Genotypic alteration of HAART-persistent HIV-1 reservoirs in vivo

Three HIV-1-infected individuals, on virally-suppressive highly active anti-retroviral therapy (HAART), were treated in vivo with anti-retroviral inhibitor intensification and cell stimulatory therapies in attempting to eradicate latent viral reservoirs. Afterwards, the patients ceased all anti-retroviral drugs. Sequences of the V3 region of HIV-1 envelope protein (ENV) from patient peripheral blood mononuclear cell (PBMC) proviral DNA, patient blood plasma viral RNA and virion-associated RNA from viruses amplified by patient cell co-culture, were obtained before, during, and certain times after the clinical regimen. As anticipated, the V3 loop sequencing results indicate diversity in viral strain complexity among the individual patients. However, the detection of unique V3 ENV signature sequences or V3 signatures of low frequency, relative to those observed prior to therapy, indicate that the expression of specific viruses, or viruses of low abundance, can be induced through stimulation in vivo. Furthermore, this stimulation or general immune activation therapy (IAT) approach, consisting of administration of the anti-T-cell receptor antibody, OKT3, and IL-2 in vivo, appeared to have subsequently altered the genotype of the persistent viral reservoir in peripheral blood cells for two of the three patients.     

Genotypic Determination of HIV Tropism in a Cohort of Patients Perinatally Infected With HIV-1 and Exposed to Antiretroviral Therapy

The aim of this study was to determine the coreceptor tropism by performing genotypic HIV-1 tropism testing in a cohort of patients perinatally infected with HIV-1 and exposed to antiretroviral therapy. Genotypic coreceptor tropism was determined in patients with HIV-1 RNA<100 copies/mL using PBMC samples by gp120 V3 sequencing followed by geno2pheno interpretation (set at a false positive rate [FPR] of 20%) and in patients with >100 copies/mL using plasma samples (set at a FPR of 20%), according to European guidelines. Out of 55 patients, 50 had an HIV-1 subtype B strain, and mean (SD) age was 18.2 (4.6) years. The median duration of antiretroviral therapy was 13 years (range, 3–23). Thirty-three (60%) patients harbored the R5 virus. At the time of the testing, the median CD4+ T lymphocyte cell count and percentage were 705 cells/mm³ (474–905) and 32.5% in group R5 and 626 cells/mm³ (450–755) and 31.7% in group X4/D-M, respectively. The nadir of CD4+ T-cell count in groups R5 and X4/D-M were 322 cells/mm³ (230–427) and 340 cells/mm³ (242–356), respectively. These differences were not statistically significant. Fifteen patients had HIV-1 RNA >50 copies/mL. The median HIV-1 RNA and HIV-1 DNA were comparable in both groups without a statistical difference. The study provides an overview of the prevalence of coreceptor tropism in a cohort of patients who were vertically infected with HIV-1. The high prevalence of X4/D-M-tropic strains may simply reflect the long-term exposure to HIV.     

Genotypic resistance profile of HIV-1 protease gene: a preliminary report from Vellore, south India

HIV-1 subtypes other than B are responsible for most new HIV infections worldwide; virus sequence data for drug resistance is described only from a limited number of non-B subtype HIV-1. This study is on mutations and polymorphisms of HIV-1 protease gene that can predict drug resistance in subtype C. The genotypic resistance assay was carried out on 38 HIV-1 strains with their plasma RNA and in nine, the proviral protease gene was sequenced. The treatment naïve strains showed minor resistance mutations, there were no major resistance mutations in the protease gene. We suggest the use of resistance testing to monitor individuals on therapy and also before initiation of therapy, gathering more sequence information for a data bank of Indian strains.     

Dendritic Cell Numbers in the Blood of HIV-1 Infected Patients Before and After Changes in Antiretroviral Therapy

Antigen presenting dendritic cells (DCs) can serve as sites for HIV replication and as vehicles for transmission of the virus to T cells. It is known that the numbers of DCs in blood is reduced during HIV-1 infection. Here we monitored the two major subsets of blood DCs in 12 individuals undergoing a change, primarily initiation, of highly active antiretroviral therapy. The numbers of plasmacytoid DCs were reliably higher on therapy, although in the 1–3 month interval we followed, these numbers did not return to those seen in HIV uninfected controls. An increase in plasmacytoid DCs was accompanied by an increase in IFN- production in response to a standard challenge in culture with UV-inactivated herpes simplex virus. The levels of myeloid DCs also demonstrated an increase while on HAART, and these numbers become comparable to the HIV uninfected controls. The numbers of plasmacytoid and myeloid DCs varied inversely with the levels of plasma HIV viremia. These longitudinal studies extend prior work showing that virus infection with HIV leads to a decrease in the number of dendritic cells in blood, and that this can be reversed at least in part by therapy.     

The Role of Virologic and Immunologic Factors in Mother-to-Child Transmission of HIV-1

PROBLEM: More than 90% of human immunodeficiency virus type 1 (HIV-1) infection in children is acquired by mother-to-child transmission. However, infection of the child occurs in between 14 and 35% of cases. METHOD OF STUDY: To understand the mechanisms involved in HIV-1 transmission, we have investigated the antigenic, molecular, and phenotypic characteristics of the virus harbored in infected mothers and their children. RESULTS: A clear correlation was observed between the transmission of the virus and the isolation of viral variants with a rapidly replicating and syncytium-inducing phenotype from the mother Furthermore, non-transmitting mothers were able to neutralize several primary isolates more frequently than transmitting mothers. The comparison of the viral phenotype and genotype of mother-child pairs showed that the transmitted virus did not have common features, suggesting that transmission is usually not a selective process. CONCLUSIONS: This study suggests that transmission is governed by an interaction of both viral and immunological factors. The results obtained indicate that different strategies can be applied for the prevention of transmission.     

对奈韦拉平耐药的HIV-1毒株诱导研究

目的 探讨对NVP耐药的Ⅰ型艾滋病病毒(HIV-1)毒株的诱导方法,获得能够产生连续稳定传代的对NVP高度耐药的HIV-1毒株.方法 MT4细胞中先后加入终浓度为100TCID50的HIV-1实验室毒株89.6与终浓度为10倍IC50的NVP药物溶液,在药物浓度不变的条件下传代,培育HIV-1病毒.提取每代培养液上清病毒RNA,逆转录后使用巢式PCR扩增HIV-1 pol区基因,收集目标片段并进行测序分析.结果 诱导培养所得耐药株由第5代开始与野生株相比,出现NVP IC50变化,倍数约为3倍,培养11代后,变化倍数高达178倍.此外,发生Y181C和Y188Y位点突变.结论 本实验中在体外经诱导所得耐药株对NVP具有较高的耐药性,并可获得稳定传代.     

Localization of HTLV-1 and HIV-1 Proviral Sequences in Chromosomes of Persistently Infected Cells

Integration sites for HTLV-1 and HIV-1proviruses were detected by FISH on the chromosomes of HTHIV27 cells persistently infected by HIV-1 (strain IIIB). HTLV-1 signals were found on 9 loci of chromosomes 4, 6, 9, 15 and 16. Integration sites of GC-rich HTLV-1 provirus are located in GC-rich isochores, confirming an ‘isopycnic’ integration, namely an integration in which the GC level of the host sequences around the integration site match the GC level of the provirus. This conclusion is not only derived from the compositional map of human chromosomes, but also from HTLV-1 hybridization on compositional fractions of human DNA. Integration of GC-poor HIV- 1 provirus was found on 4 loci of chromosomes 2, 7, 17 and 19. One copy of a complete HIV-1 provirus, which is active, was integrated in H1 isochores, whereas other defective copies were located in GC-poor L isochores. These results are discussed in terms of regional integration of retroviral sequences. This revised version was published online in August 2006 with corrections to the Cover Date.     

Cytokine Analysis at the Single Cell Level and Lymphoproliferative Responses to Mycobacterial Antigens in HIV-1 Patients with Successful Virologic Response to Potent Antiretrovirals

Immunologic parameters, known to be grossly abnormal in HIV-1-infected subjects, were analyzed in 22 patients with sustained viral load suppression (<200 copies/ml) following long-term highly active antiretroviral therapy (HAART). Responses were compared with those from 18 HIV-seronegative healthy controls. Persistent phenotypic alterations in patients' blood mononuclear cells were minimal, though the percentages of lymphocytes that could be activated to produce interleukin-2 (IL-2) remained severely depressed. Using lymphoproliferative assays, a striking deficit in the capacity of patients to respond to the common mycobacterial antigens and particularly to recombinant heat-shock proteins paralleled the absence of responses to virus p24 antigen. In view of the important immunoregulatory role of stress proteins, these findings reveal profound functional deficiencies and persistent immune dysregulation in HIV-1 patients, despite successful HAART and a considerable recovery of CD4⁺ lymphocyte numbers. Rational immunotherapeutic approaches should be aimed to correct the characterized immune abnormalities.     

广西HIV-1重组毒株env区快速基因分型方法的建立

目的建立一种快速简便的基因分型方法，对广西HIV-1重组毒株env基因区进行亚型鉴定。方法从HIV阳性样品中提取核酸，使用HIV-1M组通用引物对env区进行第一轮扩增，第二轮则使用分别检测B′/C或C亚型和CRF01-AE亚型的二套特异性引物放入同一反应管中进行扩增，根据不同亚型扩增的目的带位置不同来判断亚型。将通用引物扩增出的所有样本均进行基因测序和系统树分析以验证结果。结果50份样本中，经基因测序和系统树分析证实CRF08-BC样本3份（6％），CRF01-AE样本43份（86％），4份（8％）样本无法确定亚型。经亚型特异性引物PCR法检测得出B′/C或C亚型样本3份（100％），CRF01-AE样本39份（90．7％），灵敏度为91．3％，特异度为100％。两种方法检测结果经差异性检验显示X^2=2．25，P〉0.05，差异无统计学意义，结果一致者占92％。与基因分析结果吻合。重复实验显示CRF08-BC平均重复性为100％（10／10），CRF01．AE为93．8％（61／65）。结论该方法是一种简便、快速、低成本，具有高度灵敏性和特异性的HIV-1毒株env基因区分型法，能够直接对广西HIV-1 CRF01-AE重组毒株进行鉴定。     

26例有偿献血员HIV-1基因分型与变异特征

目的分析某地区有偿献血人员中流行的人免疫缺陷病毒1型（HIV-1）gag、pol、env基因亚型及基因变异特征。方法提取HIV-1感染者外周血单核细胞（PBMC）DNA,经巢式PCR（NestedPCR）扩增gag（p17-p24）、pol（PR＊RT）、env（C2-V5）基因片段,纯化测序后用MEGA5．0等生物学软件对核苷酸序列进行分析。结果23份样本为B亚型,2份为B亚型与C亚型重组,1份为CRF01-AE与B亚型重组。PR区未发现蛋白酶抑制剂主要耐药性突变,RT区检测到核苷类逆转录酶抑制剂耐药性突变M184V和非核苷类逆转录酶抑制剂耐药性突变K101E,G190A。结论流行于该地区的HIV-1毒株以B亚型为主。大多数毒株对常规抗病毒药物仍然敏感,使用HARRT治疗方案依然有效。CXCR4型辅助受体的毒株顶端四肽多为GPGR（91．7％）,提示GPGR可能与疾病的进展有关。     

Evolution of Hematological Parameters in HIV-1-Infected Patients With and Without Thalassemia Carriages During Highly Active Antiretroviral Therapy

Abstract

Objectives: To assess the effects of highly active antiretroviral therapy (HAART) on hematological parameters in HIV-1-infected patients with and without thalassemia carriages. Methods: Prospective study was conducted in HIV-1-infected Thai patients receiving HAART. Their hematological parameters were measured at baseline and during follow-up of 1 year. β-thalassemia and hemoglobin-E trait were diagnosed using HPLC. PCR-genotyping techniques were used to investigate α-thalassemia-1 Southeast Asian type deletion and β-thalassemia mutation. The changes of hematological parameters were compared according to thalassemia carriage. Results: During follow-up, increased levels of CD4 counts, hemoglobin, mean corpuscular volume (MCV), and mean corpuscular hemoglobin (MCH) were observed in the groups of patients with and without thalassemia. The changes in mean hemoglobin level, MCV, and MCH in both groups appeared parallel, with consistently lower levels in patients with thalassemia. At Months 6 and 12, mean MCV of patients with thalassemia was shifted from microcytic levels (<80 fL) to normocytic levels (80–100 fL) while their mean MCH was increased to normal levels (27–31 pg). Conclusion: Although HAART altered hematological parameters such as MCV and MCH, it did not induce worsening anaemia, especially in patients with thalassemia carriages. However, the increased levels of MCV and MCH crucially affect the thalassemia screening.     

Nitric Oxide Production in HIV-1 Infected Patients Receiving Intermittent Cycles of Interleukin-2 and Antiretrovirals

Abstract

Background: Interleukin-2 (IL-2) has been investigated as an adjunct to antiretroviral therapy (ART) because of its well-demonstrated capacity of stably increasing the number of peripheral CD4+ T cell lymphocytes. However, IL-2-related adverse events (AEs), including fever, tachycardia, hypotension, and respiratory failure, are typically dose- and schedule-dependent and can potentially limit the application of IL-2 therapy in an outpatient setting. Nitric oxide (NO) is a potent vasodilator potentially responsible for some of the AEs caused by IL-2. Purpose: In this study, we determined NO production in a cohort of HIV-1 infected individuals receiving ART either alone or together with IL-2. Method: NO production, detected as plasma nitrate/nitrite levels by the Griess reaction, was evaluated in 3 groups of 10 individuals each. In the first group, subcutaneous (sc) administration of 12-15 million international units per day (MIU/d) of IL-2 was administered for 5 days every 8 weeks for 6 cycles together with ART; in the second group, IL-2 (6 MIU/d) was given sc for 5 days every 4 weeks for 12 cycles together with ART; whereas the third group received ART alone. Results: At baseline, the plasma nitrate/nitrite levels in the 2 groups of patients who received high and low doses of the cytokine along with ART were 28.5 ± 18.1 μmol/L and 34.2 ± 29.0 μmol/L, respectively. These levels were comparable to those of patients treated with only ART (18.6 ± 22.4 μmol/L) and to those of 20 healthy controls (19.9 ± 5.9 μmol/L). No significant increase of plasma nitrate/nitrite levels was observed by administration of either ART or ART+IL-2. In addition, NO production was not associated significantly with different levels of tumor necrosis factor-alpha, IL-6, or soluble IL-2 receptor alpha _chain in 9 individuals with WHO grade 2 and 3 AEs. Conclusion: Our results indicate that NO is unlikely to be responsible for most side effects of IL-2 therapy in HIV-1 infected individuals. Because both IL-2 and virus multiplication have been reported to independently stimulate NO production, concomitant ART may curtail NO production through inhibition of HIV-1 replication.     

HIV-1 subtype C in vitro growth and coreceptor utilization

Human immunodeficiency virus type 1 subtype C (HIV-1C) accounts for about 50% of all HIV infections in the pandemic and is the predominant subtype in the heavily burdened region of southern Africa. HIV-1C possesses unique genetic and phenotypic features that might be associated with biological differences compared to other subtypes. Here, we generated virus isolates from individuals at different stages of HIV-1C infection and investigated the chemokine receptor repertoire that the derived HIV-1C isolates may utilize for entry. Our results show that the R5 phenotype predominates among viruses in Botswana, with a lesser contribution of viruses showing the dualtropic X4R5 phenotype. No viruses of pure X4 phenotype were found, which suggests no discernable evolution of HIV-1C to a monotropic X4 phenotype as the epidemic ages in Botswana. Usage of other coreceptors was rare and apparently insignificant. These results enhance our understanding of HIV-1C biology, with implications for designing and testing therapeutic and prophylactic agents.     

Autoproliferation in HIV-1-infected patients undergoing active HIV-1-specific immunotherapy.

We have observed a treatment-associated autoproliferative response in cultured peripheral blood mononuclear cells (PBMC) of asymptomatic HIV-1-infected subjects receiving a gp120-depleted, inactivated HIV-1 antigen in incomplete Freund's adjuvant (IFA; HIV-1 Immunogen). The frequency and magnitude of the autoproliferative response appeared to be dose-related (P < 0.05), and was not observed in subjects receiving IFA alone. Immunophenotyping of the proliferating cells demonstrated the presence of both CD4+ and CD8+ lymphocytes, with the CD4+ blasts almost exclusively expressing the CD45RO+ phenotype. A comparison of this response with the HIV-1-specific antigen stimulation responses in this cohort revealed a significant correlation between increases in HIV-1-specific cell-mediated immunity and autoproliferation (r2 = 0.61, P < 0.001). These findings suggest that immunization with the HIV-1 Immunogen induces an autoproliferative response that may reflect changes in HIV-1-specific cell-mediated immunity in infected individuals.     

Subtype-specific problems with qualitative Amplicor HIV-1 DNA PCR test

BACKGROUND: commercial HIV-1 qualitative DNA PCR tests have the potential to detect virus in patients in whom antibody tests may be ineffective, such as patients with primary HIV infection and infants born to HIV seropositive mothers. However, the genetic diversity of HIV-1 raises concern about the ability of the PCR tests to detect all current subtypes. OBJECTIVES: to asses the sensitivity of the Amplicor HIV-1 test on 126 whole-blood samples representing seven different subtypes and to investigate the sensitivity when the standard assay was modified by including the primer pair SK145 and SKCC1B. RESULTS: of the 126 HIV-1 infected persons, 113 were tested positive and 13 were DNA PCR negative. On the basis of these results, the standard Amplicor HIV-1 test had a sensitivity of 90% in our cohort. In addition, 9% of the positive samples showed a low reactivity but above the cut-off of the assay. The standard assay yielded sensitivities of 100% for subtype B (n=16), D (n=9) and G (n=1), but only 83% for subtype A (n=41), 98% for subtype C (n=43), 79% for subtype E (n=14) and 0% for subtype F (n=2). All samples with low reactivity were non-B subtype. Eight of the DNA PCR negative samples, four subtype A, one C and three E were amplified with the modified Amplicor HIV-1 test with addition of SK145/SKCC1B primers. Using this modified protocol, six samples out of eight became positive. However, two samples (one A and one C) remained DNA PCR negative. CONCLUSION: this study confirms that the Amplicor HIV-1 test does not detect all subtypes with equivalent sensitivity and 10% of the samples, tested negative. Thus, it is preferable to add the SK145/SKCC1B primers to the standard test, where infection with non-B subtype is suspected.     

Evaluation of Xpert HIV-1 Qual assay for resolution of HIV-1 infection in samples with negative or indeterminate Geenius HIV-1/2 results

BackgroundDiagnosis of HIV infection is a multistage algorithm. Following screening with 4^th generation combination immunoassay, confirmation of HIV infection is performed with an antibody assay that differentiates HIV-1 from HIV-2 infection. In the newly updated algorithm, samples that are nonreactive or indeterminate in the differentiation assay are to be tested with an HIV-1 nucleic acid amplification (NAAT) test for resolution. Xpert HIV-1 Qual is a new NAAT assay approved for the identification of HIV infection in whole and dried blood.ObjectivesTo assess the performance of Xpert HIV-1 Qual supplementary assay in resolving the clinical status of serum samples reactive by 4^th generation immunoassays and indeterminate or negative by Geenius HIV-1/2 confirmatory assay.Study designIn a retrospective study, samples from 97 individuals for whom the true HIV-1 status was already known (by follow-up samples) and which were negative or indeterminate by HIV-1/2 Geenius assay were tested with Xpert Qual HIV-1 assay.ResultsXpert Qual assay correctly classified all 97 samples from HIV-1 positive (n = 49) and negative (n = 48) individuals. The sensitivity and specificity of Xpert Qual when using the true HIV status as a reference were 100% (92.7–100% at 95% confidence interval [CI] and 92.6–100% at 95% CI, respectively).ConclusionsApplying Xpert Qual HIV-1 assay in the new HIV multi-stage diagnostic algorithm correctly classified 100% of HIV-1 infections including 49 from HIV-1 carriers who have not yet seroconverted. With this assay the total time required for acute HIV diagnosis could be significantly reduced.     

Resistance to Antiretroviral Agents in Individuals with HIV-1 Non-B Subtypes

Abstract

Naturally occurring polymorphisms at positions involved in resistance to antiretroviral agents are frequently seen in HIV-1 non-B subtypes. Although they do not seem to affect significantly the susceptibility to antiretroviral drugs in vitro, they may facilitate the selection of different pathways and/or a more rapid emergence of drug resistance and treatment failure under not fully suppressive treatment regimens.     

Correlation of immune activation with HIV-1 RNA levels assayed by real-time RT-PCR in HIV-1 subtype C infected patients in Northern India

BACKGROUND: Assays with specificity and cost effectiveness are needed for the measurement of HIV-1 burden to monitor disease progression or response to anti-retroviral therapy (ART) in HIV-1 subtype C infected patients. OBJECTIVES: The objective of this study was to develop and validate an affordable one step real-time RT-PCR assay with high specificity and sensitivity to measure plasma HIV-1 loads in HIV-1 subtype C infected patients. RESULTS: We developed an RT-PCR assay to detect and quantitate plasma HIV-1 levels in HIV-1 subtype C infected patients. An inverse correlation between plasma viral loads (PVL) and CD4+ T-cell numbers was detected at all CDC stages. Significant correlations were found between CD8+ T-cell activation and PVL, as well as with the clinical and immunological status of the patients. CONCLUSIONS: This RT-PCR assay provides a sensitive method to measure PVL in HIV-1 subtype C infected patients. Viral loads correlated with immune activation and can be used to monitor HIV care in India.