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author:("Coakley, ein")
1.  CCR5 Expression Is Reduced in Lymph Nodes of HIV Type 1–Infected Women, Compared With Men, But Does Not Mediate Sex-Based Differences in Viral Loads 
The Journal of Infectious Diseases  2013;209(6):922-930.
Background. Human immunodeficiency virus type 1 (HIV-1)–infected women have lower viral loads than men but similar rates of disease progression. We hypothesized that sex-based differences in CCR5 expression mediate viral load differences.
Methods. CCR5 was analyzed by flow cytometry in disaggregated lymph node cells from untreated HIV-1–infected women (n = 28) and men (n = 27). The frequencies of HIV-1 RNA–producing cells in the lymph node were determined by in situ hybridization. Linear and generalized linear regression models were used.
Results. The percentage of CCR5+CD3+CD4+ cells was lower in women (mean, 12%) than men (mean, 16%; P = .034). Neither the percentage of CCR5+CD3+CD4+ cells nor the CCR5 density predicted viral load or HIV-1 RNA–producing lymph node cells (P ≥ .24), after adjusting for CD4+ T-cell count, race, and age. Women had marginally fewer HIV-1 RNA–producing cells (mean, 0.21 cells/mm2) than men (mean, 0.44 cells/mm2; P = .046). After adjusting for the frequency of HIV-1 RNA–producing cells and potential confounders, the viral load in women were 0.46 log10 copies/mL lower than that in men (P = .018).
Conclusions. Reduced lymph node CCR5 expression in women did not account for the viral load difference between sexes. CCR5 expression did not predict viral load or frequencies of HIV-1 RNA–producing cells, indicating that physiologic levels of CCR5 do not limit HIV-1 replication in lymph node. Less plasma virus was associated with each HIV-1 RNA–producing cell in women as compared to men, suggesting that women may either produce fewer virions per productively infected cell or more effectively clear extracellular virus.
doi:10.1093/infdis/jit575
PMCID: PMC3935472  PMID: 24179109
Lymph node; CCR5; Immune activation; Sex differences; HIV-1
2.  HIV Drug Resistance Profiles and Clinical Outcomes in Patients with Viremia Maintained at Very Low Levels 
World journal of AIDS  2013;3(2):71-78.
We describe an observational study of clinical, virologic and drug resistance profiles in HIV-positive antiretroviral adherent subjects with stable low level viremia (LLV) 50–1,000 copies/mL for more than 12 months. Subjects were followed from time of first detectable viral load (VL). In total, 102 episodes of LLV were detected among 80 individuals. The median (mean, range) HIV copy number at genotyping was 250 (486, <50–3900) copies/mL after 14 (17.9, 0–58) months of LLV. Few patients maintained LLV for the entire 9 year period of observation, with half (52%) experiencing viremic progression following a stable period of LLV either spontaneously or after treatment interruption or failed regimen intensification. In the setting of prolonged periods of sustained LLV, mean duration 22 (range 8 – 106) months, drug resistance (DR) was almost universal. Resistance to ≥1 on-treatment drugs was defined in 97% of specimens and DR to all drugs in the treatment regimen in over half of all patients. Evolution of DR mutations during the period of LLV was observed in 20/28 (71%) subjects with specimens available for follow-up testing. This evolution was associated with viremic progression to levels >1000 copies/mL (p=0.03).
Our data suggest that DR present in patients with LLV is likely to impact long term clinical outcomes, highlighting the importance of optimizing techniques to detect the presence of drug resistant HIV in the setting of LLV and the need for larger prospective studies to assess the emergence of DR in the setting of sustained LLV and the impact of this DR on treatment outcomes.
doi:10.4236/wja.2013.32010
PMCID: PMC4319662  PMID: 25664219
HIV; low level viremia; treatment experienced patients; HIV drug resistance
3.  DETERMINATION OF VIRAL TROPISM BY GENOTYPING AND PHENOTYPING ASSAYS IN BRAZILIAN HIV-1-INFECTED PATIENTS 
The clinical application of CCR5 antagonists involves first determining the coreceptor usage by the infecting viral strain. Bioinformatics programs that predict coreceptor usage could provide an alternative method to screen candidates for treatment with CCR5 antagonists, particularly in countries with limited financial resources. Thus, the present study aims to identify the best approach using bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice. Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under clinical monitoring were analyzed in this study. Based on the Trofile results, the viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of tropism using a Geno2pheno[coreceptor] analysis with a false positive rate of 10% gave the most suitable performance in this sampling: the R5 and X4 strains were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6% concordance between the phenotypic and genotypic results. Further studies are needed to clarify how genetic diversity amongst virus strains affects bioinformatics-driven approaches for determining tropism. Although this strategy could be useful for screening patients in developing countries, some limitations remain that restrict the wider application of coreceptor usage tests in clinical practice.
doi:10.1590/S0036-46652014000400003
PMCID: PMC4131812  PMID: 25076427
HIV-1; Tropism; Brazil; V3 loop
4.  Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations 
Journal of virological methods  2010;168(0):114-120.
To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity.
doi:10.1016/j.jviromet.2010.04.030
PMCID: PMC3949620  PMID: 20451557
HIV; Single genome sequencing (SGS); pro-pol diversity; cloning and sequencing; treatment naïve
5.  HIV-1 Tropism Testing in Subjects Achieving Undetectable HIV-1 RNA: Diagnostic Accuracy, Viral Evolution and Compartmentalization 
PLoS ONE  2013;8(8):e67085.
Background
Technically, HIV-1 tropism can be evaluated in plasma or peripheral blood mononuclear cells (PBMCs). However, only tropism testing of plasma HIV-1 has been validated as a tool to predict virological response to CCR5 antagonists in clinical trials. The preferable tropism testing strategy in subjects with undetectable HIV-1 viremia, in whom plasma tropism testing is not feasible, remains uncertain.
Methods & Results
We designed a proof-of-concept study including 30 chronically HIV-1-infected individuals who achieved HIV-1 RNA <50 copies/mL during at least 2 years after first-line ART initiation. First, we determined the diagnostic accuracy of 454 and population sequencing of gp120 V3-loops in plasma and PBMCs, as well as of MT-2 assays before ART initiation. The Enhanced Sensitivity Trofile Assay (ESTA) was used as the technical reference standard. 454 sequencing of plasma viruses provided the highest agreement with ESTA. The accuracy of 454 sequencing decreased in PBMCs due to reduced specificity. Population sequencing in plasma and PBMCs was slightly less accurate than plasma 454 sequencing, being less sensitive but more specific. MT-2 assays had low sensitivity but 100% specificity. Then, we used optimized 454 sequence data to investigate viral evolution in PBMCs during viremia suppression and only found evolution of R5 viruses in one subject. No de novo CXCR4-using HIV-1 production was observed over time. Finally, Slatkin-Maddison tests suggested that plasma and cell-associated V3 forms were sometimes compartmentalized.
Conclusions
The absence of tropism shifts during viremia suppression suggests that, when available, testing of stored plasma samples is generally safe and informative, provided that HIV-1 suppression is maintained. Tropism testing in PBMCs may not necessarily produce equivalent biological results to plasma, because the structure of viral populations and the diagnostic performance of tropism assays may sometimes vary between compartments. Thereby, proviral DNA tropism testing should be specifically validated in clinical trials before it can be applied to routine clinical decision-making.
doi:10.1371/journal.pone.0067085
PMCID: PMC3731261  PMID: 23936293
6.  Transmitted Drug Resistance Among Antiretroviral-Naive Patients with Established HIV Type 1 Infection in Santo Domingo, Dominican Republic and Review of the Latin American and Caribbean Literature 
Abstract
Emergence of HIV resistance is a concerning consequence of global scale-up of antiretroviral therapy (ART). To date, there is no published information about HIV resistance from the Dominican Republic. The study's aim was to determine the prevalence of transmitted drug resistance (TDR) to reverse transcriptase and protease inhibitors in a sample of chronically HIV-1-infected patients in one clinic in Santo Domingo. The data are presented in the context of a review of the TDR literature from Latin America and the Caribbean. Genotype testing was successfully performed on 103 treatment-naive adults planning to initiate antiretroviral therapy; the World Health Organization (WHO) list of surveillance drug resistance mutations (SDRM) was used to determine the presence of TDR mutations. WHO SDRM were identified in eight patients (7.8%); none had received sdNVP. There were no significant differences in epidemiologic or clinical variables between those with or without WHO SDRM. The prevalence of WHO SDRM was 1.0% and 6.8% for nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, respectively. No WHO SDRMs for protease inhibitors were identified. Among 12 studies of TDR in the region with a sample size of at least 100 subjects, the reported prevalence of SDRM ranged from 2.8% to 8.1%. The most commonly identified SDRM was K103N. This information adds to our understanding of the epidemiology of TDR in the region and the possible role such mutations could play in undermining first-line treatment. Ongoing surveillance is clearly needed to better understand the TDR phenomenon in the Caribbean.
doi:10.1089/aid.2010.0355
PMCID: PMC3380383  PMID: 21851324
7.  Vicriviroc Resistance Decay and Relative Replicative Fitness in HIV-1 Clinical Isolates under Sequential Drug Selection Pressures 
Journal of Virology  2012;86(12):6416-6426.
We previously described an HIV-1-infected individual who developed resistance to vicriviroc (VCV), an investigational CCR5 antagonist, during 28 weeks of therapy (Tsibris AM et al., J. Virol. 82:8210–8214, 2008). To investigate the decay of VCV resistance mutations, a standard clonal analysis of full-length env (gp160) was performed on plasma HIV-1 samples obtained at week 28 (the time of VCV discontinuation) and at three subsequent time points (weeks 30, 42, and 48). During 132 days, VCV-resistant HIV-1 was replaced by VCV-sensitive viruses whose V3 loop sequences differed from the dominant pretreatment forms. A deep-sequencing analysis showed that the week 48 VCV-sensitive V3 loop form emerged from a preexisting viral variant. Enfuvirtide was added to the antiretroviral regimen at week 30; by week 48, enfuvirtide treatment selected for either the G36D or N43D HR-1 mutation. Growth competition experiments demonstrated that viruses incorporating the dominant week 28 VCV-resistant env were less fit than week 0 viruses in the absence of VCV but more fit than week 48 viruses. This week 48 fitness deficit persisted when G36D was corrected by either site-directed mutagenesis or week 48 gp41 domain swapping. The correction of N43D, in contrast, restored fitness relative to that of week 28, but not week 0, viruses. Virus entry kinetics correlated with observed fitness differences; the slower entry of enfuvirtide-resistant viruses corrected to wild-type rates in the presence of enfuvirtide. These findings suggest that while VCV and enfuvirtide select for resistance mutations in only one env subunit, gp120 and gp41 coevolve to maximize viral fitness under sequential drug selection pressures.
doi:10.1128/JVI.00286-12
PMCID: PMC3393533  PMID: 22491471
8.  HIV-1 Clinical Isolates Resistant to CCR5 Antagonists Exhibit Delayed Entry Kinetics That Are Corrected in the Presence of Drug 
Journal of Virology  2012;86(2):1119-1128.
HIV CCR5 antagonists select for env gene mutations that enable virus entry via drug-bound coreceptor. To investigate the mechanisms responsible for viral adaptation to drug-bound coreceptor-mediated entry, we studied viral isolates from three participants who developed CCR5 antagonist resistance during treatment with vicriviroc (VCV), an investigational small-molecule CCR5 antagonist. VCV-sensitive and -resistant viruses were isolated from one HIV subtype C- and two subtype B-infected participants; VCV-resistant isolates had mutations in the V3 loop of gp120 and were cross-resistant to TAK-779, an investigational antagonist, and maraviroc (MVC). All three resistant isolates contained a 306P mutation but had variable mutations elsewhere in the V3 stem. We used a virus-cell β-lactamase (BlaM) fusion assay to determine the entry kinetics of recombinant viruses that incorporated full-length VCV-sensitive and -resistant envelopes. VCV-resistant isolates exhibited delayed entry rates in the absence of drug, relative to pretherapy VCV-sensitive isolates. The addition of drug corrected these delays. These findings were generalizable across target cell types with a range of CD4 and CCR5 surface densities and were observed when either population-derived or clonal envelopes were used to construct recombinant viruses. V3 loop mutations alone were sufficient to restore virus entry in the presence of drug, and the accumulation of V3 mutations during VCV therapy led to progressively higher rates of viral entry. We propose that the restoration of pre-CCR5 antagonist therapy HIV entry kinetics drives the selection of V3 loop mutations and may represent a common mechanism that underlies the emergence of CCR5 antagonist resistance.
doi:10.1128/JVI.06421-11
PMCID: PMC3255837  PMID: 22090117
9.  Reanalysis of Coreceptor Tropism in HIV-1–Infected Adults Using a Phenotypic Assay with Enhanced Sensitivity 
The enhanced-sensitivity Trofile assay (TF-ES; Monogram Biosciences) was used to retest coreceptor tropism samples from 4 different cohorts of HIV-1–infected patients. Nine percent to 26% of patients with CCR5-tropic virus by the original Trofile assay had CXCR4-using virus by TF-ES. Lower CD4 cell counts were associated with CXCR4-using virus in all cohorts.
doi:10.1093/cid/cir072
PMCID: PMC3106234  PMID: 21427401
10.  HLA-DR+ CD38+ CD4+ T Lymphocytes Have Elevated CCR5 Expression and Produce the Majority of R5-Tropic HIV-1 RNA In Vivo ▿  
Journal of Virology  2011;85(19):10189-10200.
Percentages of activated T cells correlate with HIV-1 disease progression, but the underlying mechanisms are not fully understood. We hypothesized that HLA-DR+ CD38+ (DR+ 38+) CD4+ T cells produce the majority of HIV-1 due to elevated expression of CCR5 and CXCR4. In phytohemagglutinin (PHA)-stimulated CD8-depleted peripheral blood mononuclear cells (PBMC) infected with HIV-1 green fluorescent protein (GFP) reporter viruses, DR− 38+ T cells constituted the majority of CCR5 (R5)-tropic (median, 62%) and CXCR4 (X4)-tropic HIV-1-producing cells (median, 61%), although cell surface CCR5 and CXCR4 were not elevated in this subset of cells. In lymph nodes from untreated individuals infected with R5-tropic HIV-1, percentages of CCR5+ cells were elevated in DR+ 38+ CD4+ T cells (median, 36.4%) compared to other CD4+ T-cell subsets (median values of 5.7% for DR− 38− cells, 19.4% for DR+ 38− cells, and 7.6% for DR− 38+ cells; n = 18; P < 0.001). In sorted CD8− lymph node T cells, median HIV-1 RNA copies/105 cells was higher for DR+ 38+ cells (1.8 × 106) than for DR− 38− (0.007 × 106), DR− 38+ (0.064 × 106), and DR+ 38− (0.18 × 106) subsets (n = 8; P < 0.001 for all). After adjusting for percentages of subsets, a median of 87% of viral RNA was harbored by DR+ 38+ cells. Percentages of CCR5+ CD4+ T cells and concentrations of CCR5 molecules among subsets predicted HIV-1 RNA levels among CD8− DR/38 subsets (P < 0.001 for both). Median HIV-1 DNA copies/105 cells was higher in DR+ 38+ cells (5,360) than in the DR− 38− (906), DR− 38+ (814), and DR+ 38− (1,984) subsets (n = 7; P ≤ 0.031). Thus, DR+ 38+ CD4+ T cells in lymph nodes have elevated CCR5 expression, are highly susceptible to infection with R5-tropic virus, and produce the majority of R5-tropic HIV-1. PBMC assays failed to recapitulate in vivo findings, suggesting limited utility. Strategies to reduce numbers of DR+ 38+ CD4+ T cells may substantially inhibit HIV-1 replication.
doi:10.1128/JVI.02529-10
PMCID: PMC3196402  PMID: 21813616
11.  Connection Domain Mutations in HIV-1 Reverse Transcriptase Do Not Impact Etravirine Susceptibility and Virologic Responses to Etravirine-Containing Regimens▿† 
Connection domain mutations (CDMs) in HIV-1 reverse transcriptase (RT) alter susceptibility to some nucleoside/nonnucleoside RT inhibitors (NRTIs/NNRTIs). Their effects on susceptibility and virologic responses to etravirine were analyzed. Seventeen CDMs were evaluated: L283I, E312Q, G333D, G333E, G335C, G335D, N348I, A360I, A360T, A360V, V365I, T369I, A371V, A376S, I393L, E399D, and E399G. CDM prevalence and effects on virologic responses were analyzed retrospectively using clinical data. The effects on etravirine susceptibility were assessed in clinical samples and confirmed using site-directed mutants. The most prevalent CDMs (>10%) were A371V, E399D, A376S, N348I, A360T, G333E, and L283I. CDM presence was positively correlated with thymidine analogue-associated mutations, but not with NNRTI resistance-associated mutations (RAMs). The presence or number of CDMs did not significantly reduce etravirine susceptibility, although small reductions were seen in samples with G333D, N348I, A360V, T369I, and A376S. N348I, E399G, and N348I/T369I were associated with reduced etravirine susceptibility when present with K103N, L100I, or Y181C. N348I or T369I was associated with reduced etravirine susceptibility when present with K101P or K103R/V179D. Virologic responses to an etravirine-containing regimen were slightly diminished when G333D, G335D, or A376S was present, but this was not confirmed in subgroups with higher baseline resistance or without etravirine RAMs. CDMs alone do not confer substantial reductions in etravirine susceptibility but can further reduce etravirine susceptibility in combination with certain NNRTI mutations. Since virologic responses to etravirine were not affected by CDMs, the clinical impacts of these mutations on etravirine susceptibility appear to be minimal.
doi:10.1128/AAC.01695-10
PMCID: PMC3101386  PMID: 21464253
12.  Three-Year Safety and Efficacy of Vicriviroc, a CCR5 Antagonist, in HIV-1-Infected, Treatment-Experienced Patients 
Background
Vicriviroc, an investigational CCR5 antagonist, demonstrated short-term safety and antiretroviral activity.
Methods
Phase 2, double-blind, randomized study of vicriviroc in treatment-experienced subjects with CCR5-using HIV-1. Vicriviroc (5, 10 or 15 mg) or placebo was added to a failing regimen with optimization of background antiretroviral medications at day 14. Subjects experiencing virologic failure and subjects completing 48 weeks were offered open-label vicriviroc.
Results
118 subjects were randomized. Virologic failure (<1 log10 decline in HIV-1 RNA ≥16 weeks post-randomization) occurred by week 48 in 24/28 (86%), 12/30 (40%), 8/30 (27%), 10/30 (33%) of subjects randomized to placebo, 5, 10 and 15 mg respectively. Overall, 113 subjects received vicriviroc at randomization or after virologic failure, and 52 (46%) achieved HIV-1 RNA <50 copies/mL within 24 weeks. Through 3 years, 49% of those achieving suppression did not experience confirmed viral rebound. Dual or mixed-tropic HIV-1 was detected in 33 (29%). Vicriviroc resistance (progressive decrease in maximal percentage inhibition on phenotypic testing) was detected in 6 subjects. Nine subjects discontinued vicriviroc due to adverse events.
Conclusions
Vicriviroc appears safe and demonstrates sustained virologic suppression through 3 years of follow-up. Further trials of vicriviroc will establish its clinical utility for the treatment of HIV-1 infection.
PMCID: PMC2917795  PMID: 20672447
HIV-1; CCR5 antagonist; vicriviroc; antiretroviral therapy
13.  Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing 
PLoS Pathogens  2011;7(6):e1002106.
The emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants is associated with accelerated disease progression. CXCR4-using variants are believed to evolve from CCR5-using variants, but due to the extremely low frequency at which transitional intermediate variants are often present, the kinetics and mutational pathways involved in this process have been difficult to study and are therefore poorly understood. Here, we used ultra-deep sequencing of the V3 loop of the viral envelope in combination with the V3-based coreceptor prediction tools PSSMNSI/SI and geno2pheno[coreceptor] to detect HIV-1 variants during the transition from CCR5- to CXCR4-usage. We analyzed PBMC and serum samples obtained from eight HIV-1-infected individuals at three-month intervals up to one year prior to the first phenotypic detection of CXCR4-using variants in the MT-2 assay. Between 3,482 and 10,521 reads were generated from each sample. In all individuals, V3 sequences of predicted CXCR4-using HIV-1 were detected at least three months prior to phenotypic detection of CXCR4-using variants in the MT-2 assay. Subsequent analysis of the genetic relationships of these V3 sequences using minimum spanning trees revealed that the transition in coreceptor usage followed a stepwise mutational pathway involving sequential intermediate variants, which were generally present at relatively low frequencies compared to the major predicted CCR5- and CXCR4-using variants. In addition, we observed differences between individuals with respect to the number of predicted CXCR4-using variants, the diversity among major predicted CCR5-using variants, and the presence or absence of intermediate variants with discordant phenotype predictions. These results provide the first detailed description of the mutational pathways in V3 during the transition from CCR5- to CXCR4-usage in natural HIV-1 infection.
Author Summary
The first step in the infection of a target cell by human immunodeficiency virus type 1 (HIV-1) is binding of the envelope spike to its receptor CD4 and a coreceptor on the cellular surface. HIV-1 variants present early in the course of infection mainly use the coreceptor CCR5, while virus variants that use CXCR4 can appear later in infection. This change in coreceptor usage is associated with mutations in the third variable (V3) loop of the envelope spike, but has been difficult to study due to the low presence of intermediate variants. Using ultra-deep sequencing, we obtained thousands of sequences of the V3 loop from HIV-1 infected individuals in the year before CXCR4-using variants were first detected, including sequences from almost all intermediate variants. We show that mutations are introduced sequentially in the V3 loop during the evolution from CCR5- to CXCR4-usage. Furthermore, we describe differences and similarities between HIV-1-infected individuals that are related to this change in coreceptor usage, which provides the first detailed overview of this evolutionary process during natural HIV-1 infection.
doi:10.1371/journal.ppat.1002106
PMCID: PMC3121885  PMID: 21731496
14.  HIV Replication Capacity Is an Independent Predictor of Disease Progression in Persons With Untreated Chronic HIV Infection 
Objective
To assess the effect of pol replication capacity (RC) on the hazard ratio of progression to a composite endpoint of time to progression to <350 CD4+ cells/μL, initiation of therapy or death.
Methods
pol RC assays were performed after study closure in baseline samples obtained from 316 enrollees in a prospectively monitored cohort of treatment-naive adults with ≥450 CD4+ cells/μL and ≥1000 HIV-1 RNA copies/mL.
Results
The median RC was 79%. Patients with a lower RC had a lower median viral load (4.0 vs 4.2 Log HIV-1 RNA copies/mL, p=0.026) and a lower rate of protease inhibitor resistance 2% vs 8%, p=0.03). Otherwise, baseline demographic and laboratory characteristics were similar. The hazard ratio of progression to the composite endpoint was 0.73 (p=0.041) for persons with lower RC, 2.07 per 1.0 log10 higher viral load (p<0.001) and 0.86 per 50 cell/μL higher CD4+ cell count (p<0.001). The effect of lower RC was also significant in a separate analysis of time to initiation of therapy (p=0.04).
Conclusion
These results show that untreated patients with lower vs higher RC had a slower rate of progression as assessed by a composite outcome of time to CD4+ count ≤350 cells/μL, treatment initiation or death.
doi:10.1097/QAI.0b013e3181cae480
PMCID: PMC2837106  PMID: 20032783
disease progression; natural history; replication; HIV infections
15.  Differences in Reversion of Resistance Mutations to Wild-Type under Structured Treatment Interruption and Related Increase in Replication Capacity 
PLoS ONE  2011;6(1):e14638.
Background
The CPCRA 064 study examined the effect of structured treatment interruption (STI) of up to 4 months followed by salvage treatment in patients failing therapy with multi-drug resistant HIV. We examined the relationship between the reversion rate of major reverse transcriptase (RT) resistance-associated mutations and change in viral replication capacity (RC). The dataset included 90 patients with RC and genotypic data from virus samples collected at 0 (baseline), 2 and 4 months of STI.
Principal Findings
Rapid shift towards wild-type RC was observed during the first 2 months of STI. Median RC increased from 47.5% at baseline to 86.0% at 2 months and to 97.5% at 4 months. Between baseline and 2 months of STI, T215F had the fastest rate of reversion (41%) and the reversion of E44D and T69D was associated with the largest changes in RC. Among the most prevalent RT mutations, M184V had the fastest rate of reversion from baseline to 2 months (40%), and its reversion was associated with the largest increase in RC. Most rates of reversion increased between 2 months and 4 months, but the change in RC was more limited as it was already close to 100%. The highest frequency of concurrent reversion was found for L100I and K103N. Mutagenesis tree models showed that M184V, when present, was overall the first mutation to revert among all the RT mutations reported in the study.
Conclusion
Longitudinal analysis of combined phenotypic and genotypic data during STI showed a large amount of variability in prevalence and reversion rates to wild-type codons among the RT resistance-associated mutations. The rate of reversion of these mutations may depend on the extent of RC increase as well as the co-occurring reversion of other mutations belonging to the same mutational pathway.
doi:10.1371/journal.pone.0014638
PMCID: PMC3031504  PMID: 21297946
16.  Response to Vicriviroc in Treatment-Experienced Subjects Using an Enhanced Sensitivity Co-receptor Tropism Assay: Reanalysis of AIDS Clinical Trials Group A5211 
The Journal of infectious diseases  2009;200(11):1724-1728.
The enhanced sensitivity Trofile assay was used to re-test co-receptor usage at study screening and entry for the 118 ACTG A5211 treatment-experienced subjects who had CCR5-tropic (R5) virus by the original Trofile assay at study screening. Among 90 vicriviroc recipients, a significantly (P<0.001) greater mean reduction in HIV-1 RNA was observed in 72 subjects with R5 virus versus 15 subjects reclassified with dual/mixed-tropic viruses at screening: −1.11 vs. −0.09 (day 14), −1.91 vs. −0.57 (week 24) log10 copies/mL, respectively. Results suggest that the enhanced sensitivity assay is a better screening tool for determining patient eligibility for CCR5 antagonist therapy.
doi:10.1086/648090
PMCID: PMC2783913  PMID: 19874179
Enhanced Trofile; CCR5; CXCR4; vicriviroc
17.  Characterization of Human Immunodeficiency Virus Type 1 Populations Containing CXCR4-Using Variants from Recently Infected Individuals 
Abstract
We screened 150 individuals from two recent seroconverter cohorts and found that six (4%) had CXCR4-using viruses. Clonal analysis of these six individuals, along with a seventh individual identified during clinical care as a recent seroconverter, revealed the presence of both X4- and dual-tropic variants in these recently infected adults. The ability of individual CXCR4-using variants to infect cells expressing CD4/CXCR4 or CD4/CCR5 varied dramatically. These data demonstrate that virus populations in some newly infected individuals can consist of either heterogeneous populations containing both CXCR4-using and CCR5-tropic viruses, or homogeneous populations containing only CXCR4-using viruses. The presence of CXCR4-using viruses at early stages of infection suggests that testing for viral tropism before using CCR5 antagonists may be important even in persons with known recent infection. The presence of CXCR4-using viruses in a subset of newly infected individuals could impact the efficacies of vaccine and microbicide strategies that target CCR5-tropic viruses.
doi:10.1089/aid.2008.0252
PMCID: PMC2827835  PMID: 19678765
18.  Comparison of Human Immunodeficiency Virus Type 1 Tropism Profiles in Clinical Samples by the Trofile and MT-2 Assays▿  
Antimicrobial Agents and Chemotherapy  2009;53(11):4686-4693.
The recent availability of CCR5 antagonists as anti-human immunodeficiency virus (anti-HIV) therapeutics has highlighted the need to accurately identify CXCR4-using variants in patient samples when use of this new drug class is considered. The Trofile assay (Monogram Biosciences) has become the method that is the most widely used to define tropism in the clinic prior to the use of a CCR5 antagonist. By comparison, the MT-2 assay has been used since early in the HIV epidemic to define tropism in clinical specimens. Given that there are few data from direct comparisons of these two assays, we evaluated the performance of the plasma-based Trofile assay and the peripheral blood mononuclear cell (PBMC)-based MT-2 assay for the detection of CXCR4 use in defining the tropism of HIV isolates derived from clinical samples. The various samples used for this comparison were derived from participants of the Amsterdam Cohort Studies on HIV infection and AIDS who underwent consecutive MT-2 assay testing of their PBMCs at approximately 3-month intervals. This unique sample set was specifically selected because consecutive MT-2 assays had demonstrated a shift from negative to positive in PBMCs, reflecting the first emergence of CXCR4-using virus in PBMCs above the level of detection of the assay in these individuals. Trofile testing was performed with clonal HIV type 1 (HIV-1) variants (n = 21), MT-2 cell culture-derived cells (n = 20) and supernatants (n = 42), and plasma samples (n = 76). Among the clonal HIV-1 variants and MT-2 cell culture-derived samples, the results of the Trofile and MT-2 assays demonstrated a high degree of concordance (95% to 98%). Among consecutive plasma samples, detection of CXCR4-using virus was at or before the time of first detection by the MT-2 assay in 5/10 patients by the original Trofile assay and in 9/10 patients by the enhanced-sensitivity Trofile assay. Differences in the time to the first detection of CXCR4 use between the MT-2 assay (PBMCs) and the original Trofile assay (plasma) were greatly reduced by the enhanced-sensitivity Trofile assay, suggesting that sensitivity for the detection of minor CXCR4-using variants may be a more important determinant of discordant findings than compartmentalization. The similarities in performance of the enhanced-sensitivity Trofile and MT-2 assays suggest that either may be an appropriate methodology to define tropism in patient specimens.
doi:10.1128/AAC.00229-09
PMCID: PMC2772338  PMID: 19687240
19.  Relationship between HIV Co-Receptor Tropism and Disease Progression in Persons with Untreated Chronic HIV Infection 
Objective
To assess the effect of HIV coreceptor tropism (CRT) on the relative risk of progression to a composite outcome of CD4+ count ≤350 cells/μL, treatment initiation or death.
Methods
CRT assays were performed after study closure in baseline samples obtained from enrollees in a prospectively monitored cohort of treatment-naïve adults with ≥450 CD4+ cells/μL and ≥1,000 HIV-1 RNA copies/mL.
Results
Dual/mixed (D/M) and R5 CRT was detected in 32 and 282 patients, respectively. The baseline CD4+ count (617 vs 694 cells/μL; p=0.05) differed in patients with D/M versus R5 CRT. Otherwise, baseline laboratory characteristics were similar.
The relative risk of progression to the composite endpoint was 2.15 (p=0.002) for D/M versus R5 CRT, 2.07 per 1.0 log10 higher viral load (p<0.001) and 0.87 per 50 cell/μL higher CD4+ cell count (p<0.001). The effect of D/M CRT was also significant in separate analyses of time to initiation of antiretroviral therapy or CD4+ cell count ≤350.
Conclusion
Untreated patients with D/M rather than R5 CRT had a faster rate of disease progression, whether assessed by a composite outcome of time to CD4+ count ≤350, treatment initiation or death, or by separate analyses of time to CD4+ count ≤350 or treatment initiation.
doi:10.1097/QAI.0b013e3181989a8b
PMCID: PMC2670851  PMID: 19194318
Tropism; HIV receptors; Natural history; Progression; Prognosis
20.  Assessing Human Immunodeficiency Virus Type 1 Tropism: Comparison of Assays Using Replication-Competent Virus versus Plasma-Derived Pseudotyped Virions ▿  
Journal of Clinical Microbiology  2009;47(8):2604-2606.
Detection of CXCR4-using human immunodeficiency virus by the Trofile assay was compared to that by assays using virus isolates or replication-competent recombinants. Concordance with the Trofile assay was good, but assays using replicating viruses did not increase substantially the ability to detect the presence of CXCR4-using virus.
doi:10.1128/JCM.00632-09
PMCID: PMC2725648  PMID: 19494074
21.  Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo 
PLoS ONE  2009;4(5):e5683.
High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected from 4 chronically HIV-infected subjects in whom CCR5 antagonist (vicriviroc [VVC]) therapy failed. Between 25,000–140,000 amplified sequences were obtained per sample. Profound baseline V3 loop sequence heterogeneity existed; predicted CXCR4-using populations were identified in a largely CCR5-using population. The V3 loop forms associated with subsequent virologic failure, either through CXCR4 use or the emergence of high-level VVC resistance, were present as minor variants at 0.8–2.8% of baseline samples. Extreme, rapid shifts in population frequencies toward these forms occurred, and deep sequencing provided a detailed view of the rapid evolutionary impact of VVC selection. Greater V3 diversity was observed post-selection. This previously unreported degree of V3 loop sequence diversity has implications for viral pathogenesis, vaccine design, and the optimal use of HIV-1 CCR5 antagonists.
doi:10.1371/journal.pone.0005683
PMCID: PMC2682648  PMID: 19479085
22.  In Vivo Emergence of Vicriviroc Resistance in a Human Immunodeficiency Virus Type 1 Subtype C-Infected Subject▿ †  
Journal of Virology  2008;82(16):8210-8214.
Little is known about the in vivo development of resistance to human immunodeficiency virus type 1 (HIV-1) CCR5 antagonists. We studied 29 subjects with virologic failure from a phase IIb study of the CCR5 antagonist vicriviroc (VCV) and identified one individual with HIV-1 subtype C who developed VCV resistance. Studies with chimeric envelopes demonstrated that changes within the V3 loop were sufficient to confer VCV resistance. Resistant virus showed VCV-enhanced replication, cross-resistance to another CCR5 antagonist, TAK779, and increased sensitivity to aminooxypentane-RANTES and the CCR5 monoclonal antibody HGS004. Pretreatment V3 loop sequences reemerged following VCV discontinuation, implying that VCV resistance has associated fitness costs.
doi:10.1128/JVI.00444-08
PMCID: PMC2519584  PMID: 18495779
23.  A Novel Substrate-Based HIV-1 Protease Inhibitor Drug Resistance Mechanism 
PLoS Medicine  2007;4(1):e36.
Background
HIV protease inhibitor (PI) therapy results in the rapid selection of drug resistant viral variants harbouring one or two substitutions in the viral protease. To combat PI resistance development, two approaches have been developed. The first is to increase the level of PI in the plasma of the patient, and the second is to develop novel PI with high potency against the known PI-resistant HIV protease variants. Both approaches share the requirement for a considerable increase in the number of protease mutations to lead to clinical resistance, thereby increasing the genetic barrier. We investigated whether HIV could yet again find a way to become less susceptible to these novel inhibitors.
Methods and Findings
We have performed in vitro selection experiments using a novel PI with an increased genetic barrier (RO033-4649) and demonstrated selection of three viruses 4- to 8-fold resistant to all PI compared to wild type. These PI-resistant viruses did not have a single substitution in the viral protease. Full genomic sequencing revealed the presence of NC/p1 cleavage site substitutions in the viral Gag polyprotein (K436E and/or I437T/V) in all three resistant viruses. These changes, when introduced in a reference strain, conferred PI resistance. The mechanism leading to PI resistance is enhancement of the processing efficiency of the altered substrate by wild-type protease. Analysis of genotypic and phenotypic resistance profiles of 28,000 clinical isolates demonstrated the presence of these NC/p1 cleavage site mutations in some clinical samples (codon 431 substitutions in 13%, codon 436 substitutions in 8%, and codon 437 substitutions in 10%). Moreover, these cleavage site substitutions were highly significantly associated with reduced susceptibility to PI in clinical isolates lacking primary protease mutations. Furthermore, we used data from a clinical trial (NARVAL, ANRS 088) to demonstrate that these NC/p1 cleavage site changes are associated with virological failure during PI therapy.
Conclusions
HIV can use an alternative mechanism to become resistant to PI by changing the substrate instead of the protease. Further studies are required to determine to what extent cleavage site mutations may explain virological failure during PI therapy.
Changes in the cleavage site of the Gag substrate for the HIV protease can convey resistance to protease inhibitors and might contribute to virologic failure during therapy that includes these drugs.
Editors' Summary
Background.
Twenty-five years ago, infection with the human immunodeficiency virus (HIV)—the causative agent of AIDS—was a death sentence. However, drugs that attack various stages of the HIV life cycle were soon developed that, although not curing the infection, kept it in check when used in combination and greatly increased the life expectancy of people infected with HIV. Unfortunately, viruses resistant to these drugs have rapidly emerged and antiviral therapy now fails in many patients. The use of HIV protease inhibitors (PIs) in combination therapies, for example, has led to the stepwise selection of viral variants resistant to these drugs. Resistance is first acquired when the viral protease changes so that PIs no longer bind to it and inhibit it efficiently. These changes often reduce the efficiency with which the protease binds its substrates—polyproteins called Gag and GagPol that it chops up into smaller proteins to make new viral particles. So the next step is the accumulation of changes elsewhere in the protease that make it work better, and sometimes changes in its substrate that make it easier to cut; these compensatory changes do not directly affect viral resistance to PIs.
Why Was This Study Done?
To prevent viruses with resistance to PIs emerging, drug doses are kept high in patients and new PIs are being developed with high potency against known PI-resistant HIV variants. Both approaches set a “high genetic barrier” to the development of PI resistance by ensuring that HIV has to incorporate many changes in its protease to become resistant. But, the HIV genome naturally changes—mutates—very rapidly, so novel HIV variants could emerge that are less susceptible to the new potent PIs without the virus having to leap this high genetic barrier. In this study, the researchers have investigated whether HIV can find an alternative route to PI resistance that does not involve the introduction of multiple changes into its protease.
What Did the Researchers Do and Find?
The researchers took wild-type HIV and treated it in the laboratory with a new PI regimen that has a high genetic barrier. By gradually increasing its concentration, the researchers selected three viral populations that were able to grow in 4- to 8-fold higher concentrations of the PI than wild-type virus. None of these populations had mutations in the viral protease. Instead, they all had mutations near one of the sites—the NC/p1 site—where the protease normally cuts the Gag polyprotein. These mutations, the researchers report, enhanced the overall efficiency with which the wild-type protease cleaved the polyprotein, and a selection experiment with another PI showed that the development of PI resistance through alterations near the NC/p1 cleavage site was not unique to one PI. The researchers also investigated the potential clinical significance of this new drug resistance mechanism by looking for the same mutations in nearly 30,000 patient samples. Many of the samples did indeed have these mutations. Finally, they showed that mutations at the NC/p1 cleavage site were associated with virological failure (increased viral replication) during PI therapy in an ongoing clinical trial.
What Do These Findings Mean?
These results suggest that increased polyprotein processing because of mutations in the natural substrate of the HIV protease might be a new mechanism by which HIV can become resistant to PIs. This strategy, which occurs in the laboratory and in patients, allows HIV to develop PI resistance without the need for multiple changes in its protease and so avoids the high genetic barrier to resistance that new PIs provide. Clinical studies are now needed to test which of the mutations seen in this study contribute to virological failure, whether the degree of this failure is clinically relevant, and whether these substrate mutations enhance the effect of protease mutations. If the clinical importance of the new mechanism is confirmed, genetic examination of both the polyprotein and the protease will be needed when trying to figure out why a PI-containing therapy is failing in individual patients. Furthermore, it will be necessary to test whether this mechanism can contribute to the development of resistance when evaluating new drugs.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040036.
US National Institute of Allergy and Infectious Diseases factsheet on HIV infection and AIDS
US Department of Health and Human Services information on AIDS
US Centers for Disease Control and Prevention information on HIV/AIDS
Aidsmap information on HIV and AIDS provided by the charity NAM
BioAfrica, Bioinformatics for HIV Research, information on HIV-1 protease cleavage sites
doi:10.1371/journal.pmed.0040036
PMCID: PMC1769415  PMID: 17227139
24.  Disseminated Trichosporonosis Caused by Trichosporon loubieri 
Journal of Clinical Microbiology  2003;41(11):5317-5320.
Trichosporonosis is an emerging invasive fungal infection in immunosuppressed patients; a case of disseminated infection caused by Trichosporon loubieri presented confirms its role as a human pathogen.
doi:10.1128/JCM.41.11.5317-5320.2003
PMCID: PMC262469  PMID: 14605194
25.  Diversity of Domain V of 23S rRNA Gene Sequence in Different Enterococcus Species 
Journal of Clinical Microbiology  2000;38(11):3991-3993.
The highly conserved central loop of domain V of 23S RNA (nucleotides 2042 to 2628; Escherichia coli numbering) is implicated in peptidyltransferase activity and represents one of the target sites for macrolide, lincosamide, and streptogramin B antibiotics. DNA encoding domain V (590 bp) of several species of Enterococcus was amplified by PCR. Twenty enterococcal isolates were tested, including Enterococcus faecium (six isolates), Enterococcus faecalis, Enterococcus avium, Enterococcus durans, Enterococcus gallinarum, Enterococcus casseliflavus (two isolates of each), and Enterococcus raffinosus, Enterococcus mundtii, Enterococcus malodoratus, and Enterococcus hirae (one isolate of each). For all isolates, species identification by biochemical testing was corroborated by 16S rRNA gene sequencing. The sequence of domain V of the 23S rRNA gene from E. faecium and E. faecalis differed from those of all other enterococci. The domain V sequences of E. durans and E. hirae were identical. This was also true for E. gallinarum and E. casseliflavus. E. avium differed from E. casseliflavus by 23 bases, from E. durans by 16 bases, and from E. malodoratus by 2 bases. E. avium differed from E. raffinosus by one base. Despite the fact that domain V is considered to be highly conserved, substantial differences were identified between several enterococcal species.
PMCID: PMC87530  PMID: 11060057

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