bluuebunny/crossref_metadata_2025 huggingface dataset:
The NIQ of Lopinavir is Predictive of a 48-Week Virological Response in Highly Treatment-Experienced HIV-1-Infected Subjects Treated with a Lopinavir/Ritonavir-Containing Regimen
Authors: Castagna Antonella , Gianotti Nicola , Galli Laura , Danise Anna , Hasson Hamid , Boeri Enzo , Hoetelmans Richard , Nauwelaers David , Lazzarin Adriano
Published: April 2022

Objective

To investigate the normalized inhibitory quotient (NIQ) of lopinavir (LPV) as a predictor of 48-week virological responses to a lopinavir/ritonavir (LPV/RTV)-containing regimen in highly treatment-experienced patients.

Design

We calculated the NIQ for 59 patients who completed 48 weeks’ treatment and assessed the factors predicting a week-48 virological response.

Methods

The NIQ was calculated by dividing each subject's IQ (LPV Ctrough/fold change in LPV susceptibility, as assessed by VirtualPhenotype™) by a reference IQ (mean population LPV Ctrough/fold change in LPV IC50, as assessed by VirtualPhenotype™). HIV-1 RNA was assessed by NASBA (quantification limit: 80 copies/ml). The general linear model and multiple logistic regression, respectively, were used to estimate the independent predictors of a change in viral load and HIV-1 RNA <80 copies/ml.

Results

The median (interquartile range) baseline levels of CD4+ cells and HIV-1 RNA were 251 (141–385) cells/μl and 4.85 (4.49–5.23) log10 copies/ml, respectively. The median NIQ was 2.2 (0.5–14). At week 48, the median decrease in HIV-1 RNA was 1.4 (0.59–2.79) log10 copies/ml ( P<0.0001), with 24 subjects (41%) reaching <80 copies/ml. Baseline HIV-1 RNA ( P=0.001), CD4+ cells ( P=0.002) and NIQ ( P=0.0006) independently predicted the week-48 change in viral load, whereas baseline CD4+ cells ( P=0.011) and NIQ ( P=0.009) independently predicted a week-48 HIV-1 RNA level of <80 copies/ml.

Conclusion

The LPV NIQ independently predicts virological responses to an LPV/RTV-containing regimen in highly treatment-experienced HIV-1-infected patients.
Potent Antiviral Effect of Reverset™ in HIV-1-Infected Adults following a Single Oral Dose
Authors: Stuyver Lieven J , McBrayer Tamara R , Schürmann Dirk , Kravec Irena , Beard Amanda , Cartee Leanne , Schinazi Raymond F , Rosa Abel De La , Murphy Robert L , Otto Michael J
Published: April 2022

Reverset™ (2′,3′-didehydro-2′,3′-dideoxy-5-fluorocyti-dine, RVT) is a potent inhibitor of HIV-1 replication in cell culture, with a 90% effective concentration at or below 1 μM. In vitro, RVT retains its activity against isolates harbouring mutations in the reverse transcriptase (RT) gene that otherwise confer resistance to lamivudine and/or zidovudine. The pharmacokinetics and safety of single oral doses of RVT (10–200 mg) were evaluated in an initial Phase I clinical trial. The viral load changes were determined on 18 HIV-1-infected antiretroviral therapy-naive subjects that were randomized into three cohorts, each cohort consisting of three study periods. The subjects received up to two oral doses of active drug and one placebo dose with a 1-week washout period separating the three study periods. Quantification of viral RNA was performed on the pre-dose, 12, 24 and 48 h post-dose plasma samples. A single oral dose of RVT to antiretroviral-naive subjects significantly reduced plasma viral load by 0.45 ±0.10 log10 copies/ml ( P=0.0003). A mean drop of 0.37 ±0.12 log10 copies/ml ( P=0.001) was obtained at the lowest dose of 10 mg. Sequence analysis of the HIV-1 RT gene performed before and after RVT dosing detected no genotypic changes in this short-term study. The viral RT gene of one subject had at predose the following genotype: L41 + N103 + C181 + W210 + D215, indicating prior exposure to zidovudine and non-nucleoside analogues, and anticipating high-level resistance against these agents. A single 10 mg RVT dose resulted in a viral load drop of 0.61 ±0.05 log10 providing evidence that a viral strain with the indicated genotype is susceptible to RVT.
Clinically Validated Genotype Analysis: Guiding Principles and Statistical Concerns
Authors: Brun-Vézinet Françoise , Costagliola Dominique , Khaled Mounir Ait , Calvez Vincent , Clavel François , Clotet Bonaventura , Haubrich Richard , Kempf Dale , King Marty , Kuritzkes Daniel , Lanier Randall , Miller Michael , Miller Veronica , Phillips Andrew , Pillay Deenan , Schapiro Jonathan , Scott Janna , Shafer Robert , Zazzi Maurizio , Zolopa Andrew , DeGruttola Victor
Published: April 2022

Whereas previously the output of HIV resistance tests has been based on therapeutically arbitrary criteria, there is now an ongoing move towards correlating test interpretation with virological outcomes on treatment. This approach is undeniably superior, in principle, for tests intended to guide drug choices. However the predictive accuracy of a given stratagem that links genotype or phenotype to drug response is strongly influenced by the study design, data capture and analytical methodology used to derive it. For genotyping, the most widely used resistance tool in clinical practice, these considerations are further complicated by the range of mutational patterns present in the treated population. There is no definitively superior methodology for generating a genotype-response association for use in interpreting a resistance test, and the various approaches used to date all have their strengths and weaknesses. This review discusses the processes involved in constructing such tools, with particular emphasis on establishing validated mutation score rules, and examines the key issues and confounding factors that influence predictive accuracy outside the originating dataset. Since the size of the sample is a key influence on the statistical power to determine an effect, it is hoped that a greater understanding of the influence of study design and methodology will assist the development of standardized outcome measures and reporting formats that allow data pooling at the international level.
HIV Cohort Collaborations: Proposal for Harmonization of Data Exchange
Authors: Kjær Jesper , Ledergerber Bruno
Published: April 2022

HIV cohort studies have provided useful information on the natural history of HIV infection and the effects of antiretroviral therapy. It has become increasingly common to combine data from several cohorts into one dataset in order to address certain specific questions with more statistical power than can be achieved with the individual studies. This requires each cohort to map data into a standard format before merging. Until recently, this standard format has differed for each such collaborative analysis. We have therefore developed the HIV Cohort Data Exchange Protocol (HICDEP), which is freely available at http://www.cphiv.dk/HICDEP.pdf . Once individual cohorts have set up a means of transfering data into this format, as and when required, this should greatly facilitate data merging for future joint analyses. The HICDEP incorporates data from HIV drug resistance tests, which have been particularly challenging for cohorts to integrate into databases.
Management of Dyslipidaemia in HIV-Infected Patients Receiving Antiretroviral Therapy
Authors: Martínez Esteban , Tuset Montserrat , Milinkovic Ana , Miró José M , Gatell José M
Published: April 2022

Dyslipidaemia associated with the treatment of HIV infection, particularly with the use of protease inhibitors (PIs), can raise cholesterol and triglyceride (TG) levels to the thresholds indicated for intervention. Recent evidence from epidemiological studies has shown that there are correlations between antiretroviral drug use and increased risks for, and incidences of, cardiovascular disease, including myocardial infarction and coronary heart disease. The primary goals of dyslipidaemia therapy for HIV patients are reductions of both low-density lipoprotein cholesterol (LDL-C) and markedly elevated TG levels. Dietary strategies and exercise programs may be tried, although these have shown inconsistent results. The two options for drug therapy are switching anti-retroviral agents and using lipid-lowering drugs. Each approach is associated with advantages and limitations, and the need to maintain viral suppression must be balanced with the need to treat abnormal lipid levels. Most drug switches replace the PI component with drugs from another antiretroviral class. Selection of drug therapy for lipid lowering depends on the type of dyslipidaemia predominating and the potential for drug interactions. The use of the statins pravastatin and atorvastatin is recommended for the treatment of patients with elevated LDL-C levels and gemfibrozil or fenofibrate for patients with elevated TG concentrations. Development of new PIs with more favourable effects on the lipid profile should be of benefit.
The Correlation between Plasma Concentrations of Protease Inhibitors, Medication Adherence and Virological Outcome in HIV-Infected Patients
Authors:   the California Collaborative Treatment Group (CCTG), Yasuda Julie M , Miller Chris , Currier Judith S , Forthal Donald N , Kemper Carol A , Beall Gildon N , Tilles Jeremiah G , Capparelli Edmund V , McCutchan J Allen , Haubrich Richard H
Published: April 2022

Background

Although adherence clearly influences response to antiretroviral therapy (ART), accurate assessment of adherence is problematic. The objective of this analysis was to assess the independent predictive value of protease inhibitor (PI) concentrations as a supplement to self-report as markers of medication adherence.

Methods

This retrospective analysis was conducted from a prospective clinical trial designed to compare the outcomes of frequent versus infrequent HIV RNA measurement used to manage antiretroviral therapy. For 131 patients, self-reported medication adherence, HIV RNA levels, CD4 counts and PI concentrations (unannounced, random samples) were measured at baseline (when patients changed to a new regimen) and every 2 months thereafter. The change in HIV RNA from baseline to month 6 (area-based measure) was used to evaluate overall response. The proportion of measured PI concentrations below the detection limit was used as an alternative marker of adherence. An undetectable concentration would be expected after missing a single dose.

Results

The mean baseline CD4 count was 125 cells/mm3 and the mean HIV RNA level was 4.7 log10 copies/ml. The mean change in log10 HIV RNA was -0.73 copies/ml. The mean percentage of self-reported adherence was 91% (range: 15–100%) and the mean proportion of undetectable PI concentrations was 27% (range: 0–100%, mean 2.5 samples/patient). The correlation between the two measures was -0.23 ( P=0.009). In a multivariate model, percentage of visits with undetectable PI concentrations ( P=0.02), percentage of medication adherence ( P=0.02), baseline HIV RNA level ( P=0.005), prior PI use ( P=0.0004), prior lamivudine (3TC) use ( P=0.0009) and randomization to the frequent HIV RNA measurement group ( P<0.0001) were all related to change in HIV RNA. After accounting for adherence, patients who always had detectable PI concentrations had an average of 0.4 log10 additional HIV RNA reduction compared with those who had no detectable concentrations.

Conclusions

Repeated, random PI concentration values are independently predictive of virological response and may add to self-report of adherence in understanding the response to ART.
Effects of Zidovudine, Stavudine and β-Aminoisobutyric Acid on Lipid Homeostasis in Mice: Possible Role in Human Fat Wasting
Authors: Maisonneuve Caroline , Igoudjil Anissa , Begriche Karima , Lettéron Philippe , Guimont Marie-Christine , Bastin Jean , Laigneau Jean-Pierre , Pessayre Dominique , Fromenty Bernard
Published: April 2022

Objective

Although mitochondrial DNA (mtDNA) depletion could play a role in nucleoside reverse transcriptase inhibitor-induced lipoatrophy, poor correlations between fat mtDNA levels and lipoatrophy suggest additional mechanism(s). Stavudine (d4T), zidovudine (AZT) and the thymine catabolite, β-aminoisobutyric acid (BAIBA), but not zalcitabine (ddC) or didanosine (ddI), can increase fatty acid oxidation in liver mitochondria and plasma ketone bodies in mice. Since fat oxidation in non-adipose tissue can influence body adiposity, we sought to determine whether d4T, AZT and BAIBA can cause lipoatrophy in mice by this catabolic mechanism.

Methods

Lean or obese ob/ob mice were treated for 6 weeks with d4T, AZT or BAIBA, and lean mice with ddC or ddI. Body fat mass was assessed by dual energy X-ray absorptiometry, and mtDNA by Slot blot hybridization in epididymal fat.

Results

Whereas ddC or ddI did not change plasma β-hydroxybutyrate and body fat mass, d4T, AZT and BAIBA increased plasma β-hydroxybutyrate in lean mice suggesting increased hepatic fatty acid oxidation and ketogenesis. Despite unchanged food consumption, a supra-pharmacological dose of d4T tended to decrease, whilst AZT and BAIBA decreased body fat mass. Fat mtDNA and plasma triglycerides, cholesterol, glucose, insulin, leptin and adiponectin levels were unchanged. In obese mice, d4T, AZT and BAIBA did not increase plasma β-hydroxybutyrate, and only AZT decreased body fat mass without reducing fat mtDNA.

Conclusions

d4T and AZT can enhance hepatic fat oxidation and cause fat wasting, without decreasing adipose tissue mtDNA and without causing insulin resistance in mice. BAIBA, a thymine catabolite, reproduces these effects. These catabolic effects could play a role in the lipoatrophy, which can occur in AZT- or d4T-treated patients.
Long-Term Follow-Up of HIV-Infected Patients with Chronic Hepatitis C Virus Infection Treated with Interferon-Based Therapies
Authors: Soriano Vincent , Maida Ivana , Núñez Marina , García-Samaniego Javier , Barreiro Pablo , Martín-Carbonero Luz , González-Lahoz Juan
Published: April 2022

Background

Chronic hepatitis C virus (HCV) infection is frequent among HIV-infected patients. Clearance of serum HCV RNA 6 months after discontinuing HCV therapy is generally interpreted as a cure of HCV infection in HIV-negative subjects. However, the occurrence of liver complications (including hepatocellular carcinoma) and/or HCV relapses in coinfected patients when followed for long periods of time after HCV therapy is not well known.

Methods

All HIV-infected patients who had been treated for chronic hepatitis C at our institution and had a minimum follow-up of 6 months after discontinuing therapy were retrospectively analysed. They had received one of three HCV treatment modalities: IFN monotherapy, IFN plus ribavirin (RBV) or pegylated interferon (PEG-IFN) plus RBV.

Results

A total of 351 patients were retrospectively analysed. Sustained virological response (SVR) to HCV therapy had been reached by 77 (22%) of them: 22/119 (18.5%) with IFN monotherapy, 17/106 (16%) with IFN plus RBV and 38/126 (30.2%) with PEG-IFN plus RBV. Considering the HCV genotypes, SVR had been reached by 19/184 (10.3%) of patients with genotype 1, 54/138 (39.1%) with genotypes 2 or 3, and 4/29 (13.8%) of those with genotype 4. Within a total of 4466 patient-months follow-up (mean of 58 months), none of the 77 patients with SVR showed HCV-RNA rebounds, elevations in liver enzymes potentially linked to HCV, development of hepatocellular carcinoma or episodes of decompensated cirrhosis. In contrast, all 274 patients who did not reach SVR with HCV therapy showed evidence of persistent serum HCV RNA and 90% of them showed liver enzyme elevations during a total of 15 344 patient-months follow-up (mean of 56 months). Moreover, 11 (4%) developed clinical complications of liver cirrhosis and two of them died of end-stage liver disease.

Conclusions

HCV replication and HCV-related liver disease seem to be permanently halted in HIV/HCV-coinfected patients showing HCV-RNA clearance 6 months after completing any kind of IFN-based therapy. In contrast, complications of liver disease due to persistent HCV infection continue to occur in non-responders. The role of maintenance HCV therapy should be explored in HIV/HCV-coinfected patients.
Challenges for the Clinical Development of New Nucleoside Reverse Transcriptase Inhibitors for HIV Infection
Authors: Wainberg Mark A , Sawyer James PC , Montaner Julio SG , Murphy Robert L , Kuritzkes Daniel R , Raffi Francois
Published: April 2022

There is a need for new antiretroviral drugs with activity against HIV isolates resistant to currently available agents and improved short and long-term tolerability profiles. Clinical trial designs for nucleotide and nucleoside reverse transcriptase inhibitors (NRTIs) are restricted by the characteristics of these agents (for example, their cross-resistance, resistance threshold and interaction profiles), the ethical need to ensure that patients are not maintained on suboptimal regimens, and regulatory requirements (for example, with regards to trial designs and patient populations). For example, consideration of cross-resistance profiles must influence the way in which an NRTI in development is sequenced to minimize any impact on future treatment options. The resistance threshold is determined by the number of mutations required to diminish sensitivity to a given drug. Pharmacokinetic or pharmacodynamic interactions restrict how NRTIs may be combined during clinical development. Doses may be selected on the basis of results from short-term monotherapy studies in treatment-naive patients, but such studies cannot establish the long-term efficacy or tolerability of new agents used in combination regimens. Confirmatory studies in treatment-naive populations do not meet the medical and regulatory needs for clinical data in treatment-experienced populations, while studies in treatment-experienced populations are subject to numerous clinical and logistical difficulties. Intensification, switch and hybrid study designs all offer suitable approaches to the evaluation of NRTIs with novel resistance profiles. Switch studies are particularly useful for agents with resistance profiles that suggest a specific sequencing approach in treatment and for those with the potential, based on pharmacokinetic data, for interactions with other agents. The successful development of new NRTIs will depend upon a thorough appreciation of these many and complex issues, not only among those involved in the design of clinical studies, but also those contributing to their review and conduct.
The HIV Protease Inhibitors Nelfinavir and Saquinavir, but Not a Variety of HIV Reverse Transcriptase Inhibitors, Adversely Affect Human Proteasome Function
Authors: Piccinini Marco , Rinaudo Maria T , Anselmino Annalisa , Buccinnà Barbara , Ramondetti Cristina , Dematteis Antonio , Ricotti Emanuela , Palmisano Lucia , Mostert Michael , Tovo Pier-Angelo
Published: April 2022

Background

In HIV-infected patients some clinical and immunological benefits of antiretroviral therapy, which frequently include a combination of HIV protease inhibitors (PIs) and reverse transcriptase inhibitors (RTIs), cannot be solely explained by the drugs’ action on viral enzymes. Proteasomes constitute the central protease of the ubiquitin ATP-dependent pathway involved in many cellular processes, as well as in HIV maturation and aggressiveness. Objective: To explore whether the PIs nelfinavir and saquinavir and the RTIs abacavir, nevirapine, delavirdine, stavudine and didanosine affect proteasome function in vitro and in vivo.

Methods

Peptidase activity of purified human 26S and 20S proteasomes was assayed with and without the drugs at different concentrations. Intracellular proteasome proteolytic activity was evaluated by searching for ubiquitin-tagged proteins in HL60 cells incubated with and without the drugs.

Results

At therapeutic dosages, nelfinavir and saquinavir inhibited proteasome peptidase activity and caused intracellular accumulation of polyubiquitinated proteins, a hallmark of proteasome proteolytic inhibition in vivo; the RTIs failed to evoke either effect.

Conclusion

Proteasomes are targeted by the two PIs but not the RTIs. Therefore, in HIV-infected patients the beneficial effect of a therapy including one of the two PIs should partly rely on inhibition of host proteasome function.
Pre-Incubation of Cell-Free HIV-1 Group M Isolates with Non-Nucleoside Reverse Transcriptase Inhibitors Blocks Subsequent Viral Replication in Co-Cultures of Dendritic Cells and T Cells
Authors: Njai Harr F , Lewi Paul J , Janssen Cornelus GM , Garcia Sergio , Fransen Katrien , Kestens Luc , Vanham Guido , Janssen Paul AJ
Published: April 2022

In order to study the inhibitory effect of various reverse transcriptase inhibitors (RTIs) on cell-free HIV, we adapted a recently described in vitro system, based on co-cultures of dendritic cells and resting CD4 T cells, modelling early target cells during sexual transmission. The compounds tested included the second-generation non-nucleoside RTI (NNRTI) TMC-120 (R147681, dapivirine) and TMC-125 (R165335, travertine), as well as the reference nucleoside RTI AZT (zidovudine), the nucleotide RTI PMPA (tenofovir) and the NNRTI UC-781. The virus strains included the reference strain HIV-1Ba-L and six primary isolates, representative of the HIV-1 group M pandemic. They all display the non-syncytium-inducing and CCR5 receptor-using (NSI/R5) phenotype, important in transmission. Cell-free virus was immobilized on a poly-L-lysine (PLL)-treated microwell plate and incubated with compound for 1h. Afterwards, the compound was thoroughly washed away; target cells were added and cultured for 2 weeks, followed by an extended culture with highly susceptible mitogen-activated T cells. Viral production in the cultures was measured on supernatant with HIV antigen ELISA. Negative results were confirmed by showing absence of proviral DNA in the cells.

TMC-120 and TMC-125 inhibited replication of HIV-1Ba-L with average EC50 values of 38 nM and 117 nM, respectively, whereas the EC50 of UC-781 was 517 nM. Complete suppression of virus and provirus was observed at compound concentrations of 100, 300 and 1000 nM, respectively. Inhibition of all primary isolates followed the same pattern as HIV-1Ba-L. In contrast, pre-treating the virus with the nucleotide RTI PMPA and AZT failed to inhibit infection even at a concentration of 100000 nM. These data clearly suggest that NNRTIs inactivate RT enzymatic activity of different viral clades (predominant in the epidemic) and might be proposed for further testing as a sterilizing microbicide worldwide.
Dynamic Changes in Clinical Features and Cytokine/Chemokine Responses in Sars Patients Treated with Interferon Alfacon-1 plus Corticosteroids
Authors: Ward Sarah E , Loutfy Mona R , Blatt Lawrence M , Siminovitch Katharine A , Chen Jiabing , Hinek Anna , Wolff Bryan , Pham Dieu H , Deif Hassan , LaMere Elizabeth A , Kain Kevin C , Farcas Gabriella A , Ferguson Patti , Latchford Mary , Levy Gary , Fung Liasum , Dennis James W , Lai Enoch KY , Fish Eleanor N
Published: April 2022

Severe acute respiratory syndrome (SARS), caused by a novel coronavirus, emerged in early 2003 as a major international health crisis. We report on serum cytokine levels, viral load and clinical parameters over the course of the disease in a cohort of nine adult SARS patients treated with steroids and interferon alfacon-1 at North York General Hospital in Toronto, Ontario. Considerable variation among SARS patients with respect to circulating viral load and patterns of SARS-CoV-evoked cytokine responses was recorded. No single cytokine profile was observed in all patients, yet serum concentrations of interferon (IFN)-γ, interleukin (IL)-10, CXCL10, CCL5 and CXCL8 were found to be elevated above normal levels during the course of the disease in all patients. Expression levels for IL-10, IFN-γ and CXCL10 consistently peaked within 4 days of peak viral load. IL-12p70, IL-4 and tumour necrosis factor-α concentrations were consistently highest within 5 days of peak viral load. These results suggest that elevated levels of inflammatory cytokines are sensitive correlates of disease severity, including lung abnormalities and viral load in serum, and may provide a tool for monitoring disease progression in affected individuals.
Incidence and Risk Factors for Mitochondrial Toxicity in Treated HIV/HCV-Coinfected Patients
Authors: Laguno Montse , Milinkovic Ana , de Lazzari Elisa , Murillas Javier , Martínez Esteban , Blanco Jose Luis , Loncá Montse , Biglia Alejandra , Leon Agathe , García Mercedes , Larrousse Maria , García Felipe , Miró Jose Maria , Gatell Jose Maria , Mallolas Josep
Published: April 2022

Background

Coinfection with hepatitis C virus (HCV) and HIV is not uncommon and therapies for both infections are currently available. A major drawback, however, could be a potentially higher risk for mitochondrial toxicity (MT), defined as the elevation of pancreatic enzymes or lactate levels due to the nucleoside analogue reverse transcriptase inhibitors contained in both therapies.

Methods

Prospective analyses of clinical and laboratory data, including plasma lactate levels and pancreatic enzymes, of 113 consecutive HIV/HCV-coinfected patients were assigned to receive ribavirin (RBV) plus interferon (IFN)-α.

Results

Fourteen patients (12%) showed increased levels of amylase/lipase and/or hyperlactataemia. No patient developed clinical pancreatitis. Four patients with hyperlactataemia had clinical symptoms of lactic acidosis and recovered uneventfully by 2 weeks after treatment withdrawal. The variables significantly associated with MT in the univariate analysis were: therapy with didanosine (ddI), ddI plus stavudine (d4T), previous history of diabetes and the baseline lactate level. However, ddI use was the only independent risk factor for MT identified in the multivariate analysis. MT was not associated with gender, age, alcohol consumption, type of IFN, degree of steatosis and fibrosis in liver biopsy, presence of lipodystrophy, CD4+ cell count, HCV or HIV viral load, mitochondrial DNA and COXII-expression in liver tissue, or antiretroviral therapy containing d4T or protease inhibitors.

Conclusions

12% of HIV/HCV-coinfected patients receiving IFN plus RBV concomitantly with highly active antiretroviral therapy developed laboratory markers of MT. Although most of cases were asymptomatic, our study suggests that concomitant use of RBV plus ddI should be avoided, and that routine monitoring of lactate and pancreatic enzymes may be recommended.
Evaluation of Methods for Monitoring Drug Resistance in Chronic Hepatitis B Patients during Lamivudine Therapy Based on Mass Spectrometry and Reverse Hybridization
Authors: Kim Hyon-Suk , Han Kwang-Hyub , Ahn Sang Hoon , Kim Eun-Ok , Chang Hye-Young , Moon Myoung Soon , Chung Hyun Jae , Yoo Wangdon , Kim Soo-Ok , Hong Sun Pyo
Published: April 2022

A matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based genotyping assay, termed restriction fragment mass polymorphism (RFMP) has been recently developed for detecting hepatitis B virus (HBV) mutants. The assay is based on PCR amplification and mass measurement of oligonucleotides containing sites of mutations that confer resistance to lamivudine. We compared the efficacy and usefulness of the RFMP assay with a commercial assay using a reverse hybridization line probe technology, namely INNO-LiPA HBV DR (referred to henceforth as the LiPA assay), for the detection of lamivudine-resistant HBV mutants. A total of 60 patient samples were analysed for the presence of mutations at rtL180M and rtM204I/V of HBV polymerase by the LiPA and RFMP assays. The ability to detect mutations at rtM204I/V was compared with defined mixtures of wild-type and mutant HBV cloned in plasmids at relative concentrations ranging from 1–25%. Concordance between methods was found to be 95.0% (57/60) when only the presence of resistance mutations was considered, regardless of quasispecies. In three cases, additional minor populations of resistant viruses were identified by RFMP. Defined mixtures were consistently successfully identified at a 1% relative concentration of mutant versus wild-type viruses by the RFMP assay and 4% by the LiPA assay. The RFMP assay proved to be an accurate and reliable tool for detection of lamivudine-resistant mutations and was more sensitive than the LiPA assay in detecting mixtures of mutant and wild-type viruses. The improved sensitivity of the RPMP assay can help monitor drug resistance as it develops, enabling early intervention and prevention.
Comparison of Tests and Procedures to Build Clinically Relevant Genotypic Scores: Application to the Jaguar Study
Authors: Flandre Philippe , Marcelin Anne-Geneviève , Pavie Juliette , Shmidely Nathalie , Wirden Marc , Lada Olivier , Bernard Marie-Charlotte , Molina Jean-Michel , Calvez Vincent
Published: April 2022

Objective

To compare non-parametric tests and procedures of selection in building clinically validated genotypic scores.

Design and patients

In the Jaguar study, 111 patients on a stable antiretroviral regimen experiencing virological failure were randomized in the didanosine (ddI) arm to receive ddI for 4 weeks in addition to their current combination therapy.

Methods

The virological response was HIV-1 RNA reduction from baseline to week 4. The univariate impact of each mutation associated with resistance to ddI on virological response was quantified by comparing reduction in plasma HIV-1 RNA in patients with or without the specific mutation, using a Wilcoxon–Mann–Whitney test. The next step was to select the combination of mutations most strongly associated with the virological response. Two procedures and two tests were compared using either the set of resistance mutations or the set of resistance mutations and mutations providing a better virological response. The Kruskal–Wallis and the Jonckheere test for ordered alternatives were compared in order to build a genotypic score using the two distinct procedures.

Results

Eight mutations were associated with a reduced virological response to ddI: M41L, D67N, T69D, L74V, V118I, L210W, T215Y/F and K219Q/E and two mutations with a better virological response: K70R and M184V/I. The Jonckheere–Terpstra test for trend provided the combination of mutations (M41L+T69D-K70R+L74V-M184V /I+T215Y/F+ K219A/E) that were the most predictive for the week 4 virological response, that is, leading to the lowest P value. The ‘removing’ procedure, starting from a set of mutations retained and removing mutations one by one to find the best combination, provides lower P values than the ‘adding’ procedure starting with a single mutation and adding mutations one by one. Whatever the set of mutations and the procedure used, the Jonckheere–Terpstra test selects combinations of mutations leading to lower P values than the Kruskal–Wallis test.

Conclusion

The Jonckheere–Terpstra test for trend is recommended for building a genotypic score when compared with the Kruskal–Wallis. The choice of the selection procedure is discussed here and may be dependent on the objective of the score.
Early Virological Failure after Tenofovir + Didanosine + Efavirenz Combination in HIV-Positive Patients upon Starting Antiretroviral Therapy
Authors:   KARINA-SISTHER Collaboration Group of the MASTER Cohort, Torti Carlo , Quiros-Roldan Eugenia , Regazzi Mario , Antinori Andrea , Patroni Andrea , Villani Paola , Tirelli Valeria , Cologni Giuliana , Zinzi Daniela , Caputo Sergio Lo , Perini Paolo , Carosi Giampiero , Torti C , Quiros-Roldan E , Patroni A , Tirelli V , Cologni G , Lapadula G , Castelnuovo F , Paraninfo G , Casari S , Moretti F , Costarelli S , Carosi G , Zinzi D , Zaccarelli M , Marconi P , Antinori A , Lo Caputo S , Pierotti P , Mazzotta F , Perini P , Orani AM , Villani P , Cusato M , Regazzi M , Gargiulo F , Manca N , Tinelli C
Published: April 2022

A prospective, randomized pilot trial was conducted in naive patients comparing three different combinations: zidovudine+lamivudine+lopinavir/ritonavir (arm A) versus tenofovir+lamivudine+efavirenz (arm B) versus tenofovir+didanosine+efavirenz (arm C). HIV-RNA slope (days 1, 3, 7, 14 and 28) was slower in arm C with respect to arm B ( P<0.0001). Seven out of eight patients (87.5%) reached undetectable HIV-RNA by week 28 in arm A, 10/10 (100%) in arm B and 6/10 (60%) in arm C. Among arm C patients who failed at week 4, one HIV isolate showed 67N and 219Q, and another one showed 210F and 215D substitutions in the HIV reverse transcriptase gene at baseline, respectively. Non-nucleoside reverse transcriptase inhibitor resistance-related mutations appeared first, followed by 65R mutations in all cases. Efavirenz AUC0–24 values were lower in arm C with respect to arm B, especially in patients who failed early. A high virological failure rate after tenofovir+didanosine+efavirenz correlated with a slower HIV-RNA decrease and a peculiar accumulation of resistance mutations. A constellation of factors could be correlated with early failure events in patients receiving this combination such as resistance mutations or polymorphisms present at baseline, low CD4+ T-cell count or advanced disease and unexpectedly low efavirenz plasma levels.
Evolution of Hepatitis C Virus Quasispecies during Therapy with Il2 Combinated to Alpha Interferon and Ribavirin
Authors: Boulestin Anne , Sandres-Saune Karine , Alric Laurent , Pipy Bernard , Dubois Martine , Vinel Jean-Pierre , Izopet Jacques
Published: April 2022

This study analyses the impact of interleukin 2 (IL2) combined with alpha interferon (IFN-α) and ribavirin on the heterogeneity of hepatitis C virus (HCV). We studied 10 patients who took part in a clinical trial that assessed the effects of retreatment with IL2, IFN-α and ribavirin in patients who failed to clear the virus after a previous bitherapy. The heterogeneity of HCV quasispecies was assessed by cloning and sequencing the hypervariable region 1 (HVR1) in samples obtained at baseline (W0), after 12 weeks of treatment with IFN-α and ribavirin (W12), after a cycle of administration of IL2 in combination with the classical bitherapy (W21 and W24) in the eight patients who failed to clear the virus under treatment. The mean viral load at W21 and at W24 was not different from that at W12. The heterogeneity of HVR1 quasispecies after the administration of IL2 was not different from that at baseline or after 12 weeks of bitherapy. Furthermore, the proportion of nonsynonymous substitutions was unchanged after the IL2 cycles. Thus, the efficacy of the tritherapy with IL2, IFN-α and ribavirin is similar to that of the classical bitherapy. Treatment with IL2 in combination with IFN-α and ribavirin had no effect on the selective pressure on HCV quasispecies. IL2 is not the best option to treat hepatitis C.
Haematological Changes in Adults Receiving a Zidovudine-Containing Haart Regimen in Combination with Cotrimoxazole in Côte D'ivoire
Authors: Moh Raoul , Danel Christine , Sorho Souleymane , Sauvageot Delphine , Anzian Amani , Minga Albert , Gomis Olivier Ba , Kanga Constance , Inwoley André , Gabillard Delphine , Bissagnene Emmanuel , Salamon Roger , Anglaret Xavier
Published: April 2022

Objective

Neutropenia is the most frequent side effect of cotrimoxazole in sub-Saharan Africa. We estimated the incidence of haematological disorders during the first 6 months of a zidovudine-containing highly active anti-retroviral therapy (HAART) regimen in sub-Saharan African adults receiving cotrimoxazole.

Methods

Prospective cohort study in Abidjan, with blood cell count measurement at baseline (HAART initiation), month 1, month 3 and month 6.

Results

A total of 498 adults [baseline: 80% currently on cotrimoxazole prophylaxis; median CD4 count 237/mm3 [interquartile range (IQR) 181;316]; median neutrophil count 1647/mm3 (IQR 1221;2256); median haemoglobin 113 g/l (IQR 102;122)] started zidovudine (AZT)/lamivudine/efavirenz. During follow-up, 118 patients had a grade 3–4 neutropenia [(56.3/100 person-years (PY)], 23 had a grade 3–4 anaemia (9.6/100 PY) and no cases of grade 3–4 thrombocytopenia. Of the 118 patients with grade 3–4 neutropenia, 86 (73%) had to stop cotrimoxazole because neutropenia persisted, and one (<1%) had to stop AZT because of persistent neutropenia after cotrimoxazole was stopped (neutropenia-related HAART modification: 0.4/100 PY). Of the 23 patients with grade 3–4 anaemia, 11 had to stop AZT (anaemia-related HAART modification: 4.4/100 PY). In patients who stopped cotrimoxazole but not AZT, the median gain in neutrophils at 1 month was +540/mm3 (IQR +150;+896).

Conclusions

At baseline, most patients had a normal neutrophil count and 80% of them were already receiving cotrimoxazole. An unexpectedly high rate of grade 3–4 neutropenia occurred shortly after introduction of AZT. Almost all of the persistent severe neutropenia disappeared after cotrimoxazole was stopped. This suggests an accentuated drug interaction between the two drugs in these sub-Saharan African individuals. Grade 3–4 anaemia was much less frequent, but remained the first cause of AZT discontinuation.
Comparison of Three Different Interventions for the Correction of HIV-Associated Facial Lipoatrophy: A Prospective Study
Authors: Guaraldi Giovanni , Orlando Gabriella , De Fazio Domenico , Lorenzi Ilario De , Rottino Antonio , Santis Giorgio De , Pedone Antonio , Spaggiari Antonio , Baccarani Alessio , Borghi Vanni , Esposito Roberto
Published: April 2022

Objective

To compare autologous fat transfer (AFT), injections of reabsorbable [polylactic acid (PLA)] and non-reabsorbable [polyacrylamide hydrogel (PAAG)] filler materials for the treatment of HIV-related facial lipoatrophy.

Design and methods

Eligible individuals with enough residual subcutaneous fat in the abdomen or in the dorso-cervical region were offered AFT surgery. Other individuals were blindly assigned to two different surgical teams, who administered a set of PLA or PAAG injections every 4 weeks. The primary endpoint was the measurement of Bichat's fat pad region, determined by the result of dermal plus subcutaneous thickness. Secondary endpoints included body image evaluation (determined by ABCD questionnaire), facial aesthetic satisfaction (determined by Visual Analogue Scale), and aesthetic pre- and post-picture comparisons by independent reviewers. All variables were measured at baseline and at 24 weeks after the last treatment session.

Results

Twenty-four individuals received AFT and 35 were selectively randomized to PLA (20) or PAAG (15) infiltrations. PLA and PAAG groups received a mean of 5 and 6 injections respectively ( P=NS). The mean change in dermal and subcutaneous thickness was 3.3 ±4.1 mm, 3.5 ±4.0 mm; 2.1 ±3.0 mm ( P=0.687), respectively. The mean change in ABCD score result was poorer in the AFT arm, but there were no other differences in other measured factors. Four serious adverse events were documented in the AFT arm only.

Conclusions

All three interventional techniques were highly effective in improving the aesthetic satisfaction of the patients. Longer follow-up is necessary to determine the most durable and suitable treatment.
Role of the Inhibitory Quotient in HIV Therapy
Authors: Hoefnagel Jolanda GM , Koopmans Peter P , Burger David M , Schuurman Rob , Galama Jochem MD
Published: April 2022

A systemic review is presented of all studies that have evaluated the inhibitory quotient (IQ). The IQ is defined as the ratio between (trough) drug concentration and level of drug resistance of the HIV isolate. From the studies presented, it can be concluded that for protease inhibitors (PIs) and efavirenz, the phenotypic IQ is associated with virological response. The genotypic IQ (GIQ) for PIs was also demonstrated to be associated with virological response. An intrinsic limitation of the GIQ is that it is only applicable for PIs, of which resistance is based on the cumulative effect of mutations. As the IQ can be modified by adjustment of the drug dosage, it may be of clinical value. Its application in patient care should therefore be further investigated.
Mitochondrial Studies in Haart-Related Lipodystrophy: From Experimental Hypothesis to Clinical Findings
Authors: Miró Òscar , López Sònia , Cardellach Francesc , Casademont Jordi
Published: April 2022

Chronic use of antiretrovirals (ARVs) to treat HIV infection, along with more prolonged patient survival, has been associated with an increase in adverse drug effects in HIV-infected patients on treatment. It has been proposed that some of these adverse effects (including myopathy, cardiomyopathy, anaemia, hyperlactataemia/ lactic acidosis, pancreatitis, polyneuritis and lipodystrophy) could be mediated by mitochondrial (mt) toxicity. From the experimental data, it has been proposed that nucleoside analogue reverse transcriptase inhibitors (NRTIs) also inhibit γ-polymerase, the enzyme devoted to replicate (and, to a lesser extent, repair) mtDNA. It is now widely accepted that the use of most NRTIs in HIV-infected patients is associated with mtDNA depletion. Although cross-sectional studies suggest that certain ARVs, especially stavudine, are more toxic to mitochondria, the differences among different highly active ARV therapy (HAART) schedules detected in the analysis of longitudinal studies are not so clear. These types of study in previously untreated individuals suggest that the greatest mtDNA loss appears at the beginning of the treatment. Conversely, in ARV-experienced patients, the potential beneficial effects of HAART changes in terms of mtDNA content remain controversial and must be further investigated. Functional studies accompanying genetic investigations are needed for the correct pathogenic interpretation of the mtDNA abnormalities.
Mitochondrial Dna Levels of Peripheral Blood Mononuclear Cells and Subcutaneous Adipose Tissue from Thigh, Fat and Abdomen of HIV-1 Seropositive and Negative Individuals
Authors: Gerschenson Mariana , Shiramizu Bruce , LiButti Daniel E , Shikuma Cecilia M
Published: April 2022

Mitochondrial dysfunction has been demonstrated in subcutaneous adipose tissue from lipoatrophic HIV-1-infected patients treated with nucleoside reverse transcriptase inhibitors (NRTIs). To further assess mitochondrial toxicity, mitochondrial DNA (mtDNA) copies/cell were measured in subcutaneous fat from various sites. Peripheral adipose tissues were obtained from the abdominal wall near the umbilicus, anterior lateral thigh, and dorsal cervical region of the neck of individuals from four cohorts: 1) seven lipoatrophic HIV-1-infected patients receiving a regimen with nucleoside reverse transcriptase inhibitors (NRTIs) as part of highly active antiretroviral therapy (HAART) for >6 months; 2) seven non-lipoatrophic HIV-1-infected patients receiving NRTIs-containing HAART; 3) five HIV-1-infected patients on antiretroviral therapy <2 weeks (naive); 4) and five HIV-1-negative participants. Along with the adipose tissue samples, peripheral blood mononuclear cells (PBMC) were also obtained from each patient for mtDNA depletion examination. Total DNA was isolated and mtDNA copies/cell quantitated by competitive and realtime PCR. MtDNA copies/cell in abdomen, thigh, and neck fat were depleted in lipoatrophic HIV-1 seropositive compared to the seropositive naive and seronegative cohorts. MtDNA copies/cell in thigh and neck fat were also decreased in non-lipoatrophic subjects exposed to NRTIs compared with NRTI-naive and HIV seronegative controls. PBMC values did not differ among the cohorts and there was no correlation with lipoatrophy state or HIV-1 serostatus. Additionally, differences in mtDNA copies/cell were observed in the fat depots from seronegative subjects. Thigh fat mtDNA levels were 45–55% lower than abdomen and neck. These studies help demonstrate that mtDNA levels can vary in different subcutaneous adipose depots suggesting possible metabolic differences.
Altered Mitochondrial Rna Production in Adipocytes from HIV-Infected Individuals with Lipodystrophy
Authors: Galluzzi Lorenzo , Pinti Marcello , Guaraldi Giovanni , Mussini Cristina , Troiano Leonarda , Roat Erika , Giovenzana Chiara , Nemes Elisa , Nasi Milena , Orlando Gabriella , Salomoni Paolo , Cossarizza Andrea
Published: April 2022

Background

Damage to mitochondria (mt) is a major side effect of highly active antiretroviral therapy (HAART) that includes a nucleoside reverse transcriptase inhibitor (NRTI). Such damage is associated with the onset of lipodystrophy in HAART-treated HIV+ patients. To further investigate mt changes during this syndrome, we analysed the expression of mtRNA in adipocytes from lipodystrophic HIV+ patients taking NRTI-containing HAART and compared it with similar cells from healthy individuals.

Materials and methods

Total RNA was extracted from adipocytes collected from different anatomical locations of 11 HIV+ lipodystrophic patients and seven healthy control individuals. RNA was reverse transcribed and Taqman-based real-time PCR was used to quantify three different mt transcripts (ND1, CYTB and ND6 gene products). mtRNA content was normalized versus the housekeeping transcript L13.

Results

ND1, CYTB and ND6 expression was significantly reduced in HIV+ lipodystrophic patients. HIV+ men and women did not differ in a statistically significant way regarding the levels of ND1 and ND6, whereas the opposite occurred for CYTB.

Conclusions

Lipodystrophy following treatment with NRTI-containing HAART is associated with a decrease in adipose tissue mtRNAs.
A Human Neutralizing Antibody against a Conformational Epitope Shared by Oligomeric Sars S1 Protein
Authors: Duan Jinzhu , Ji Xin , Feng Jing , Han Wei , Zhang Panhe , Cao Wuchun , Guo Xueming , Qi Cai , Yang Dongling , Jin Gang , Gao Guangxia , Yan Xiyun
Published: April 2022

An antibody phage-display library was constructed from the B cells of convalescent severe acute respiratory syndrome (SARS) patients and screened using inactivated SARS coronavirus (CoV) virions as antigens. More than 80 positive clones were isolated from the library and one of them, scFv H12, was extensively characterized. scFv H12 bound to SARS-CoV with high affinity (equilibrium dissociation constant, Kd=73.5 nM), and neutralized SARS virions in vitro. The facts that scFv H12 bound to the SARS-S1 protein under non-reducing conditions and that it did not bind to monomeric S1 protein under reducing conditions strongly suggest that scFv H12 recognizes a conformational epitope shared by oligomeric S1 proteins. This study should aid in the manufacture of neutralizing antibody, provide a better understanding the immunological characteristics of SARS protein and facilitate the design of a SARS vaccine.
Clinical Performance of the New Roche Cobas® Taqman HCV Test and High Pure System for Extraction, Detection and Quantitation of HCV RNA in Plasma and Serum
Authors: Gelderblom Huub C , Menting Sandra , Beld Marcel G
Published: April 2022

We evaluated the Roche COBAS® TaqMan HCV Test For Use With The High Pure System (TaqMan HPS; Roche Diagnostics), for the extraction, detection and quantitation of hepatitis C virus (HCV) RNA in serum or plasma of HCV-infected individuals. The TaqMan HPS is a real-time PCR assay with a reported linear dynamic range of 3.0x101 to 2.0x108 HCV RNA IU/ml, and a reported lower limit of detection (LLD) of 10 IU/ml. Calculation of the HCV RNA titre is based upon an external standard curve in the presence of an internal control. Intra-assay and inter-assay variation were small in reference panel members with HCV RNA ≥100 IU/ml. Genotype performance and quantitative correlation between the TaqMan HPS and the bDNA (VERSANT® HCV 3.0 assay; Bayer Diagnostics), assessed in 59 patient samples, were good for HCV genotype 1 but poor for genotypes 2, 3 and 4. For genotypes 2, 3 and 4, values obtained from the TaqMan HPS were in general 0.5 log lower than those from the bDNA. Sensitivity was poor in low viral titre samples of genotypes 1, 2, 3 and 4. The LLD (95%) was estimated at 41 HCV RNA IU/ml for genotype 4. The TaqMan HPS underestimates HCV RNA at all levels in plasma and serum from HCV-infected individuals, and the LLD should be reconsidered. This is clinically relevant because underestimation of HCV RNA levels during therapy may lead physicians into making incorrect treatment decisions.