bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting HIV Coreceptor Usage on the Basis of Genetic and Clinical Covariates
Authors: Sing Tobias , Low Andrew J , Beerenwinkel Niko , Sander Oliver , Cheung Peter K , Domingues Francisco S , Büch Joachim , Däumer Martin , Kaiser Rolf , Lengauer Thomas , Harrigan P Richard
Published: April 2022

Background

We compared several statistical learning methods for the prediction of HIV coreceptor use from clonal HIV third hypervariable (V3) loop sequences, and evaluated and improved their effectiveness on clinical samples.

Methods

Support vector machines (SVM), artificial neural networks, position-specific scoring matrices (PSSM) and mixtures of localized rules were estimated and tested using 10x ten-fold cross-validation on a clonal dataset consisting of 1,100 matched clonal genotype-phenotype pairs from 332 patients. Different SVMs were also trained and tested on a clinically derived dataset, representing 920 patient samples from British Columbia, Canada. Methods were evaluated using receiver operating characteristic (ROC) curves.

Results

In the clonal analysis, the sensitivity of the 11/25 rule at 92.5% specificity was 59.5%. PSSMs and SVMs increased sensitivity to 71.9% and 76.4%, respectively, at the same specificity ( P<<0.05). In clinical samples, the sensitivity of the 11/25 rule and SVM decreased to 25.9% (specificity 93.9%) and 39.8% (specificity 93.5%), respectively. However, the integration of clinical data resulted in a further 2.4-fold increase in sensitivity over the 11/25 rule (63%). Univariate analyses identified 41 V3 mutations significantly associated with coreceptor usage.

Conclusion

For all methods tested, a substantial sensitivity decrease is observed on clinical data, probably owing to the heterogeneity of the viral population in vivo. In response to these complications, we present an SVM-based approach that integrates sequence information with clinical and host data, resulting in improved performance and sensitivity compared with purely sequence-based approaches.
Viral and Clinical Factors associated with Surface Gene Variants among Hepatitis B Virus Carriers
Authors: Roque-Afonso Anne Marie , Férey Marie-Pierre , Ly Thoai Duong , Graube Arielle , Costa-Faria Luciana , Samuel Didier , Dussaix Elisabeth
Published: April 2022

Background

Understanding the prevalence of potential antigenic variation of the hepatitis B virus (HBV) surface antigen (HBsAg) is fundamental for assay design and to future changes in vaccine formulation. In this study, the nature and frequency of HBsAg polymorphisms occurring in France in chronic carriers and in newly diagnosed patients were determined. We focused on variations in the major hydrophilic region (MHR), the central core of HBsAg known to be exposed on the surface and involved in antibody binding.

Methods

Two patient groups were identified: 51 chronic HBV carriers followed at our institution for >1 year; and 129 newly diagnosed patients (63 of whom had a first HBsAg-positive result at our hospital laboratory and 66 a first positive result in a private laboratory). DNA sequences of HBsAg were obtained from these 180 patients and compared with consensus sequences built with 168 full-length HBV sequences imported from GenBank. Polymorphisms of the MHR of HBsAg were analysed with the Mutation Master Software. Literature review and BLOSUM scores were used to define potentially altered antigenicity.

Results

The global frequency of MHR variants was 27.8%. Occurrence of MHR variants was independent of viral load, HBeAg status and sex, but was associated with the chronic carriers’ group, advancing age, the presence of antibodies to HBsAg, immunoprophylaxis administration, antiviral treatment and genotypic resistance to antivirals. In multivariate analysis, the independent variables associated with MHR variants were advancing age and the presence of genotypic resistance to nucleoside or nucleotide analogues.

Conclusion

Most MHR variants emerge with longer disease duration and upon indirect selective pressure. Variation of the MHR may serve to restore virus replication of resistant strains. Combined envelope and polymerase variants could impair diagnostic assays and limit treatment alternatives.
Activity of the Anti-Orthopoxvirus Compound ST-246 against Vaccinia, Cowpox and Camelpox Viruses in Cell Monolayers and Organotypic Raft Cultures
Authors: Duraffour Sophie , Snoeck Robert , De Vos Rita , Van Den Oord Joost J , Crance Jean-Marc , Garin Daniel , Hruby Dennis E , Jordan Robert , De Clercq Erik , Andrei Graciela
Published: April 2022

Background

The potential use of variola virus as a biological weapon has renewed efforts in the development of antiviral agents against orthopoxviruses. ST-246 [4-trifluoromethyl-W-(3,3a,4,4a,5,5a,6,6a-octahydro-1,3-dioxo-4,6-ethenocycloprop [f]isoindol-2(1H)-yl)-benza-mide] is an anti-orthopoxvirus compound active against several orthopoxviruses including vaccinia virus (VV), cowpox virus (CPV), camelpox virus (CMLV), ectromelia virus (ECTV) and variola virus in cell culture. The compound has been shown to inhibit the release of extracellular virus by targeting the F13L VV protein and to protect mice from VV, CPV and ECTV orthopoxvirus-induced disease.

Methods

The antiviral activity of ST-246 was assessed against extracellular and intracellular VV, CPV and CMLV production in human embryonic lung (HEL) fibroblasts and primary human keratinocyte (PHK) cell monolayers, as well as in three-dimensional raft cultures.

Results

ST-246 inhibited preferentially the production of extracellular virus compared with intracellular virus production in HEL and PHK cells (for VV) and in PHK cells (for CMLV). In organotypic epithelial raft cultures, ST-246 at 20 μg/ml inhibited extracellular VV and CMLV production by 6 logs, whereas intracellular virus yield was reduced by 2 logs. In the case of CPV, both extracellular and intracellular virus production were completely inhibited by ST-246 at 20 μg/ml. Histological sections of the infected rafts, treated with increasing amounts of drug, confirmed the antiviral activity of ST-246: the epithelium was protected and there was no evidence of viral infection. Electron microscopic examination confirmed the absence of intracellular enveloped virus forms in VV-, CPV- and CMLV-infected cells treated with 10 μg/ml of ST-246.

Conclusions

These data indicate that ST-246 is a potent anti-orthopoxvirus compound; the mode of inhibition is dependent on the virus and cell type.
Predictive Factors for Response to a Boosted Dual HIV-Protease Inhibitor Therapy with Saquinavir and Lopinavir in Extensively Pre-Treated Patients
Authors: Von Hentig Nils , Babacan Errol , Staszewski Schlomo , Stürmer Martin , Doerr Hans W , Lötsch Jörn
Published: April 2022

Objective

To evaluate predictive factors for therapy outcome of a boosted double-protease inhibitor (PI) regimen in 58 extensively pre-treated patients with HIV.

Methods

Patients received lopinavir/ritonavir 400/100 mg and saquinavir 1,000 mg twice daily without reverse transcriptase inhibitors (RTI). The primary outcome parameter was HIV RNA <400 copies/ml at week 48, secondary parameters were HIV-1 RNA and CD4+ T-cell count changes from baseline to week 48. Pharmacokinetics, genotypic resistance and clinical and individual parameters were correlated with the clinical outcome in regression analyses. Covariates for the analyses were minimum plasma concentration (Cmin), maximum plasma concentration, area under the concentration versus time curve, half-life and clearance of lopinavir and saquinavir, the genotypic inhibitory quotients (GIQ) of archived (GIQarch) and baseline PI resistance mutations, previously taken antiretrovirals, archived and baseline viral resistance mutations, baseline HIV-1 RNA and CD4+ T-cell count.

Results

The analyses detected correlations between the primary outcome parameter and several factors: baseline CD4+ T-cell count ( P=0.001); absence of mutations at V82T/A/F/I/S plus I54M/V/L ( P=0.002) or K20M/R ( P=0.010); and lopinavir CminGIQarch ( P=0.046). This regression model had a predictability of 97.0% for response to therapy. Covariates for the decrease of HIV-1 RNA from baseline to week 48 were baseline HIV-1 RNA ( P<0.001), lopinavir CminGIQarch ( P=0.013), presence/absence of mutations at V82T/A/F/I/S or I84A/V plus L10I/R/V/F, I54M/V/L or L63P ( P=0.018), and previously taken antiretrovirals ( P=0.034).

Conclusions

Baseline HIV-1 RNA <5.0 log10 and CD4+ T-cell count >200 cells/μl, lopinavir CminGIQarch >2,000 ng/ml and the absence of viral resistance mutations at V82T/A/F/I/S and I54M/V/L are highly predictive for therapeutic success of a regimen of saquinavir/lopinavir/ ritonavir without RTI in a heterogenic cohort of patients with an extensive pre-treatment history and highly variable pharmacokinetics.
Adverse Events to Antiretrovirals in the Swiss HIV Cohort Study: Effect on Mortality and Treatment Modification
Authors: Keiser Olivia , Fellay Jacques , Opravil Milos , Hirsch Hans H , Hirschel Bernard , Bernasconi Enos , Vernazza Pietro L , Rickenbach Martin , Telenti Amalio , Furrer Hansjakob ,   Swiss HIV Cohort Study, Battegay M , Bernasconi E , Böni J , Bucher H , Bürgisser Ph , Cattacin S , Cavassini M , Dubs R , Egger M , Elzi L , Erb P , Fischer M , Flepp M , Fontana A , Francioli P , Furrer H , Gorgievski M , Günthard H , Hirschel B , Hösli I , Kahlert Ch , Kaiser L , Karrer U , Keiser O , Kind C , Klimkait Th , Ledergerber B , Martinez B , Müller N , Nadal D , Opravil M , Paccaud F , Pantaleo G , Perrin L , Piffaretti J-C , Rickenbach M , Rudin C , Schmid P , Schultze D , Schüpbach J , Speck R , Taffé P , Tarr P , Telenti A , Trkola A , Vernazza P , Weber R , Yerly S
Published: April 2022

Background

Antiretroviral therapy (ART) decreases morbidity and mortality in HIV-infected patients but is associated with considerable adverse events (AEs).

Methods

We examined the effect of AEs to ART on mortality, treatment modifications and drop-out in the Swiss HIV Cohort Study. A cross-sectional evaluation of prevalence of 13 clinical and 11 laboratory parameters was performed in 1999 in 1,078 patients on ART. AEs were defined as abnormalities probably or certainly related to ART. A score including the number and severity of AEs was defined. The subsequent progression to death, drop-out and treatment modification due to intolerance were evaluated according to the baseline AE score and characteristics of individual AEs.

Results

Of the 1,078 patients, laboratory AEs were reported in 23% and clinical AEs in 45%. During a median follow up of 5.9 years, laboratory AEs were associated with higher mortality with an adjusted hazard ratio (HR) of 1.3 (95% confidence interval [CI] 1.2–1.5; P<0.001) per score point. For clinical AEs no significant association with increased mortality was found. In contrast, an increasing score for clinical AEs (HR 1.11, 95% CI 1.04–1.18; P=0.002), but not for laboratory AEs (HR 1.07, 95% CI 0.97–1.17; P=0.17), was associated with antiretroviral treatment modification. AEs were not associated with a higher drop-out rate.

Conclusions

The burden of laboratory AEs to antiretroviral drugs is associated with a higher mortality. Physicians seem to change treatments to relieve clinical symptoms, while accepting laboratory AEs. Minimizing laboratory drug toxicity seems warranted and its influence on survival should be further evaluated.
Respiratory Syncytial Virus Infection in Adults
Authors: Murata Yoshihiko , Falsey Ann R
Published: April 2022

Originally considered as only a paediatric pathogen, respiratory syncytial virus (RSV) has recently been shown to be a significant cause of respiratory illness among elderly and high-risk adults. Approximately 170,000 hospitalizations and 10,000 deaths associated with RSV occur annually in people over the age of 65 years in the United States. Although rhinorrhoea and wheezing are common symptoms among adults, the clinical syndrome associated with RSV is not distinctive and thus laboratory methods are required for specific diagnosis. Presently, the combination of reverse transcription PCR and enzyme immunoassay serology offers the best sensitivity and specificity for diagnosis of RSV. Treatment options are limited at present, with inhaled ribavirin being the only licensed drug for use in hospitalized children. Vaccines against RSV remain an unachieved goal. Promising new agents that inhibit the virus-cell fusion, cell-cell fusion, or viral gene expression are currently in development.
Influenza Virus Susceptibility and Resistance to Oseltamivir
Authors: Aoki Fred Y , Boivin Guy , Roberts Noel
Published: April 2022

Oseltamivir phosphate is a prodrug of oseltamivir carboxylate, a highly specific inhibitor of influenza virus neuraminidases. Given that oseltamivir carboxylate binds to highly conserved, essential amino acids in the catalytic site of the enzyme, and that the activity of neuraminidase is critical for virus release from infected cells and subsequent virus spread, the drug was expected to have a low propensity to select for viable resistant mutants. Indeed, viruses with neuraminidase (and haemagglutinin) substitutions conferring reduced susceptibility to oseltamivir have been generated with difficulty in vitro, and these mutants generally have reduced infectivity and transmissibility compared with wild-type virus in animal models. Studies of seasonal influenza isolates collected before the introduction of oseltamivir show an absence of naturally occurring resistance. Few resistant mutants have arisen during clinical trials of oseltamivir in seasonal influenza, with cumulative data from all Roche-sponsored studies indicating an incidence of resistance of 0.32% in adults (0.4%, including low-level mutants detected by genotyping alone in mixed virus populations) and 4.1% (5.4%) in children. Higher incidences of resistance were observed in two small Japanese studies, in which children received a different dosing schedule from their Western counterparts. In summary, the overall incidence of influenza virus resistance associated with the seasonal use of oseltamivir is currently low and resistant viruses might be of little clinical significance, except perhaps in immunocompromised individuals. However, continued vigilance, especially of emerging avian H5N1 strains, combined with careful, systematic laboratory-based monitoring, is essential.
Severe Acute Respiratory Syndrome Coronavirus Entry as a Target of Antiviral Therapies
Authors: Kuhn Jens H , Li Wenhui , Radoshitzky Sheli R , Choe Hyeryun , Farzan Michael
Published: April 2022

The identification in 2003 of a coronavirus as the aetiological agent of severe acute respiratory syndrome (SARS) intensified efforts to understand the biology of corona-viruses in general and SARS coronavirus (SARS-CoV) in particular. Rapid progress was made in describing the SARS-CoV genome, evolution and lifecycle. Identification of angiotensin-converting enzyme 2 (ACE2) as an obligate cellular receptor for SARS-CoV contributed to understanding of the SARS-CoV entry process, and helped to characterize two targets of antiviral therapeutics: the SARS-CoV spike protein and ACE2. Here we describe the role of these proteins in SARS-CoV replication and potential therapeutic strategies aimed at preventing entry of SARS-CoV into target cells.
Molecular Pathogenesis of H5N1 Influenza Virus Infections
Authors: Neumann Gabriele , Shinya Kyoko , Kawaoka Yoshihiro
Published: April 2022

Highly pathogenic H5N1 influenza viruses have become endemic in poultry populations throughout Southeast Asia and continue to infect humans with a greater than 50% case fatality rate. So far, human-to-human transmission of these viruses has been limited. Here, we discuss the molecular features of H5N1 influenza viruses that might affect their pathogenicity, and explain the current lack of efficient human-to-human transmission. Such knowledge is critical in evaluating the pandemic risk these viruses pose.
VII International Symposium on Respiratory Viral Infections
Authors: Bermingham Alison , Henrickson Kelly , Hayden Frederick , Zambon Maria
Published: April 2022

The VII International Symposium on Respiratory Viral Infections was a multidisciplinary forum for the presentation of recent advances in respiratory virus research with special emphasis on antiviral therapies and vaccine strategies. Topics covered in invited lectures included detection of novel respiratory viral pathogens and viral evolution, characterization of the 1918 pandemic virus, human metapneumovirus infections, human respiratory epithelial cultures for studying viral pathogenesis, the role of respiratory viruses in the pathogenesis of asthma, influenza-bacterial interactions, advances in generating vaccine candidates against global respiratory threats like avian influenza and SARS, antiviral resistance surveillance in influenza viruses, and a mini-symposium on advances in viral diagnostics. Other talks covered the live, attenuated intranasal influenza vaccine, monoclonals for respiratory syncytial virus (RSV), mechanisms of antiviral resistance in influenza B, and novel inhibitors for influenza, RSV and rhinovirus infections.
Major Causes of Antiviral drug Resistance and Implications for Treatment of Hepatitis B virus Monoinfection and Coinfection with HIV
Authors: Locarnini Stephen , Warner Nadia
Published: April 2022

The two key events in the life-cycle of the hepatitis B virus (HBV) involve (1) the generation from viral genomic DNA of the covalently closed circular DNA transcriptional template, and (2) the reverse transcription of the viral pregenomic RNA to form the HBV DNA genome. Diversity in the HBV genome is ensured by the low fidelity of the viral reverse transcriptase (rt). Particular selection pressures such as antiviral therapy readily select out escape mutants from this pre-existing quasispecies pool. Antiviral drug resistance in chronic hepatitis B can be caused by many factors, including the viral mutation frequency, the intrinsic mutability of the antiviral target site, the selective pressure exerted by the drug, the magnitude and rate of virus replication, the overall replication fitness of the mutant, the genetic barrier of the >compound and the availability of replication space. In the setting of HIV coinfection, the rate of replication is increased by one to two orders of magnitude, accelerating the emergence of drug resistance in this setting. The HBV genome is arranged into frame-shifted and overlapping reading frames in such a manner that antiviral drug-resistance-associated changes in the rt can result in changes in the viral envelope protein. These HBV isolates with altered surface antigens exhibit reduced binding of specific and neutralizing antibody and so have diagnostic and public health implications, especially in the setting of HIV coinfection where the risk of transmission is increased. Thus, prevention of resistance requires the adoption of strategies that effectively control virus replication, including the use of combination chemotherapy.
Darunavir: Pharmacokinetics and Drug Interactions
Authors: Back David , Sekar Vanitha , Hoetelmans Richard MW
Published: April 2022

Darunavir (TMC114) is a new HIV protease inhibitor that has demonstrated substantial antiretroviral activity against wild-type HIV-1 virus and multidrug-resistant strains. Darunavir inhibits and is primarily metabolized by cytochrome P450 3A (CYP3A) isoenzymes and is coadministered with low-dose ritonavir (darunavir/r); ritonavir is an inhibitor of CYP3A isoenzymes and pharmacologically enhances darunavir, resulting in increased plasma concentrations and allowing for a lower daily dose. The t1/2 (terminal elimination half-life) of darunavir is 15 h in the presence of ritonavir. An extensive darunavir/r drug-drug interaction programme has been undertaken, covering a wide range of therapeutic areas. Studies conducted in HIV-negative healthy volunteers and in HIV-infected patients show that the potential for interactions is well characterized and the interactions are manageable. For most drugs investigated, no dose adjustments of darunavir/r or the co-administered drug are required. This article reviews all the pharmacokinetic and drug-drug interaction studies conducted to date for darunavir/r, providing guidance on how to co-administer darunavir/r with many other antiretroviral or non-antiretroviral medications commonly used in HIV-infected individuals.
Self-Reported Non-Adherence to Antiretroviral Therapy Repeatedly assessed by Two Questions Predicts Treatment Failure in Virologically Suppressed Patients
Authors:   the Swiss HIV Cohort Study, Glass Tracy R , De Geest Sabina , Hirschel Bernard , Battegay Manuel , Furrer Hansjakob , Cavassini Matthias , Vernazza Pietro L , Bernasconi Enos , Rickenbach Martin , Weber Rainer , Bucher Heiner C
Published: April 2022

Background

The aim of this study was to explore the predictive value of longitudinal self-reported adherence data on viral rebound.

Methods

Individuals in the Swiss HIV Cohort Study on combined antiretroviral therapy (cART) with RNA <50 copies/ml over the previous 3 months and who were interviewed about adherence at least once prior to 1 March 2007 were eligible. Adherence was defined in terms of missed doses of cART (0, 1, 2 or >2) in the previous 28 days. Viral rebound was defined as RNA >500 copies/ml. Cox regression models with time-independent and -dependent covariates were used to evaluate time to viral rebound.

Results

A total of 2,664 individuals and 15,530 visits were included. Across all visits, missing doses were reported as follows: 1 dose 14.7%, 2 doses 5.1%, >2 doses 3.8%, taking <95% of doses 4.5% and missing ≥2 consecutive doses 3.2%. In total, 308 (11.6%) patients experienced viral rebound. After controlling for confounding variables, self-reported non-adherence remained significantly associated with the rate of occurrence of viral rebound (compared with zero missed doses: 1 dose, hazard ratio [HR] 1.03, 95% confidence interval [CI] 0.72–1.48; 2 doses, HR 2.17, 95% CI 1.46–3.25; >2 doses, HR 3.66, 95% CI 2.50–5.34). Several variables significantly associated with an increased risk of viral rebound irrespective of adherence were identified: being on a protease inhibitor or triple nucleoside regimen (compared with a non-nucleoside reverse transcriptase inhibitor), >5 previous cART regimens, seeing a less-experienced physician, taking co-medication, and a shorter time virally suppressed.

Conclusions

A simple self-report adherence questionnaire repeatedly administered provides a sensitive measure of non-adherence that predicts viral rebound.
Low Rate of Emergence of Nevirapine and Lamivudine Resistance after Post-Partum Interruption of a Triple-Drug Regimen
Authors: Pérez Héctor , Vignoles Moira , Laufer Natalia , Gómez Alejandro , Coll Patricia , Lattner Jorge , Rolón María , Salomón Horacio , Cahn Pedro
Published: April 2022

Introduction

Emergence of nevirapine (NVP) resistance may be a consequence of its use in monotherapy to prevent HIV mother-to-child transmission (MTCT). The aim of this study was to evaluate the emergence of strains resistant to NVP and lamivudine (3TC) after discontinuation of anti-retroviral therapy (ART) with 3TC/zidovudine (ZDV)/NVP.

Methods

Twenty pregnant women (ART-naive or pre-exposed only to ZDV), to whom 3TC/ZDV/NVP was prescribed as MTCT prophylaxis, were studied. They received ART for a median of 4 months with median viral load (VL) at labour <50 copies/ml. Samples were collected between 1 and 15 months (median: 3 months) after ART interruption. Sequence-selective real-time PCR (SPCR), which quantifies minority viral populations containing K103N, Y181C and M184V mutations, and standard genotypic sequencing were assayed.

Results

No mutations associated with resistance to 3TC or NVP were found by standard population sequencing. Analysis of K103N by SPCR showed that 35% of the patients contained ≤0.1% of viruses carrying either the AAC or AAT mutations. For Y181C mutation, 10% of the patients contained <0.5% of viruses with TGT codon change. For M184V mutation, one patient contained 6.2% of virus with GTG mutation and 13 patients (65%) contained <0.9% of mutated viruses. Four women were re-exposed to 3TC/ZDV/NVP and achieved HIV VL <50 copies/ml. No perinatal transmission occurred in any of the 22 births.

Conclusions

NVP associated with ZDV/3TC as a regimen to prevent MTCT may involve a low risk for the selection of antiretroviral-resistant strains and may not jeopardize the use of these same drugs for future treatment.
Cytokine Profiling in Abacavir Hypersensitivity Patients
Authors: Almeida Coral-Ann M , Martin Annalise M , Nolan David , Lucas Andrew , Cameron Paul U , James Ian , Phillips Elizabeth , Mallal Simon
Published: April 2022

Background

Abacavir hypersensitivity in genetically susceptible individuals implicates an abacavir-specific T-cell response to either the parent drug or a metabolite generated in vivo. We have analysed the cytokine profile in antigen-presenting cells and the T-lymphocytes that are involved in the pathological immune response to abacavir.

Methods

In this study, we compared abacavir-specific cytokine responses in cultured peripheral blood mononuclear cells (PBMCs) from HIV-infected abacavir hypersensitive, tolerant and naive individuals. Cells were cultured in the presence or absence of abacavir. Cytokine expression was determined by microarray analysis, enzyme-linked immunosorbent assays and flow cytometry.

Results

We demonstrated using in vitro models of immune activation that the production of interferon-γwas specifically induced by abacavir treatment in PBMCs obtained from hypersensitive patients carrying the HLA-B*5701 allele (median 123.86 compared with -30.83 for tolerant controls, P=0.001).

Conclusion

These results provide further insight into the immunological and metabolic basis of abacavir hypersensitivity syndrome. In vitro assays could assist in the identification of susceptible loci by providing a surrogate marker for the hypersensitivity reaction. Such a marker could be studied in unexposed individuals to shed further light on the immunopathogenesis of the abacavir hypersensitivity syndrome.
Use of Diet, Nutritional Supplements and Exercise in HIV-Infected Patients Receiving Combination Antiretroviral Therapies: A Systematic Review
Authors: Leyes Pere , Martínez Esteban , de Talló Forga Maria
Published: April 2022

Background

The use of combination antiretroviral therapy (cART) has improved the prognosis of HIV infection, but it has also been linked to a spectrum of body composition changes and metabolic alterations known as the lipodystrophy syndrome. Nutritional status could influence body composition changes.

Methods

We performed a systematic search of published peer-reviewed data on the effects of diet, nutrition support and exercise on body composition and metabolic complications in patients receiving cART.

Results

Few controlled studies, most of them with small sample size, were found. Oral nutritional support increases protein and energy intake, and results in body weight and fat mass gains. Resistance exercise, with or without an aerobic component, increases lean mass and can improve insulin resistance. Low-fat diets or exercise can result in loss of fat mass, and they should be used with caution in subjects with lipoatrophy.

Conclusions

Nutritional support and exercise result in small but significant body composition changes and can be used as complementary interventions. There is a need for further research on nutritional interventions in HIV-infected patients receiving cART.
Silver Nanoparticles Inhibit Hepatitis B virus Replication
Authors: Lu Lei , Sun Raymond Wai-Yin , Chen Rong , Hui Chee-Kin , Ho Chi-Ming , Luk John M , Lau George KK , Che Chi-Ming
Published: April 2022

Background

Silver nanoparticles have been shown to exhibit promising cytoprotective activities towards HIV-infected T-cells; however, the effects of these nanoparticles towards other kinds of viruses remain largely unexplored. The aim of the present study was to investigate the effects of silver nanoparticles on hepatitis B virus (HBV).

Methods

Monodisperse silver nanoparticles with mean particle diameters of ∼10 nm (Ag10Ns) and ∼50 nm (Ag50Ns) were prepared from AgNO3 in HEPES buffer. The in vitro anti-HBV activities of these particles were determined using the HepAD38 cell line as infection model.

Results

Ag10Ns and Ag50Ns were able to reduce the extracellular HBV DNA formation of HepAD38 cells by >50% compared with the vehicle control (that is, HepAD38 cells in the absence of silver nanoparticles). Silver nanoparticles had little effect on the amount of HBV covalently closed circular DNA (cccDNA), but could inhibit the formation of intracellular HBV RNA. Gel mobility shift assays indicated that Ag10Ns bound HBV double-stranded DNA at a DNA:silver molar ratio of 1:50; an absorption titration assay showed that the nanoparticles have good binding affinity for HBV DNA with a binding constant ( Kb) of (8.8 ±1.0)x105 dm3mol-1. As both the viral and Ag10Ns systems are in the nanometer size range, we found that Ag10Ns could directly interact with the HBV viral particles as revealed by transmission electronic microscopy.

Conclusions

Silver nanoparticles could inhibit the in vitro production of HBV RNA and extracellular virions. We hypothesize that the direct interaction between these nanoparticles and HBV double-stranded DNA or viral particles is responsible for their antiviral mechanism.
Virological Response to Darunavir/Ritonavir-Based Regimens in Antiretroviral-Experienced Patients (PREDIZISTA Study)
Authors:   the ANRS Co3 Aquitaine Cohort, Pellegrin Isabelle , Wittkop Linda , Joubert Laurence Morand , Neau Didier , Bollens Diane , Bonarek Mojgan , Girard Pierre-Marie , Fleury Hervé , Winters Bart , Saux Marie-Claude , Pellegrin Jean-Luc , Thiébaut Rodolphe , Breilh Dominique
Published: April 2022

Background

We assessed the association of baseline HIV-1 mutations, phenotypic sensitivity and pharmacokinetics with virological failure (VF) at week 12 (W12) after onset of a darunavir/ritonavir (DRV/r)-based regimen in a cohort of 67 antiretroviral-experienced HIV-patients failing on highly active antiretroviral therapy (HAART).

Methods

VF was defined as HIV RNA >2.3 log10copies/ml at W12. HIV reverse transcriptase and protease sequencing was performed at W0; mutations with a P-value <0.25 in univariable analyses were used for a backward selection to find the best mutation set for VF prediction. Genotypic and phenotypic sensitivity scores were calculated and virtual phenotype predicted fold change (FC) assessed. DRV Cmin, Cmax, AUC0→12 h and genotypic inhibitory quotient (GIQ) were determined.

Results

Patients had a median of 15 previous treatments for 10 years. Median W0 values included a T-cell count of 129 cells/μl, 4.7 log10 HIV RNA copies/ml, four major protease and six nucleoside reverse transcriptase inhibitor resistance mutations. At W12, median HIV RNA decrease was -2.1 log10 copies/ml with a gain of +67 CD4+ T-cells/μl; 40% of patients failed. We determined the genotypic score I13V+V32I+L33F/I/V+E35D+ M36I/L/V+I47V+F53L+I62V According to <4, 4–5 and >5 mutations, failure occurred in 11%, 48% and 100% of patients. Failure was associated with CDC stage, baseline CD4+ T-cell count, number of major protease inhibitor resistance mutations, FC and DRV/r score. Pharmacokinetics were not associated with failure, but GIQ was.

Conclusion

At W12, 60% of heavily pretreated patients responded on DRV/r-based HAART. Genotypic and phenotypic information constituted the main virological response determinant in patients with optimal drug concentrations.
Virological Pattern in Plasma, Peripheral Blood Mononuclear Cells and Liver Tissue and Clinical Outcome in Chronic Hepatitis B and C virus Coinfection
Authors: Coppola Nicola , Pisapia Raffaella , Tonziello Gilda , Martini Salvatore , Imparato Michele , Piai Guido , Stanzione Maria , Sagnelli Caterina , Filippini Pietro , Piccinino Felice , Sagnelli Evangelista
Published: April 2022

Background

We aim to evaluate in chronic hepatitis B virus–hepatitis C virus (HBV–HCV) coinfection the interplay of these viruses in liver tissue, peripheral blood mononuclear cells (PBMC), and plasma and to analyze the effect on disease course and response to treatment.

Methods

We enrolled 19 patients with chronic HBV–HCV coinfection, 20 with chronic HCV and 20 with chronic HBV infection at their first liver biopsy, all were naive for antiviral therapy. The patients’ plasma, PBMC and liver biopsy samples were tested for HBV DNA and/or HCV RNA by real-time PCR, according to the presence/absence of hepatitis B surface antigen and antibodies against HCV in the serum.

Results

Contemporary presence of HBV DNA and HCV RNA was rare in plasma (5.3% of cases) and PBMC (10.6%), but frequent in liver tissue (52.6%). Of 10 cases circulating only HCV RNA and treated with pegylated interferon (PEG-IFN) plus ribavirin for 12 months, two showed a sustained response, and eight cleared HCV RNA but became HBV-DNA-positive in plasma; these eight had detectable HBV DNA in liver at baseline. One patient, who was plasma HBV-DNA-positive/HCV-RNA-negative at baseline, showed a sustained response after 18 months of PEG-IFN treatment; another, who was plasma HBV-DNA/HCV-RNA-positive at baseline, cleared only HCV RNA during 12 months of PEG-IFN plus ribavirin treatment. Seven cases remained untreated.

Conclusion

Despite a reciprocal inhibition in plasma, HBV and HCV frequently coexist in liver tissue, a condition to be taken into consideration when deciding therapy.
A Systematic Review of T-cell Epitopes in Hepatitis B Virus: Identification, Genotypic Variation and Relevance to Antiviral Therapeutics
Authors: Desmond Christopher P , Bartholomeusz Angeline , Gaudieri Silvana , Revill Peter A , Lewin Sharon R
Published: April 2022

Background

The immune response to hepatitis B virus (HBV) is important for both viral control and disease pathogenesis. A detailed understanding of the HBV-specific T-cell responses may potentially lead to novel therapeutic strategies for HBV.

Methods

All English language journal articles (including articles in press) up to October 2007 were retrieved using searches of MEDLINE, EMBASE and the Cochrane Controlled Trial Registry. An extensive database of HBV sequences (SeqHepB) and GenBank were used to assess the degree of sequence variation in each epitope. The new standardized nomenclature for HBV amino acid position number was applied to all previously defined epitopes.

Results

Forty-four HBV-specific human leukocyte antigen (HLA) class I restricted and 32 HBV-specific HLA class II restricted epitopes have been defined and have been identified in all HBV genes. The majority of HLA class I restricted epitopes have been defined in HLA-A2-positive individuals in the setting of acute HBV infection. There is significant sequence variation of these epitopes within and between HBV genotypes. Newer HBV immunotherapeutics appear promising but are still in early phases of development.

Conclusions

Identification of HBV-specific epitopes in non-HLA-A2-positive individuals and recognition of genotypic variation across epitopes are important for the future development of novel immunotherapeutic strategies for the management of chronic HBV infection.
Long-Term Efficacy and Safety of First-Line Therapy with Once-Daily Saquinavir/Ritonavir
Authors:   Staccato Thailand Study Group, Ananworanich Jintanat , Gayet-Ageron Angele , Ruxrungtham Kiat , Chetchotisakd Ploenchan , Prasithsirikul Wisit , Kiertiburanakul Sasisopin , Munsakul Warangkana , Raksakulkarn Phitsanu , Tansuphasawadikul Somboon , LeBraz Michelle , Jupimai Thidarat , Ubolyam Sasiwimol , Schutz Malte , Hirschel Bernard
Published: April 2022

Background

The aim of this study was to assess the long-term efficacy and safety of first-line treatment with once-daily saquinavir/ritonavir plus two nucleoside reverse transcriptase inhibitors (NRTIs).

Methods

A total of 272 antiretroviral-naive patients with a CD4+ T-cell count of 200–350 cells/mm3 were treated with two NRTIs and saquinavir/ritonavir 1,600/100 mg per day for ≥24 weeks. Patients were followed up every 12 weeks for CD4+ T-cell counts, HIV RNA levels, clinical and laboratory toxicities. Intention-to-treat analyses were used for the first 24 weeks of treatment and as-treated analysis after week 24.

Results

The median baseline CD4+ T-cell count was 269 cells/mm3 and HIV RNA was 4.7 log10 copies/ml. At a median follow-up time of 56 (interquartile range [IQR] 25–113) weeks, 262/272 (96.3%) had HIV RNA <400 copies/ml, with a median HIV RNA decline of -2.89 (IQR 3.31–2.37) log10 copies/ml ( P<0.001) and a median rise in CD4+ T-cell count of 192 (IQR 117–317) cells ( P<0.001). At weeks 24, 48, 72 and 96, 249/272 (91.5%), 157/164 (95.7%), 113/126 (89.7%) and 84/90 (93.3%) had HIV RNA <400 copies/ml, respectively; at the same time points, 83.8%, 92.7%, 85.7% and 85.6% had HIV RNA <50 copies/ml. Drug-related adverse events were reported in 6.3%. Significant rises in total cholesterol, triglyceride, low-density lipoprotein and high-density lipoprotein were seen.

Conclusion

First-line highly active antiretroviral therapy with once-daily saquinavir/ritonavir plus two NRTIs showed strong antiviral efficacy.
A Randomized Study to Evaluate Injection Site Reactions using Three Different Enfuvirtide Delivery Mechanisms (the OPTIONS Study)
Authors: Boyd Mark A , Truman Matt , Hales Gillian , Anderson Jonathan , Dwyer Dominic E , Carr Andrew
Published: April 2022

Background

The antiretroviral enfuvirtide (ENF) is injected subcutaneously using a 27-gauge needle. Injection site reactions (ISRs) can affect long-term ENF tolerability. Alternative ENF delivery methods may ameliorate ISRs.

Methods

We conducted a multicentre, open-label, randomized controlled trial in which patients receiving ENF were randomized to continue receiving ENF by a 27-gauge needle, a shorter 31-gauge needle or a gas-powered, needle-free injection device (NFID). The primary study endpoint was the proportion of participants with <grade 2 ISR induration at week 12.

Results

Sixty patients received treatment and were included in the intention-to-treat population. The cohort was predominantly male (95%) with a mean age of 49.1 (SD ±7.7) years who had injected ENF for a mean of 821 (SD ±561) days. Response rates for ISR induration at week 12 were 38%, 25% and 42% for the 27-gauge, 31-gauge and NFID groups, respectively (all pairwise treatment comparison P-values >0.2). There was no significant between-group difference for any ISR endpoint, except for changes in the composite ISR score (that is, no ongoing pain of ≥grade 1 or ISR for ongoing pain ≥grade 1 with induration ISR <grade 3 and for nodules <grade 2), which favoured the 27-gauge needle and NFID groups over the 31-gauge group ( P=0.012 and 0.047, respectively). Plasma HIV RNA load was unaffected. There were seven adverse events related to the delivery system: five attributed to the NFID. At week 12, 85% of participants elected to use the NFID.

Conclusion

Needle-free ENF injection offers a reasonable, reliable alternative to needle-based injecting in this population, at least in the short term.
Rapid Semiquantitative Real-Time PCR for the Detection of Human Cytomegalovirus UL97 Mutations Conferring Ganciclovir Resistance
Authors: Göhring Katharina , Mikeler Elfriede , Jahn Gerhard , Rohde Frank , Hamprecht Klaus
Published: April 2022

Background

The development of infections with ganci-clovir (GCV)-resistant human cytomegalovirus (HCMV) remains a serious problem in recipients of stem cell or organ transplants. Nearly all GCV-resistant clinical isolates have mutations in the viral UL97 gene. The rapid detection of GCV-resistant HCMV infections is necessary and the relative proportions of wild-type and mutant strains are predictive for the efficiency of antiviral therapy. To date, genotypical resistance screening has been limited to restriction fragment length polymorphism (RFLP) and sequencing analyses. Here, we present a comprehensive real-time PCR approach for the detection of most frequent mutations in the UL97 gene associated with GCV resistance.

Methods

The laboratory strains AD169 and Towne, different wild-type isolates and plasmids constructed by site-directed mutagenesis and overlap extension with specific point-mutations in the UL97 gene were analysed by LightCycler PCR and compared with UL97 RFLP and sequencing analyses.

Results

A new and comprehensive set of LightCycler PCRs was created using specific hybridization probes with melting-point analysis for the relevant codons 594, 595, 603 and 607. Different wild-type isolates and plasmids containing specific UL97 mutations conferring GCV resistance were investigated in the real-time PCR assay. Total processing time was 80 min per assay, whereas combinations of RFLP and sequencing needed at least 3–4 days. Proportions of co-existing wild-type and mutant strains in mixed viral populations can be obtained.

Conclusions

We established a rapid real-time PCR approach for the detection of most frequent HCMV UL97 mutations associated with GCV resistance. Moreover, the method allows semiquantitative differentiation of the proportions of co-existing wild-type and mutant strains. This approach represents a new alternative for laborious RFLP analysis.
Modelled in vivo HIV Fitness under drug Selective Pressure and Estimated Genetic Barrier Towards Resistance are Predictive for Virological Response
Authors:   the EuroSIDA Study Group, Deforche Koen , Cozzi-Lepri Alessandro , Theys Kristof , Clotet Bonaventura , Camacho Ricardo J , Kjaer Jesper , Van Laethem Kristel , Phillips Andrew , Moreau Yves , Lundgren Jens D , Vandamme Anne-Mieke
Published: April 2022

Background

A method has been developed to estimate a fitness landscape experienced by HIV-1 under treatment selective pressure as a function of the genotypic sequence thereby also estimating the genetic barrier to resistance.

Methods

We evaluated the performance of two estimated fitness landscapes (nelfinavir [NFV] and zidovudine [AZT] plus lamivudine [3TC]) to predict week 12 viral load (VL) change for 176 treatment change episodes (TCEs) and probability of week 48 virological failure for 90 TCEs, in treatment experienced patients starting these drugs in combination.

Results

A higher genetic barrier for AZT plus 3TC, (quantified per additional mutation required to develop resistance against these drugs) was associated with a 0.54 (95% confidence interval [CI] 0.30–0.77) larger log10 VL reduction at 12 weeks ( P<0.0001) and a 0.39 (95% CI 0.23–0.66) lower odds of virological failure at 48 weeks ( P=0.0005), in analyses adjusting for the pre-TCE VL and the exact time-lag between the TCE and the date of determining response VL. The strength of these associations was comparable with those seen with expert interpretation systems (Rega, ANRS and HIVDB). A higher genetic barrier to NFV resistance was the only genotypic predictor that tended to be associated with a 0.19 (95% CI 0–0.39) higher log10 VL reduction at 12 weeks ( P=0.05) and a 0.63 (95% CI 0.36–1.09) lower odds of virological failure at 48 weeks ( P=0.10) per additional mutation.

Conclusions

These results suggest that an estimated genetic barrier derived from fitness landscapes may contribute to an improvement of predicted treatment outcome for NFV and this approach should be explored for other drugs.
Prediction of Sustained Virological Response by Ribavirin Plasma Concentration at Week 4 of Therapy in Hepatitis C virus Genotype 1 Patients
Authors: Maynard Marianne , Pradat Pierre , Gagnieu Marie-Claude , Souvignet Claude , Trepo Christian
Published: April 2022

Background

Pegylated interferon/ribavirin combination is currently the standard treatment for chronic hepatitis C virus (HCV) infection. Body weight adjustment of ribavirin is crucial for response. However, previous studies found no relation between ingested dose and plasma concentration. The aim of this study was to define the ribavirin trough plasma concentration at week 4 (W4) associated with sustained virological response (SVR).

Methods

Thirty-one HCV genotype 1 patients (8 naive and 23 non-responders to a previous pegylated interferon/ribavirin therapy) were treated with pegylated interferon/ribavirin and assessed by HPLC for ribavirin plasma concentration at W4.

Results

Eleven patients (35%) achieved SVR, whereas 20 (65%) were non-responders. The median ribavirin plasma concentration at W4 (1.90 mg/l) varied from 1.62 mg/l in patients with subsequent non-response to 2.28 mg/l in sustained responders ( P=0.007). Receiver operating characteristic curve analysis indicated that the 2.01 mg/l threshold gave the best sensitivity and specificity (73% and 80%, respectively, area under the curve=0.80; P=0.007). Sixty-seven percent of patients with median ribavirin plasma concentration >2 mg/l achieved SVR versus only 16% below this level ( P=0.007). Multivariate regression analysis indicated that a ribavirin plasma concentration >2 mg/l at W4 was associated with SVR independent of gender, age, weight, baseline viral load and response to previous therapy.

Conclusion

These results, which remain to be confirmed in large clinical trials, highlight the potential relevance of ribavirin plasma level monitoring at an early stage of treatment. This monitoring could be of help in guiding antiviral therapy by offering dose adjustment in patients with ribavirin plasma level below the 2 mg/l threshold.
Comparison of DNA- and mRNA-Transfected Mouse Dendritic Cells as Potential Vaccines against the Human Papillomavirus Type 16 associated Oncoprotein E7
Authors: Dell Kerstin , Klein Corinna , Gissmann Lutz
Published: April 2022

Background

Dendritic cells (DCs) mediate the generation of strong cytotoxic T-lymphocyte (CTL) responses by functioning in antigen presentation and exerting adjuvant properties. We compared several activation markers and parameters of biological activity of DNA- and mRNA-transfected DCs in vitro and in vivo.

Methods

CpG-matured, bone marrow derived C57BL/6 mouse DCs were electroporated either with enhanced green fluorescence protein (EGFP) or human papillomavirus type 16 (HPV16) E7 expression plasmids or in vitro transcribed mRNAs encoding for the codon-optimized E7 or a shuffled version thereof. Activation marker expression and antigen presentation was analysed by fluorescence-activated cell sorting. The migratory behaviour of transfected DCs were investigated by in vitro chemotaxis experiments and cytokine expression by ELISA. CTL-priming capacity of transfected DCs were determined by vaccination of mice.

Results

mRNA transfection produced a two- to fourfold increase of the activation markers CD40, CD80, CD86 and MHC I and MHC II molecules. Predominately antigen-expressing DCs migrated after mRNA transfection. Furthermore, mRNA-transfected DCs were capable of inducing a chemokine gradient. After maturation, electroporation and activation with soluble CD40 ligand and interferon-γ, DCs displayed a T-helper cell type 2 cytokine expression pattern. Nevertheless, E7-transfected DCs were able to prime E7-specific CTL responses in vivo. The highest E7-specific CTL frequencies were found in mice immunized with mRNA-transfected DCs. The in vitro expanded CTLs exerted functional E7-specific cytotoxic activity.

Conclusions

Genetically modified DCs are suitable vehicles for the induction of E7-specific CTL responses in mice and hence could help to eradicate HPV-associated lesions in humans.