complexity of subtype variation, which has important implications for HIV-1 vaccine design.
doi:10.1089/aid.2009.0127
PMCID: PMC2785855  PMID: 19803713
23.  Impaired Viral Entry Cannot Explain Reduced CD4+ T Cell Susceptibility to HIV Type 1 in Certain Highly Exposed Individuals 
AIDS research and human retroviruses  2008;24(11):1415-1427.
Rare individuals report repeated unprotected HIV-1 sexual exposures, yet remain seronegative for years. We investigated the possibility that reduced in vitro CD4+ T cell susceptibility to HIV-1 infection protects such highly exposed seronegative (ES) individuals. Susceptibility to three R5-tropic HIV-1 isolates, regardless of inoculating dose, was remarkably similar between 81 ES and 33 low-risk controls. In 94% (99/105) of donors, we observed a 1.36 log-unit range in HIV-1JR-CSF production, with similar results for HIV-11192. The median frequency of intracellular Gag+ T cells after single-round infection was similar in ES (5.2%) and controls (7.2%), p = 0.456. However, in repeated testing, CD4+ T cells from two controls (6.1%) and four ES (4.9%) exhibited a 10- to 2500-fold reduction in HIV-1 production and required 5- to 12-fold greater HIV-11192 and HIV-1JR-CSF inocula to establish infection (TCID50). Reduced viral entry cannot explain the low producer phenotype; no differences in CCR5 receptor density or β-chemokine production were observed. In conclusion, we have identified a remarkably narrow range of HIV-1 susceptibility in seronegative donors regardless of risk activity, which can be applied as a benchmark to assess vaccine-induced antiviral effector activities. However, CD4+ T cells from a subset of individuals demonstrated reduced HIV-1 susceptibility unexplained by impaired entry, lending support to the possibility that cellular restriction of HIV-1 may account for continued seronegativity in some of those having repeated sexual exposure. Identifying the host–virus interactions responsible for diminished in vitro susceptibility may contribute to the development of novel therapeutic strategies.
doi:10.1089/aid.2007.0256
PMCID: PMC2764523  PMID: 19000021
24.  A Decrease in Albumin in Early SIV Infection Is Related to Viral Pathogenicity 
A decrease in circulating albumin levels after seroconversion has been reported as a predictor of disease progression in HIV-infected adults. We hypothesized that a similar decrease would be seen in pig-tailed macaques in early SIV infection, and that the degree of this decrease would be related to the pathogenicity of the infecting viral strain. Ten juvenile pig-tailed macaques were previously inoculated with virus derived from molecular clones representing different stages of infection: early (SIVMneCL8, n = 2), intermediate (SIVMne35wkSU, n = 2), late blood (SIVMne170, n = 3), or late lymph node (SIVMne027, n = 3). Albumin was measured in stored samples. Changes from baseline were evaluated by paired sample t tests and by linear regression with generalized estimating equations (GEE). Albumin levels decreased in the week after SIV inoculation (p = 0.02), increased above baseline at week 5, then fell, returning below baseline by week 16 (p = 0.03). In GEE modeling, albumin decreased significantly in both early and chronic infection (weeks 0–3, p < 0.001; weeks 5–16, p = 0.004) and this change differed significantly between infections caused by late versus early or intermediate virus variants (weeks 0–3, p = 0.002; weeks 5–16, p = 0.001).A decrease in albumin levels occurs in both early and chronic SIV infection, and is more marked in macaques infected with more pathogenic virus variants. These results suggest that both early and late events in SIV pathogenesis are influenced by properties of the infecting viral strain.
doi:10.1089/aid.2008.0267
PMCID: PMC2768648  PMID: 19320603
25.  HIV Type 1 Viremia on ART Is Positively Associated with Polyclonal T Cell Proliferation in Subjects with T Cell IFN-γ Secretion Levels Comparable to Those of Uninfected Subjects 
AIDS research and human retroviruses  2008;24(9):1203-1208.
We investigated the association between plasma HIV-1 RNA, immune activation, and polyclonal T cell function in viremic subjects whether on or off antiretroviral therapy (ART). The surface expression of activation/functional molecules on T cells and monocytes as well as cytokine secretion and T cell proliferation were assessed in 23 HIV-1− and 79 HIV-1+-infected subjects with different levels of viral suppression and CD4+ T cell count >250 cells/mm3 for >6 months. Viral replication was associated with increased T cell and monocyte activation irrespective of ART. In subjects with a detectable viral load on ART, we found a positive association with anti-CD3/CD28-induced T cell proliferation compared to patients with undetectable viral load (<400 copies/ml). No difference among groups was observed for anti-CD3/CD28-mediated IFN-γ responses. The presence of an unexpected positive association between polyclonal T cell proliferation and viral load in subjects with levels of T cell IFN-γ responses comparable to those of uninfected subjects is of potential relevance to an increase in T cell activation response before the loss of polyclonal cytokine secretion and proliferation observed with disease progression. This finding suggests that T cell hyperresponsiveness may play a role in the pathogenesis of immune comorbidities on ART.
doi:10.1089/aid.2008.0054
PMCID: PMC2762279  PMID: 18788911

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