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Find video protocols related to scientific articles indexed in Pubmed.
A very low geno2pheno false positive rate is associated with poor viro-immunological response in drug-naïve patients starting a first-line HAART.
PLoS ONE
PUBLISHED: 08-25-2014
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We previously found that a very low geno2pheno false positive rate (FPR ? 2%) defines a viral population associated with low CD4 cell count and the highest amount of X4-quasispecies. In this study, we aimed at evaluating whether FPR ? 2% might impact on the viro-immunological response in HIV-1 infected patients starting a first-line HAART.
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Microbiological Infections in Women With Cervical Cytological Reports of Atypical Squamous Cells of Undetermined Significance.
J Low Genit Tract Dis
PUBLISHED: 08-21-2014
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To study the role of cervicovaginal infections in women with cytological reports of atypical squamous cells of undetermined significance (ASC-US).
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Phylogenetic and evolutionary analysis of influenza A H7N9 virus.
New Microbiol.
PUBLISHED: 07-01-2014
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Recently, human infections with the novel avian-origin influenza A H7N9 virus have been reported from various provinces in China. Human infections with avian influenza A viruses are rare and may cause a wide spectrum of clinical symptoms. This is the first time that human infection with a low pathogenic avian influenza A virus has been associated with a fatal outcome. Here, a phylogenetic and positive selective pressure analysis of haemagglutin (HA), neuraminidase (NA), and matrix protein (MP) genes of the novel reassortant H7N9 virus was carried out. The analysis showed that both structural genes of this reassortant virus likely originated from Euro-Asiatic birds, while NA was more likely to have originated from South Korean birds. The Bayesian phylogenetic tree of the MP showed a main clade and an outside cluster including four sequences from China. The United States and Guatemala classical H7N9-isolates appeared homogeneous and clustered together, although they are distinct from other classical Euro-Asiatic and novel H7N9 viruses. Selective pressure analysis did not reveal any site under statistically significant positive selective pressure in any of the three genes analyzed. Unknown certain intermediate hosts involved might be implicated, so extensive global surveillance and bird-to-person transmission should be closely considered in the future.
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Optimizing HIV therapy. A consensus project on differences between cytidine analogues and regime compactness.
New Microbiol.
PUBLISHED: 07-01-2014
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The identification of the most effective HAART regimens in different clinical settings is still an issue. The aim of the study was to analyze how the compactness of HAART regimens is perceived and if differences between lamivudine (3TC) and emtricitabine (FTC) do exist according to a panel of Italian HIV/AIDS clinicians, using the Delphi method.
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Understanding HIV compartments and reservoirs.
Curr HIV/AIDS Rep
PUBLISHED: 04-15-2014
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The spectrum of HIV-1 cellular reservoirs is highly diversified, and their role varies according to the milieu of the anatomical sites in which the virus replicates. In this light, mechanisms underlying HIV-1 persistence in anatomical compartments may be profoundly different from what is observed in peripheral blood. This scenario is further complicated by sub-optimal drug penetration in tissues allowing persistent and cryptic HIV-1 replication in body districts despite undetectable viremia. On this basis, this review aims at providing recent insights regarding the critical role of HIV-1 cellular reservoirs in different anatomical compartments, and their relationship with the pathogenesis of HIV-1 infection. A comprehensive definition of the complex interplay between the virus and its reservoir is critical in order to set up prophylactic and therapeutic strategies aimed at achieving the maximal virological suppression and hopefully in the near future the cure of HIV-1 infection (either functional or biological).
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Analysis of single-nucleotide polymorphisms (SNPs) in human CYP3A4 and CYP3A5 genes: potential implications for the metabolism of HIV drugs.
BMC Med. Genet.
PUBLISHED: 03-24-2014
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Drug metabolism via the cytochrome P450 (CYP450) system has emerged as an important determinant in the occurrence of several drug interactions (adverse drug reactions, reduced pharmacological effect, drug toxicities). In particular, CYP3A4 and CYP3A5 (interacting with more than 60% of licensed drugs) exhibit the most individual variations of gene expression, mostly caused by single nucleotide polymorphisms (SNPs) within the regulatory region of the CYP3A4 and CYP3A5 genes which might affect the level of enzyme production.In this study, we sought to improve the performance of sensitive screening for CYP3A polymorphism detection in twenty HIV-1 infected patients undergoing lopinavir/ritonavir (LPV/r) monotherapy.
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Screening of respiratory pathogens by Respiratory Multi Well System (MWS) r-gene™ assay in hospitalized patients.
New Microbiol.
PUBLISHED: 03-04-2014
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Novel respiratory viruses have been identified as possible agents of upper and lower respiratory tract infections. Multiplex real-time PCRs have been developed to identify clinically relevant respiratory pathogens. In this study, 178 respiratory samples already screened for influenza virus types A and B by Flu A/B ASR real-time PCR kit were retrospectively analyzed with the Respiratory Multi Well System (MWS) r-gene™ real-time PCR kit which detects a wide spectrum of respiratory pathogens. The goal was to demonstrate the importance of a wide spectrum screening compared to a single diagnostic request. The Flu A/B ASR kit detected influenza B virus in 1.7% of the samples (3/178) and no influenza A virus. The MWS r-gene™ kit detected influenza virus in 6.7% (12/178) of samples (0.6% influenza A, and 6.2% influenza B), while the overall detection rate for respiratory pathogens was 54% (96/178). Co-infections were detected in 8/178 (4.5%) samples. Adenovirus was the infectious agent detected most frequently, followed by respiratory syncytial virus. The risk of being infected by respiratory syncytial virus is almost threefold higher in patients older than 65 years compared to the younger age group (OR:2.7, 95% CI: 1.2-6.2). Wide spectrum screening of respiratory pathogens by real-time PCR is an effective means of detecting clinically relevant viral pathogens.
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Less drug regimens and PI/r-based strategies in HIV infection: focus on best practices using the HIV patient's journey methodology.
New Microbiol.
PUBLISHED: 02-06-2014
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During these last two years less drug regimens (LDRs) in HIV, and in particular protease inhibitor (PI)/r-based strategies, have been explored both in clinical trials and in clinical practice. Many results are now available and more is known about how to use them safely and effectively. Understanding that an LDR strategy represents a real tailored therapeutic approach for the patient is crucial for the long-term success and positive management of HIV infection. Trust between patients and HIV specialists and a real focus on the patient's life are key factors for long life treatment success, in particular when using a LDR strategy. This is clearly shown by the HIV patient's journey (HPJ) methodology, used in an Italian national workshop to better define the criteria and challenges of LDR strategies. This paper shows the results of this complex process.
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Reliability and clinical relevance of the HIV-1 drug resistance test in patients with low viremia levels.
Clin. Infect. Dis.
PUBLISHED: 01-14-2014
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We evaluated reliability and clinical usefulness of genotypic resistance testing (GRT) in patients for whom combination antiretroviral therapy (cART) was unsuccessful with viremia levels 50-1000 copies/mL, for whom GRT is generally not recommended by current guidelines.
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Randomized trial of DRV/r or LPV/r QD monotherapy vs maintaining a PI/r-based antiretroviral regimen in persons with suppressed HIV replication.
J Int AIDS Soc
PUBLISHED: 01-01-2014
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PI/r monotherapy has been suggested as an attainable maintenance strategy in patients achieving stable HIV suppression in plasma. The objective of trial was to compare the virological outcome of two different PI/r QD monotherapy strategies (LPV/r or DRV/r) with maintaining a triple PI/r-based ARV regimen.
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Potential implications of CYP3A4, CYP3A5 and MDR-1 genetic variants on the efficacy of Lopinavir/Ritonavir (LPV/r) monotherapy in HIV-1 patients.
J Int AIDS Soc
PUBLISHED: 01-01-2014
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Several genetic single nucleotide polymorphisms (SNPs) in biotransformation enzymes (CYP3A4, CYP3A5) or transporter proteins (multidrug resistance MDR1 gene product, P-gp) are involved in PI metabolism so that PI pharmacokinetics is characterized by a large inter-individual variability. The aim of this study was: (i) to develop an in-house PCR/direct sequencing, based on DNA purification of full-length CYP3A4 and CYP3A5 genes (SNPs) and MDR1 C3435T variant; (ii) to investigate association of CYP3A4 and CYP3A5 reported or unreported genetic polymorphisms and MDR1-C3435T (CC homozygote, CT heterozygote, TT homozygote) with clinical outcome of HIV-1 infected subjects treated with PI.
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Durability of Lopinavir/ritonavir mono-therapy in individuals with viral load ?50 copies/mL in the observational setting.
Antivir. Ther. (Lond.)
PUBLISHED: 09-04-2013
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The main objective is to evaluate the efficacy and durability of Lopinavir-ritonavir monotherapy (LPV/r-MT) in virologically-controlled HIV-positive individuals switching from combination antiretroviral therapy (cART).
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HIV-1 drug resistance in recently HIV-infected pregnant mothers naïve to antiretroviral therapy in Dodoma urban, Tanzania.
BMC Infect. Dis.
PUBLISHED: 08-07-2013
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HIV resistance affects virological response to therapy and efficacy of prophylaxis in mother-to-child-transmission. The study aims to assess the prevalence of HIV primary resistance in pregnant women naïve to antiretrovirals.
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A multi-targeted drug candidate with dual anti-HIV and anti-HSV activity.
PLoS Pathog.
PUBLISHED: 07-01-2013
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Human immunodeficiency virus (HIV) infection is often accompanied by infection with other pathogens, in particular herpes simplex virus type 2 (HSV-2). The resulting coinfection is involved in a vicious circle of mutual facilitations. Therefore, an important task is to develop a compound that is highly potent against both viruses to suppress their transmission and replication. Here, we report on the discovery of such a compound, designated PMEO-DAPym. We compared its properties with those of the structurally related and clinically used acyclic nucleoside phosphonates (ANPs) tenofovir and adefovir. We demonstrated the potent anti-HIV and -HSV activity of this drug in a diverse set of clinically relevant in vitro, ex vivo, and in vivo systems including (i) CD4(+) T-lymphocyte (CEM) cell cultures, (ii) embryonic lung (HEL) cell cultures, (iii) organotypic epithelial raft cultures of primary human keratinocytes (PHKs), (iv) primary human monocyte/macrophage (M/M) cell cultures, (v) human ex vivo lymphoid tissue, and (vi) athymic nude mice. Upon conversion to its diphosphate metabolite, PMEO-DAPym markedly inhibits both HIV-1 reverse transcriptase (RT) and HSV DNA polymerase. However, in striking contrast to tenofovir and adefovir, it also acts as an efficient immunomodulator, inducing ?-chemokines in PBMC cultures, in particular the CCR5 agonists MIP-1?, MIP-1? and RANTES but not the CXCR4 agonist SDF-1, without the need to be intracellularly metabolized. Such specific ?-chemokine upregulation required new mRNA synthesis. The upregulation of ?-chemokines was shown to be associated with a pronounced downmodulation of the HIV-1 coreceptor CCR5 which may result in prevention of HIV entry. PMEO-DAPym belongs conceptually to a new class of efficient multitargeted antivirals for concomitant dual-viral (HSV/HIV) infection therapy through inhibition of virus-specific pathways (i.e. the viral polymerases) and HIV transmission prevention through interference with host pathways (i.e. CCR5 receptor down regulation).
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Recurrent miscarriage and cervical human papillomavirus infection.
Am. J. Reprod. Immunol.
PUBLISHED: 06-15-2013
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To investigate the possible relationship between human papillomavirus (HPV) infection and recurrent miscarriage (RM).
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Identification of a rare mutation at reverse transcriptase Lys65 (K65E) in HIV-1-infected patients failing on nucleos(t)ide reverse transcriptase inhibitors.
J. Antimicrob. Chemother.
PUBLISHED: 06-07-2013
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The HIV reverse transcriptase (RT) mutation K65R confers resistance to nucleos(t)ide reverse transcriptase inhibitors (NRTIs). Here, analysing a large database, we report the selection of another rare K65E mutation in patients failing on NRTI-containing regimens.
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An HIV type 2 case series in Italy: a phylogenetic analysis.
AIDS Res. Hum. Retroviruses
PUBLISHED: 05-25-2013
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In recent years, the increase of migration from countries where human immunodeficiency virus type 2 (HIV-2) is endemic to industrialized countries has facilitated the spread of the virus in individuals previously unexposed to this threat. In this report, we performed a phylogenetic analysis on pol and env sequences of HIV-2 strains identified in foreigners and native citizens to trace the origin of infection. All but one of the 17 pol gene sequences were classified as group A. HIV-2 strains were aggregated in several clusters depending by the country of origin and/or infection. One patient (1AA) was classified as being infected with a recombinant between HIV-2 group A and HIV-2 group B, because the pol gene sequence was clearly in the group A, but an env V3 region sequence from this patient was more similar to group B viruses. Therefore, it is urgent to strengthen the surveillance and use adequate molecular virological tools to diagnose and monitor HIV-2 infection.
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Structural modifications induced by specific HIV-1 protease-compensatory mutations have an impact on the virological response to a first-line lopinavir/ritonavir-containing regimen.
J. Antimicrob. Chemother.
PUBLISHED: 05-17-2013
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This study evaluates the impact of specific HIV-1 protease-compensatory mutations (wild-type amino acids in non-B subtypes) on virological response to a first-line lopinavir/ritonavir-containing regimen in an HIV-1 subtype B-infected population.
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Molecular analysis of hepatitis B virus in Bulgaria.
J. Med. Virol.
PUBLISHED: 04-18-2013
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Hepatitis B virus infection is a global health problem. Based on the sequence divergence of the entire genome, hepatitis B virus has been classified into eight genotypes which have a characteristic geographic distribution. To date, no data are available on the molecular epidemiology of hepatitis B virus in Bulgaria. The aim of the present study was to reconstruct the epidemiological history of HBV genotypes/subgenotypes circulating in Bulgaria using a phylodynamic approach and a Bayesian statistical inference framework. Sequence analysis of the HBsAg/Reverse Transcriptase overlapping genomic regions revealed that D1 and A2 were the subgenotypes detected most frequently in the patients examined. The tMRCA estimations of the few HBV D1 Bulgarian significant clades dated back to 23-27 years ago, corresponding to the early 1980s. The HBV A2 Bulgarian sequences fell into two closely related supported clusters dated to 2003 and 1996 years, respectively, suggesting a more recent introduction of subgenotype A2 into Bulgaria. The study provides new information about the HBV subgenotypes in Bulgaria.
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Nucleotide polymorphisms in the 5-UTR region of HCV can affect the ability of two widely used assays to assign an HCV genotype.
J. Virol. Methods
PUBLISHED: 03-08-2013
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Determination of hepatitis C virus genotype is crucial for establishing the duration of antiviral therapy and predicts response to treatment. In this study, consecutive serum samples collected from two patients with chronic hepatitis C infection were tested by two assays used widely, the Abbott RealTime HCV Genotype II and the Versant HCV Genotype 2.0 assays, in order to assign a genotype to the virus. The obtained results were verified by phylogenetic analysis of the NS5B region and sequencing of the 5-UTR of the viral genome. Testing of the serum samples from both patients gave an indeterminate result with the Abbott assay. By contrast, the Versant assay gave an indeterminate result for one patient and identified an HCV-2b subtype in the other patient. Phylogenetic analysis of the NS5B region confirmed the presence of HCV-2b in this latter patient and disclosed the presence of HCV-3h in the other patient. Sequencing of the 5-UTR revealed the presence of nucleotide changes at positions -166 and -119 of HCV-2b, and at positions -138, -108 and -99 of HCV-3h. Nucleotide mutations located in the 5-untraslated region of hepatitis C virus may impair the ability of commercial assays to assign an HCV genotype.
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Anti-HBV treatment induces novel reverse transcriptase mutations with reflective effect on HBV S antigen.
J. Infect.
PUBLISHED: 02-04-2013
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The identification of novel reverse-transcriptase (RT) drug-resistance mutations is critical in predicting the probability of success to anti-HBV treatment. Furthermore, due to HBV-RT/HBsAg gene-overlap, they can have an impact on HBsAg-detection and quantification.
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Monitoring of KI and WU polyomaviruses in hematopoietic stem cell transplant patients.
J. Med. Virol.
PUBLISHED: 01-29-2013
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Primary infection with KIPyV and WUPyV polyomaviruses occurs early in childhood followed by lifelong persistence in the body. Polyomavirus reactivation can occur in the presence of impaired immunity as in hematological malignancies or during immunosuppresssion induced by medications. In this study, reactivation of KIPyV and WUPyV was monitored by conventional PCR in plasma samples of 26 stem cell transplant patients and in 26 related bone marrow donors. Plasma samples from transplant patients were collected immediately after the end of conditioning regimen and up to 270 days after transplant. All plasma samples from transplant patients were negative for KIPyV and WUPyV DNA. Instead, KIPyV DNA was detected in two bone marrow donors. There was no evidence of KIPyV transmission from the donor to the recipient. The data suggest that detection of KIPyV in plasma is sporadic and that KPIyV and WUPyV do not affect the post-transplant clinical course. However, further studies on a larger sample size and more sensitive PCR methods are needed to confirm these observations.
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Description of the L76V resistance protease mutation in HIV-1 B and "non-B" subtypes.
PLoS ONE
PUBLISHED: 01-18-2013
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To describe the prevalence of the L76V protease inhibitors resistance-associated mutation (PI-RAM) in relation with patients characteristics and protease genotypic background in HIV-1 B- and "non-B"-infected patients.
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The genotypic false positive rate determined by V3 population sequencing can predict the burden of HIV-1 CXCR4-using species detected by pyrosequencing.
PLoS ONE
PUBLISHED: 01-14-2013
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The false-positive rate (FPR) is a percentage-score provided by Geno2Pheno-algorithm indicating the likelihood that a V3-sequence is falsely predicted as CXCR4-using. We evaluated the correlation between FPR obtained by V3 population-sequencing and the burden of CXCR4-using variants detected by V3 ultra-deep sequencing (UDPS) and Enhanced-Sensitivity Trofile assay (ESTA).
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The human polyomaviruses KI and WU: virological background and clinical implications.
APMIS
PUBLISHED: 01-09-2013
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In 2007, two novel polyomaviruses KI and WU were uncovered in the respiratory secretions of children with acute respiratory symptoms. Seroepidemiological studies showed that infection by these viruses is widespread in the human population. Following these findings, different biological specimens and body compartments have been screened by real-time PCR in the attempt to establish a pathogenetic role for KI polyomavirus (KIPyV) and WU polyomavirus (WUPyV) in human diseases. Although both viruses have been found mainly in respiratory tract samples of immunocompromised patients, a clear causative link with the respiratory disease has not been established. Indeed, the lack of specific clinical or radiological findings, the frequent co-detection with other respiratory pathogens, the detection in subjects without signs or symptoms of respiratory disease, and the variability of the viral loads measured did not allow drawing a definitive conclusion. Prospective studies carried out on a large sample size including both immunocompromised and immunocompetent patients with and without respiratory symptoms are needed. Standardized quantitative real-time PCR methods, definition of a clear clinical cutoff value, timing in the collection of respiratory samples, are also crucial to understand the pathogenic role, if any, of KIPyV and WUPyV in human pathology.
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Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage.
Bioinformatics
PUBLISHED: 01-06-2013
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To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo.
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Inhibition of dual/mixed tropic HIV-1 isolates by CCR5-inhibitors in primary lymphocytes and macrophages.
PLoS ONE
PUBLISHED: 01-01-2013
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Dual/mixed-tropic HIV-1 strains are predominant in a significant proportion of patients, though little information is available regarding their replication-capacity and susceptibility against CCR5-antagonists in-vitro. The aim of the study was to analyze the replication-capacity and susceptibility to maraviroc of HIV-1 clinical isolates with different tropism characteristics in primary monocyte-derived-macrophages (MDM), peripheral-blood-mononuclear-cells (PBMC), and CD4(+) T-lymphocytes.
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HIV-1 Genetic Variability and Clinical Implications.
ISRN Microbiol
PUBLISHED: 01-01-2013
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Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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When phylogenetic analysis complements the epidemiological investigation: a case of HIV-2 infection, Italy.
New Microbiol.
PUBLISHED: 01-01-2013
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Human immunodeficiency virus type 2 (HIV-2) infection is geographically restricted, affecting West African countries such as Guinea- Bissau and Cape Verde. We describe a recent case of HIV-2 infection in an Italian patient. Phylogenetic analysis of the V3 region of HIV-2 indicated that the Italian patient was infected by HIV-2 subtype A2. The sequence obtained from the Italian patient clustered significantly with a sequence isolated from Senegal. A phylogenetic doubt may arise from a Guinea Bissau sequence because it was in a major clade with the Italian and Senegal sequences, but was not statistically significant. The discovery of another Italian case over a short time frame stresses the importance of strengthening the surveillance system for HIV-2 because of the increase in migration from endemic areas to Italy.
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Identification and structural characterization of novel genetic elements in the HIV-1 V3 loop regulating coreceptor usage.
Antivir. Ther. (Lond.)
PUBLISHED: 10-26-2011
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The interaction between HIV-1 gp120 and CCR5 N terminus is critical for R5-virus entry and affects CCR5 antagonists activity. Knowledge of how different genetic signatures of gp120 V3 domain effect the strength of this interaction is limited.
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The HIV-1 integrase G118R mutation confers raltegravir resistance to the CRF02_AG HIV-1 subtype.
J. Antimicrob. Chemother.
PUBLISHED: 09-19-2011
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Most of the previous studies that explored the molecular basis of raltegravir resistance were conducted studying the HIV-1 B subtype. It has been shown that the CRF02_AG subtype in relation to its natural integrase (IN) sequence could develop different genetic pathways associated with raltegravir resistance. The aim of this study was to explore resistance pathways preferably used by CRF02_AG viruses compared with subtype B.
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Sentinel mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing.
J. Antimicrob. Chemother.
PUBLISHED: 09-02-2011
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This proof-of-concept study aimed to identify whether mutations considered not yet relevant for drug resistance (but located at key drug-resistance positions) can act as sentinels of minority resistant variants in HIV-1 drug-naive patients.
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Novel HBsAg markers tightly correlate with occult HBV infection and strongly affect HBsAg detection.
Antiviral Res.
PUBLISHED: 08-18-2011
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Occult HBV infection (OBI) is a threat for the safety of blood-supply, and has been associated with the onset of HBV-related hepatocellular carcinoma and lymphomagenesis. Nevertheless, genetic markers in HBsAg (particularly in D-genotype, the most common in Europe) significantly associated with OBI in vivo are missing. Thus, the goal of this study is to define: (i) prevalence and clinical profile of OBI among blood-donors; (ii) HBsAg-mutations associated with OBI; (iii) their impact on HBsAg-detection. OBI was searched among 422,278 blood-donors screened by Nucleic-Acid-Testing. Following Taormina-OBI-definition, 26 (0.006%) OBI-patients were identified. Despite viremia <50IU/ml, HBsAg-sequences were obtained for 25/26 patients (24/25 genotype-D). OBI-associated mutations were identified by comparing OBI-HBsAg with that of 82 chronically-infected (genotype-D) patients as control. Twenty HBsAg-mutations significantly correlated for the first time with OBI. By structural analysis, they localized in the major HBV B-cell-epitope, and in HBsAg-capsid interaction region. 14/24 OBI-patients (58.8%) carried in median 3 such mutations (IQR:2.0-6.0) against 0 in chronically-infected patients. By co-variation analysis, correlations were observed for R122P+S167L (phi=0.68, P=0.01), T116N+S143L (phi=0.53, P=0.03), and Y100S+S143L (phi=0.67, p<0.001). Mutants (obtained by site-directed mutagenesis) carrying T116N, T116N+S143L, R122P, R122P+Q101R, or R122P+S167L strongly decreased HBsAg-reactivity (54.9±22.6S/CO, 31.2±12.0S/CO, 6.1±2.4S/CO, 3.0±1.0S/CO and 3.9±1.3S/CO, respectively) compared to wild-type (306.8±64.1S/CO). Even more, Y100S and Y100S+S143L supernatants show no detectable-HBsAg (experiments in quadruplicate). In conclusions, unique HBsAg-mutations in genotype-D, different than those described in genotypes B/C (rarely found in western countries), tightly correlate with OBI, and strongly affect HBsAg-detection. By altering HBV-antigenicity and/or viral-particle maturation, they may affect full-reliability of universal diagnostic-assays for HBsAg-detection.
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Intratype variations of HPV 31 and 58 in Italian women with abnormal cervical cytology.
J. Med. Virol.
PUBLISHED: 08-13-2011
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Oncogenic human papillomaviruses (HPVs) are the recognized etiological agents of cervical cancer. A number of epidemiological, etiological, and molecular data suggest that variants of the same HPV type are distinct biologically and may confer differential pathogenic risks. Therefore, investigation of genome variants of clinically important HPV types may be important for the identification of pathogenically important variants. In this study, the genomic regions of L1, E6, E7, and long control region (LCR) of HPV 31 and 58, identified in women with abnormal cervical smear, were investigated. Several mutations were identified in the regions examined. Of the mutations found in the L1 region of HPV 31 and 58, the novel mutations described in this study fall within a protein region which may play a critical role in the binding of neutralizing antibodies against different HPV types. No significant association was found between the E6 and E7 mutations of both HPV types and the cytological lesion found. Some mutations found in the LCR of HPV 31 and 58 encompassed known transcription binding sites with possible consequences on the transcription of the oncogenic genes. Intratype genetic characterization of HPV types may help to define the pathogenetic risk of HPV variants.
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Drug resistance among drug-naive and first-line antiretroviral treatment-failing children in Cameroon.
Pediatr. Infect. Dis. J.
PUBLISHED: 08-06-2011
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Scale-up to antiretroviral therapy (ART) requires surveillance for HIV drug resistance. With the goal of attaining 100% pediatric ART coverage in Cameroon, strategies to limit the spread of HIV resistance among children are very important.
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Docking analysis and resistance evaluation of clinically relevant mutations associated with the HIV-1 non-nucleoside reverse transcriptase inhibitors nevirapine, efavirenz and etravirine.
ChemMedChem
PUBLISHED: 07-25-2011
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An integrated computational and statistical approach was used to determine the association of non-nucleoside reverse transcriptase inhibitors (NNRTIs) nevirapine, efavirenz and etravirine with resistance mutations that cause therapeutic failure and their impact on NNRTI resistance. Mutations detected for nevirapine virological failure with a prevalence greater than 10% in the used patient set were: K103N, Y181C, G190A, and K101E. A support vector regression model, based on matched genotypic/phenotypic data (n=850), showed that among 6365 analyzed mutations, K103N, Y181C and G190A have the first, third, and sixth greatest significance for nevirapine resistance, respectively. The most common indicator of treatment failure for efavirenz was K103N mutation present in 56.7% of the patients where the drug failed, followed by V108I, L100I, and G190A. For efavirenz resistance, K103N, G190, and L100I have the first, fourth, and eighth greatest significance, respectively, as determined in support vector regression model. No positive interactions were observed among nevirapine resistance mutations, while a more complex situation was observed with treatment failure of efavirenz and etravirine, characterized by the accumulation of multiple mutations. Docking simulations and free energy analysis based on docking scores of mutated human immunodeficiency virus (HIV) RT complexes were used to evaluate the influence of selected mutations on drug recognition. Results from support vector regression were confirmed by docking analysis. In particular, for nevirapine and efavirenz, a single mutation K103N was associated with the most unfavorable energetic profile compared to the wild-type sequence. This is in line with recent clinical data reporting that diarylpyrimidine etravirine, a very potent third generation drug effective against a wide range of drug-resistant HIV-1 variants, shows increased affinity towards K103N/S mutants due to its high conformational flexibility.
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Late hepatitis B virus reactivation after lamivudine prophylaxis interruption in an anti-HBs-positive and anti-HBc-negative patient treated with rituximab-containing therapy.
J. Infect.
PUBLISHED: 07-23-2011
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We describe a case of an anti-HBs-positive patient who experienced hepatitis B reactivation 18 months after the discontinuation of rituximab and after 12 months of lamivudine prophylaxis. The patient carried a hepatitis B genotype D virus harbouring a single immune escape mutation, sT118K. No consensus guidelines regarding the optimal length of treatment or the best elective drug have been defined for antiviral prophylaxis for HBsAg-negative, anti-HBc- and/or anti-HBs-positive patients undergoing immunosuppressive treatment. Screening based on HBV serological markers and HBV DNA testing is a critical issue to recognise hepatitis B reactivation as early as possible. Furthermore, it is of outstanding importance to identify alternative markers (e.g. cccDNA, HBV core related antigen, etc.), that could be predictive of HBV reactivation.
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Performance evaluation of the Artus hepatitis C virus QS-RGQ assay.
J. Virol. Methods
PUBLISHED: 07-19-2011
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Accurate determination of hepatitis C virus RNA level is essential for evaluating the response to antiviral therapy, to determine the duration of treatment, and to predict treatment outcome. Currently, two real-time based polymerase chain reaction assays are used widely to monitor the hepatitis C RNA level: the Abbott RealTime HCV assay and the Cobas Taqman HCV assay. Recently, a third assay has become commercially available: the Artus HCV QS-RGQ assay, which uses the QIAsymphony SP/AS platform for sample preparation and PCR-setup, and the Rotor-Gene Q for amplification and detection. In this study, the performance of the Artus HCV QS-RGQ assay was tested on 105 plasma samples and compared to that of the Cobas Taqman HCV assay. Linear regression analysis showed a good agreement between the two assays. A slightly better sensitivity was observed with the Cobas Taqman assay, while higher hepatitis C viral RNA levels were measured by the Artus HCV QS-RGQ assay in samples positive for hepatitis C genotypes 4. Taken together, the data suggest that the Artus HCV QS-RGQ assay is useful in a diagnostic setting. The combination with the versatile QIAsymphony SP/AS system may represent a major advantage for clinical virological laboratories aiming at optimizing their workflow.
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Molecular analysis of hepatitis C virus infection in Bulgarian injecting drug users.
J. Med. Virol.
PUBLISHED: 07-09-2011
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Intravenous drug users constitute a group at risk for hepatitis C virus (HCV) infection. Today, no data are available on the molecular epidemiology of HCV in Bulgaria despite the fact that in recent years the incidence of acute hepatitis C infection among Bulgarian intravenous drug users increased sixfold and about 2/3 of them developed a chronic infection. The aim of this study was to determine the circulation of hepatitis C genotypes among drug users and to study the evolution and transmission history of the virus by molecular clock and Bayesian methods, respectively. Sequencing of NS5B gene showed that the genotype 3a was the most prevalent type among intravenous drug users. In the Bayesian tree, the 3a subtypes grouped in one main clade with one small cluster well statistically supported. The root of the tree was dated back to the year 1836, and the main clade from Bulgaria was dated 1960. The effective number of infections remained constant until about years 1950s, growing exponentially from the 1960s to the 1990s, reaching a plateau in the years 2000. The not significant intermixing with isolates from other countries may suggest a segregated circulation of the epidemic between 1940s and 1980s. The plateau reached by the epidemic in the early 2000s may indicate the partial success of the new preventive policies adopted in Bulgaria.
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The potential role of pre-transplant HBcIgG seroposivity as predictor of clinically relevant cytomegalovirus infection in patients with lymphoma undergoing autologous hematopoietic stem cell transplantation: a study from the Rome Transplant Network.
Am. J. Hematol.
PUBLISHED: 07-02-2011
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Despite the increased use of intensive immunosuppressive chemo-immunotherapies in patients with lymphoma observed in the last decade, current data on cytomegalovirus (CMV) infection following autologous stem cell transplantation (Auto-SCT) are very limited. To address this peculiar aspect, a retrospective study on a cohort of 128 adult patients consecutively transplanted for lymphoma in three Hematology Institutions was performed with the aim to determine the incidence of and the risk factors for CMV symptomatic infection and/or end-organ disease. Sixteen patients (12.5%) required specific antiviral therapy and 4/16 died (25%); transplant-related mortality (TRM) was significantly influenced by CMV infection (P = 0.005). In univariate analysis, a pre-transplant HBcIgG seropositivity, HBV infection according to clinical-virological definitions, a pre-transplant Rituximab treatment, a diagnosis of B-cell non-Hodgkin lymphoma, and age at transplant were significantly associated with the risk of developing a clinically relevant CMV infection. In multivariate analysis, only a pre-transplant HBcIgG seropositivity (P = 0.008) proved to be an independent predictor of a clinically relevant CMV infection. These results suggest that a pre-transplant HBcIgG seropositivity could be considered as an independent predictor factor of clinically relevant CMV infection after Auto-SCT.
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Human papillomaviruses 53 and 66: clinical aspects and genetic analysis.
Virus Res.
PUBLISHED: 06-21-2011
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Variants of HPV types may have different oncogenic potential. While HPV 16 and 18 variants have been extensively studied, little is known on the less frequent high-risk types such as HPV 53 and 66. Here, we analyzed the genetic variability of HPV 53 and 66 by sequencing the E6, E7, L1 genes and the Long Control Region (LCR) sequences of HPV 53 and HPV 66 from infected women. Fishers exact-test was performed to correlate viral variants with cervical lesions. Higher-order interactions among identified mutations were analyzed by co-variation and cluster analyses. Antigenic-index alterations following L1 mutations were predicted by Jameson-Wolf algorithm. In HPV53, novel variants were identified in L1 (N=9) and E6 (N=1) genes. The novel L1 mutation P432L was statistically associated with L-SIL lesions (P=0.04) and its development reduced the L1 predicted antigenicity (up to -2.3 for Glu433). HPV 53 E6 and L1 sequences clustered phylogenetically into two main clades. In HPV 66, novel polymorphisms were identified in L1 (N=4) and E6 (N=4) genes. The L1 protein mutations S405P and D458N were exclusively found in patients with L-SILs. Seven E7 variants and 10 LCR variants were for the first time analyzed. Novel HPV 53 and 66 variants were identified in this study. Some of these mutations were significantly associated with L-SIL lesions and affected the antigenic index of the L1 protein with possible interesting implications in vaccine design.
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Selected amino acid mutations in HIV-1 B subtype gp41 are associated with specific gp120v? signatures in the regulation of co-receptor usage.
Retrovirology
PUBLISHED: 05-12-2011
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The third variable loop (V3) of the HIV-1 gp120 surface protein is a major determinant of cellular co-receptor binding. However, HIV-1 can also modulate its tropism through other regions in gp120, such as V1, V2 and C4 regions, as well as in the gp41 protein. Moreover, specific changes in gp41 are likely to be responsible for of damage in gp120-CCR5 interactions, resulting in potential resistance to CCR5 inhibitors.In order to genetically characterize the two envelope viral proteins in terms of co-receptor usage, we have analyzed 526 full-length env sequences derived from HIV-1 subtype-B infected individuals, from our and public (Los Alamos) databases. The co-receptor usage was predicted by the analysis of V3 sequences using Geno2Pheno (G2P) algorithm. The binomial correlation phi coefficient was used to assess covariation among gp120V3 and gp41 mutations; subsequently the average linkage hierarchical agglomerative clustering was performed.
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HIV-2 A-subtype gp125c?-v?-c? mutations and their association with CCR5 and CXCR4 tropism.
Arch. Virol.
PUBLISHED: 05-11-2011
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The early events of the HIV replication cycle involve the interaction between viral envelope glycoproteins and their cellular CD4-chemokine (CCR5/CXCR4) receptor complex. In this study, for the first time, the HIV-2 A-subtype gp125(C2-V3-C3) mutations and their tropism association were characterized by analyzing 149 HIV-2 sequences from the Los Alamos database. The analysis has strengthened the importance of C2-V3-C3 region as a determinant factor for co-receptor selection. Moreover, statistically significant correlations were observed between C2-V3-C3 mutations, and several correlated mutations were associated with CXCR4 and CCR5 co-receptor usage. A dendrogram showed two distinct clusters, with numerous associated mutations grouped, thus dividing CCR5- and CXCR4-tropic viruses. Fourteen X4-tropic virus mutations, all in V3 and C3 domains and forming highly significant subclusters, were found. Finally, R5 associations, two strong subclusters were observed, grouping several C2-V3-C3 mutated positions. These data indicate the possible contribution of C2-V3-C3 mutational patterns in regulating HIV-2 tropism.
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Molecular epidemiology of HIV type 1 CRF02_AG in Cameroon and African patients living in Italy.
AIDS Res. Hum. Retroviruses
PUBLISHED: 05-06-2011
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HIV-1 CRF02_AG accounts for >50% of infected individuals in Cameroon. CRF02_AG prevalence has been increasing both in Africa and Europe, particularly in Italy because of migrations from the sub-Saharan region. This study investigated the molecular epidemiology of CRF02_AG in Cameroon by employing Bayesian phylodynamics and analyzed the relationship between HIV-1 CRF02_AG isolates circulating in Italy and those prevalent in Africa to understand the link between the two epidemics. Among 291 Cameroonian reverse transcriptase sequences analyzed, about 70% clustered within three distinct clades, two of which shared a most recent common ancestor, all related to sequences from Western Africa. The major Cameroonian clades emerged during the mid-1970s and slowly spread during the next 30 years. Little or no geographic structure was detected within these clades. One of the major driving forces of the epidemic was likely the high accessibility between locations in Southern Cameroon contributing to the mobility of the population. The remaining Cameroonian sequences and the new strains isolated from Italian patients were interspersed mainly within West and Central African sequences in the tree, indicating a continuous exchange of CRF02_AG viral strains between Cameroon and other African countries, as well as multiple independent introductions in the Italian population. The evaluation of the spread of CRF02_AG may provide significant insight about the future dynamics of the Italian and European epidemic.
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Genetic and structural analysis of HIV-1 Rev responsive element related to V38A and T18A enfuvirtide resistance mutations.
Intervirology
PUBLISHED: 05-04-2011
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For the expression of late viral genes, HIV-1 efficiently exploits the nuclear export by using Rev viral protein, which specifically binds the RNA Rev Responsive Element (RRE). This region is contained within the gp120-gp41 encoding sequence. Enfuvirtide is the first approved HIV-1 fusion-inhibitor, and gp41 codons associated with primary enfuvirtide-resistance (amino-acids 36-45) are localized within the RRE structure. We previously found the co-presence of V38A+T18A resistance mutations in patients failing enfuvirtide.
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Phylogenesis and Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection.
Open Virol J
PUBLISHED: 04-07-2011
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During the spring of 2009, a new influenza A (H1N1) virus of swine origin emerged and spread worldwide causing a pandemic influenza. Here, 329 naso-pharyngeal swabs collected from patients with flu-like symptoms were analyzed by real-time PCR for the presence of H1N1 2009 pandemic virus. Twenty-five samples collected from immunocompetent and immunodepressed patients contained the H1N1 pandemic virus. Phylogenetic analysis of the hemagglutinin and neuraminidase genes showed no obvious differences in terms of similarity and/or homology between the sequences identified in immunocompetent individuals and those obtained from immunocompromised patients. Pre-existing clinical conditions may influence the outcome of H1N1 disease.
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Prevalence of resistance mutations related to integrase inhibitor S/GSK1349572 in HIV-1 subtype B raltegravir-naive and -treated patients.
J. Antimicrob. Chemother.
PUBLISHED: 04-07-2011
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To compare the frequency of previously in vitro-selected integrase mutations (T124A, T124A/S153F, S153Y, T124A/S153Y and L101I/T124A/S153Y) conferring resistance to S/GSK1349572 between HIV-1 subtype B integrase inhibitor (INI)-naive and raltegravir-treated patients.
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Comparative antiviral activity of integrase inhibitors in human monocyte-derived macrophages and lymphocytes.
Antiviral Res.
PUBLISHED: 04-04-2011
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The activity of raltegravir and 4 other integrase inhibitors (MK-2048, L870,810, IN2, and IN5) was investigated in primary human macrophages, PBMC and C8166-lymphocytic T cells, in order to determine their relative potency and efficacy in different cellular systems of HIV infection. Raltegravir showed better protective efficacy in all cell types; MK-2048, L870,810 and IN5 showed a potent anti-HIV-1 activity in macrophages, while in lymphocytes only MK-2048 and L870,810 showed an inhibitory effect comparable to raltegravir. IN2 was a poorly effective anti-HIV-1 compound in all cellular systems. All effective integrase inhibitors exhibited a potent antiviral activity against both X4 and R5 HIV-1 strains. In general, raltegravir, MK-2048, L870,810 and IN5 showed anti HIV activity similar or slightly higher in macrophages compared to PBMC and C8166 T cells: for MK-2048, the EC(50) was 0.4, 0.9, 11.5 nM in macrophages, in PBMCs and T cells, respectively; for L870,810, the EC(50) was 1.5, 14.3, and 10.6 nM, respectively; for IN5 the EC(50) was 0.5, 13.7, and 5.7 nM, respectively.
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A case of Italian HIV type 2 infection: a genetic analysis.
AIDS Res. Hum. Retroviruses
PUBLISHED: 04-02-2011
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Human immunodeficiency virus type 2 (HIV-2), originally restricted to Western Africa, is now spreading to Western European countries because of migration from endemic areas. Therefore, it is mandatory to enforce the surveillance and improve the diagnostics of this neglected infection. In this report, we describe a case of HIV-2 infection affecting an Italian citizen along with three cases from India. Phylogenetic analysis showed that the viral strain identified in the Italian patient clustered with a strain isolated from an immigrant living in France. Of the three Indian strains, two clustered together and were statistically supported, whereas one clustered with a strain from Guinea Bissau. The description of the first case of HIV-2 infection in an Italian citizen indicates that the virus is spreading from endemic areas to countries involved in migration. A strict monitoring and improvement of the diagnostic molecular tools are necessary to avoid misdiagnosis with relevant clinical consequences.
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Topical tenofovir, a microbicide effective against HIV, inhibits herpes simplex virus-2 replication.
Cell Host Microbe
PUBLISHED: 03-25-2011
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The HIV reverse-transcriptase inhibitor, tenofovir, was recently formulated into a vaginal gel for use as a microbicide. In human trials, a 1% tenofovir gel inhibited HIV sexual transmission by 39% and, surprisingly, herpes simplex virus-2 (HSV-2) transmission by 51%. We demonstrate that the concentration achieved intravaginally with a 1% tenofovir topical gel has direct antiherpetic activity. Tenofovir inhibits the replication of HSV clinical isolates in human embryonic fibroblasts, keratinocytes, and organotypic epithelial 3D rafts, decreases HSV replication in human lymphoid and cervicovaginal tissues ex vivo, and delays HSV-induced lesions and death in topically treated HSV-infected mice. The active tenofovir metabolite inhibits HSV DNA-polymerase and HIV reverse-transcriptase. To exert dual antiviral effects, tenofovir requires topical administration to achieve a drug concentration higher than systemic levels achieved by oral treatment. These findings indicate that a single topical treatment, like tenofovir, can inhibit the transmission of HIV and its copathogens.
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Performance evaluation of the COBAS/TaqMan HIV-1 v2.0 in HIV-1 positive patients with low viral load: a comparative study.
J. Virol. Methods
PUBLISHED: 03-04-2011
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HIV-1 viral load determination is a crucial step for monitoring the efficacy of highly active antiretroviral therapy (HAART) and predicts disease progression. Real-time PCR based assays are available for monitoring the viral load. They differ in sensitivity, genomic target region and dynamic range. In this study, the performance of the Roche Cobas Taqman HIV-1 v2.0 was evaluated on plasma samples from HIV-1 positive patients in parallel with the Abbott RealTime HIV-1 assay in a routine diagnostic setting. Overall, there was a good agreement between the two assays. However, some samples detected by the Abbott RealTime HIV-1 assay but below the limit of quantitation of the assay were found negative result when tested with the Roche Cobas Taqman HIV-1 v2.0. It is conceivable that signal anomalies or background noise may affect the lower-end precision of the Abbott RealTime HIV-1 assay. Based on these results, it is concluded that it is not recommended to switch platform during longitudinal viral load monitoring of HIV-1 positive patients.
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HIV-1 dual/mixed tropic isolates show different genetic and phenotypic characteristics and response to maraviroc in vitro.
Antiviral Res.
PUBLISHED: 02-10-2011
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Dual/mixed-tropic HIV-1 strains are predominant in a significative proportion of patients, though few information is available regarding the genetic characteristics, quasispecies composition, and susceptibility against CCR5-antagonists of the primary-isolates. For this reason, we investigated in deep details, both phenotypically and genotypically, the characteristics of 54 HIV-1 primary-isolates obtained from HIV-infected patients. Tropism was assessed by multiple-cycles phenotypic-assay on U87MG-CD4(+)-CCR5(+)-/CXCR4(+)-expressing cells. In vitro selection in PBMCs of X4-tropic viral strains following maraviroc-treatment was also performed. Phenotypic-assay reported pure R5-tropic viruses in 31 (57.4%) isolates, dual/mixed-tropic viruses in 22 (40.7%), and pure X4-tropic virus in only 1 (1.8%). Among dual/mixed-tropic isolates, 12 showed a remarkably higher replication-efficacy in CCR5-expressing cells (R5(+)/X4), and 2 in CXCR4-expressing cells (R5/X4(+)). Genotypic-tropism testing showed a correlation between PSSM-scores, geno2pheno false-positive-rate, and V3-net-charge with both CCR5-usage and syncytium-inducing ability. Moreover, specific gp120- and gp41-mutations were significantly associated with tropism and/or syncytium-inducing ability. Ultra-deep V3-pyrosequencing showed the presence of a swarm of genetically distinct species with a preference for CCR5-coreceptor not only in all pure R5-isolates, but also in 6/7 R5(+)/X4-tropic isolates. In both pure-X4 and R5/X4(+)-isolates, we observed extensive prevalence of X4-using species. In vitro selection-experiments with CCR5-inhibitor maraviroc (up to 2 months) showed no-emergence of X4-tropic variants for all R5- and R5(+)/X4-isolates tested (while X4-virus remained fully-resistant). In conclusion, our study shows that dual/mixed-tropic viruses are constituted by different species, whereby those with characteristics R5(+)/X4 are genotypically and phenotypically similar to the pure-R5 isolates; thus the use of CCR5-antagonists in patients with R5(+)/X4-tropic viruses may be a therapeutic-option that deserves further investigations.
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Safety of complete and sustained prophylaxis withdrawal in patients liver-transplanted for HBV-related cirrhosis at low risk of HBV recurrence.
J. Hepatol.
PUBLISHED: 01-18-2011
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HBV reactivation after liver transplantation may be related to persistence of covalently closed circular (ccc) DNA. We investigated the safety of HBV prophylaxis withdrawal in selected HBV transplanted patients.
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The novel KI, WU, MC polyomaviruses: possible human pathogens?
New Microbiol.
PUBLISHED: 01-15-2011
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Recently, three novel human polyomaviruses KIPyV, WUPyV and MCPyV were uncovered in biological specimens of patients with different underlying clinical conditions. Although it is too early to draw firm conclusions on their role in human pathology, this finding has revitalized the scientific debate on the Polyomaviridae family and their relation to human disease. Seroepidemiological studies showed that, similarly to BKPyV and JCPyV, benign primary exposure to these new viruses occurs early in childhood. The viruses then remain latent in the body, and reactivate in immunosuppressed patients with possible pathological consequences. Furthermore, the discovery of MCPyV in a rare and aggressive skin cancer named Merckel cell carcinoma and its clonal integration within the tumor genome suggests that MCPyV infection may represent an early event in the pathogenesis of this disease. This review describes the general aspects of human polyomavirus infection and pathogenesis. Current topics of investigation and future directions in the field are also discussed.
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Epidemiological network analysis in HIV-1 B infected patients diagnosed in Italy between 2000 and 2008.
Infect. Genet. Evol.
PUBLISHED: 01-13-2011
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This study, through a phylogenetic analysis, is aimed to identify potential epidemiological networks and sequence interrelationships between acute/early and chronic infections in both drug-naïve and drug-experienced individuals within a local, well-defined setting and to investigate the population dynamics of transmitted resistance and the potential contribution of untreated patients to the spread of antiretroviral resistance. A total of 884 HIV-1 B subtype pol gene sequences from 306 drug-naïve (40 recently and 266 chronically infected) and 578 drug-treated HIV-1 infected patients were collected through routine drug-resistance testing between 2000 and 2008 in a single center (Division of Infectious Disease, Bergamo, Northern Italy). Bayesian phylogenetic tree was reconstructed and transmission clusters were recognized using a posterior probability as statistical support of each cluster. Differences among clustered and non-clustered drug-resistance mutations were assessed by Fishers exact test. In our cohort we identified five clusters including ?6 sequences with the root posterior probability of 100%. Dated phylogenies reconstructed through Bayesian Markov chain Monte Carlo model was possible for only two main clade (?10 sequences) originated between 1990 and 2002. Among the 306 drug-naïve individuals, 12% carried a viral strain with at least 1 major mutation associated with transmitted drug resistance and 36% of these strains were involved in significant clusters. We report for the first time that many (34%) of HIV-1 subtype B transmission clusters identified in Italy were only composed by drug-naïve individuals and that the 14% of transmitted drug resistance was linked to transmission clusters composed only of newly diagnosed individuals. The phylogenetic analysis was performed on a large cohort of drug-naïve recently/chronically infected individuals where drug-experienced patients represent almost all infected individuals in a restricted geographical area. Our findings highlight the role of newly diagnosed individuals, not yet exposed to antiretroviral drugs, in the transmission of drug-resistant HIV-1 strains, providing new insights for the planning and management of treatment programs in developing countries.
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Molecular and structural aspects of clinically relevant mutations related to the approved non-nucleoside inhibitors of HIV-1 reverse transcriptase.
Drug Resist. Updat.
PUBLISHED: 01-07-2011
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In recent years relevant progress has been made in the treatment of HIV-1 with a consequent decrease in mortality. The availability of potent antiretroviral drugs and the ability of viral load assays that accurately evaluate the true level of viral replication, have led to a better understanding of pathogenesis of the disease and how to obtain improved therapeutic profiles. The highly active antiretroviral therapy (HAART), based on a combination of three or more antiretroviral drugs, has radically changed the clinical outcome of HIV. In particular, reverse transcriptase non-nucleoside inhibitors (NNRTIs) play an essential role in most protocols and are often used in first line treatment. The high specificity of these inhibitors towards HIV-1 has increased the number of structural and molecular modeling studies of enzyme complexes and that have led to chemical syntheses of more selective second and third-generation NNRTIs. However, a considerable percentage of new HIV-1 infections are caused by the emergence of drug-resistant mutant viruses that complicate treatment strategies. In this review we discuss relevant clinical and structural aspects for the management of antiretroviral drug resistance, with detailed explanations of mechanisms and mutation patterns useful to better understand the relation between drug resistance and therapy failure.
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Specific HIV-1 integrase polymorphisms change their prevalence in untreated versus antiretroviral-treated HIV-1-infected patients, all naive to integrase inhibitors.
J. Antimicrob. Chemother.
PUBLISHED: 09-03-2010
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To define whether the prevalence of mutations associated with integrase inhibitor (INI) resistance is different in untreated versus antiretroviral-treated HIV-1-infected individuals (all INI naive).
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Different evolution of genotypic resistance profiles to emtricitabine versus lamivudine in tenofovir-containing regimens.
J. Acquir. Immune Defic. Syndr.
PUBLISHED: 08-27-2010
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To investigate genotypic resistance profiles to emtricitabine + tenofovir (FTC + TDF) in-vivo and in-vitro, and compare them with lamivudine + tenofovir (3TC + TDF).
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KI and WU polyomaviruses and CD4+ cell counts in HIV-1-infected patients, Italy.
Emerging Infect. Dis.
PUBLISHED: 08-26-2010
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To investigate an association between KI and WU polyomavirus (KIPyV and WUPyV) infections and CD4+ cell counts, we tested HIV-1-positive patients and blood donors. No association was found between cell counts and virus infections in HIV-1-positive patients. Frequency of KIPyV infection was similar for both groups. WUPyV was more frequent in HIV-1-positive patients.
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Population dynamics of HIV-1 subtype B in a cohort of men-having-sex-with-men in Rome, Italy.
J. Acquir. Immune Defic. Syndr.
PUBLISHED: 08-13-2010
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A recent increase in HIV diagnoses among men-having-sex-with-men (MSM) has been shown by surveillance data from Europe and Italy, and new approaches to inferring viral population dynamics from heterochronously sampled gene sequences have been developed. The aim of this study was to reconstruct the epidemiological history of HIV-1 subtype B in a homogeneous group of Italian MSM using a coalescent-based Bayesian framework. A total of 125 HIV-1 subtype B pol sequences were analyzed using Bayesian methods and a relaxed molecular clock to reconstruct their dated phylogeny and estimate population dynamics. At least 10 epidemiological clusters of 3-9 isolates were identified: half including the largest clades originated in the early 1990s and the other half radiated from 1999. Demographic analysis showed that the HIV epidemic grew in accordance with a logistic model characterized by a rapid exponential increase in the effective number of infections (r = 1.54 year) starting from the early 1980s and reaching a plateau 10 years later. Our data suggest that the HIV B epidemic entered our MSM population through multiple transmission chains about 20 years later than in other Western European country. Epidemiological clusters originating in the early 2000s suggest a recent re-emergence of HIV in Italian MSM.
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Persistent epithelial defect after penetrating keratoplasty caused by adenoviral infectious keratitis.
New Microbiol.
PUBLISHED: 06-04-2010
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A causal role of herpes simplex infection in persistent epithelial defect following penetrating keratoplasty (PKP) has been documented in the past. Instead, not much information is available on the role of adenovirus infection in delayed epithelization following PKP. Here, we describe a case of persistent epithelial defect due to adenoviral infection keratitis confirmed by PCR analysis. Adenovirus keratitis can be an unusual cause of delayed epithelization after PKP.
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Secondary integrase resistance mutations found in HIV-1 minority quasispecies in integrase therapy-naive patients have little or no effect on susceptibility to integrase inhibitors.
Antimicrob. Agents Chemother.
PUBLISHED: 05-17-2010
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The goal of this study was to explore the presence of integrase strand transfer inhibitor (InSTI) resistance mutations in HIV-1 quasispecies present in InSTI-naïve patients and to evaluate their in vitro effects on phenotypic susceptibility to InSTIs and their replication capacities. The RT-RNase H-IN region was PCR amplified from plasma viral RNA obtained from 49 HIV-1 subtype B-infected patients (21 drug naïve and 28 failing highly active antiretroviral therapy [HAART] not containing InSTIs) and recombined with an HXB2-based backbone with RT and IN deleted. Recombinant viruses were tested against raltegravir and elvitegravir and for replication capacity. Three-hundred forty-four recombinant viruses from 49 patients were successfully analyzed both phenotypically and genotypically. The majority of clones were not phenotypically resistant to InSTIs: 0/344 clones showed raltegravir resistance, and only 3 (0.87%) showed low-level elvitegravir resistance. No primary resistance mutations for raltegravir and elvitegravir were found as major or minor species. The majority of secondary mutations were also absent or rarely present. Secondary mutations, such as T97A and G140S, found rarely and only as minority quasispecies, were present in the elvitegravir-resistant clones. A novel mutation, E92G, although rarely found in minority quasispecies, showed elvitegravir resistance. Preexisting genotypic and phenotypic raltegravir resistance was extremely rare in InSTI-naïve patients and confined to only a restricted minority of secondary variants. Overall, these results, together with others based on population and ultradeep sequencing, suggest that at this point IN genotyping in all patients before raltegravir treatment may not be cost-effective and should not be recommended until evidence of transmitted drug resistance to InSTIs or the clinical relevance of IN minor variants/polymorphisms is determined.
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Rapid prediction of sustained virological response in patients chronically infected with HCV by evaluation of RNA decay 48h after the start of treatment with pegylated interferon and ribavirin.
Antiviral Res.
PUBLISHED: 05-07-2010
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The combination of pegylated interferons (PEG-IFNs) and ribavirin represents the standard of care for the treatment of chronic HCV-infected patients, yet with a success rate around 50% in genotypes 1 and 4, high costs and side effects. Therefore, early prediction of sustained virological response (SVR) is a relevant issue for HCV-patients. We evaluated the association between SVR and decline of HCV-RNA at 48h in a prospective cohort of 145 HCV-patients treated with PEG-IFNs and ribavirin (males=69.1%; genotypes 1/4=51.0%; HIV-1 coinfected=6.7%). SVR was obtained in 65.5% of patients, while 16.6% experienced relapse and 17.9% no response. The first-phase of HCV-RNA decline clearly differentiated patients with SVR from relapsers and non-responders, independently of genotype (P<0.001). In univariate and multivariate analyses, different infralogaritmic thresholds of HCV-RNA decay at 48h were tested, observing the highest predictive potential at 0.5log: decays above this threshold showed a 76.2% negative predictive value for SVR, whereas decays >0.5log indicated a 6.8 odds ratio (95% C.I.: 2.0-23.2) for SVR after controlling for genotype, baseline viremia, adherence to therapy and HIV coinfection. Decays beyond the 0.5log threshold were also strongly associated with and highly predictive of early virological response (95.0% positive predictive value, P<0.001).
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The novel swine-origin H1N1 influenza A virus riddle: is it a domestic bird H1N1-derived virus?
New Microbiol.
PUBLISHED: 04-21-2010
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To understand the role of domestic birds in the 2009 H1N1 influenza A outbreak, a phylogenetic analysis of hemagglutinin, neuraminidase and matrix protein genes from human, avian and swine H1N1 viruses was carried out. Analysis of the H1 sequences revealed that the virus evolved most likely from American swine as well as intermixing between Asian swine and American domestic bird H1N1 viruses. Neuroaminidase and matrix protein analysis showed that the H1N1 2009 viruses were more closely related to the H1N1 isolates from Euro-Asiatic domestic birds and swine than wild birds. Domestic birds could act as intermediate hosts of H1N1 reassortants.
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A multicenter evaluation of the Abbott RealTime HCV Genotype II assay.
J. Virol. Methods
PUBLISHED: 03-16-2010
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Genotype determination is recommended before starting anti-HCV therapy to determine the duration of treatment (PEG-Interferon+ribavirin). The Versant HCV Genotype 2.0 assay, based on the reverse hybridization of the 5UTR segment and core region of hepatitis C virus (HCV), has been one of the assays used most widely for HCV genotyping. A multicenter evaluation of the more automated Abbott RealTime HCV Genotype II assay was carried out on 124 HCV positive sera tested previously with the Versant HCV Genotype 2.0 assay. There was good agreement between the two assays. Type concordance was 95.9% (117/122) while concordance at the subtype level for genotype 1 was 95.6% (43/45). The Abbott RealTime HCV Genotype II assay is automated, allowing a substantial reduction of time-to results and hands-on time. The combined features of full automation, objective interpretation and digital archiving make this assay useful in a diagnostic setting.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.