Prevalence of natural polymorphisms at the HCV NS5A gene associated with resistance to daclatasvir, an NS5A inhibitor.

BACKGROUND: Daclatasvir (BMS-790052) is an investigational molecule that inhibits the HCV NS5A protein and shows potent antiviral activity apparently across all HCV genotypes. Selection of drug resistance mutations has been reported only for HCV genotype 1, and no information exists for other HCV variants and/or in HIV-HCV-coinfected individuals. METHODS: All interferon-α-naive, HIV-HCV-coinfected patients newly attended at Hospital Carlos III (Madrid, Spain) in 2011 were identified. Changes reported to be associated with daclatasvir resistance in the in vitro replication system for HCV genotype/subtypes 1a/1b (M28T, Q30H/R, L31F/M/V, P32L and Y93C/H/N) were examined. RESULTS: A total of 78 HIV-HCV-coinfected individuals as well as 635 NS5A sequences deposited at Los Alamos HCV database were analysed. None of the NS5A sequences from HCV-1a or HCV-3 showed changes associated with daclatasvir resistance. By contrast, all NS5A sequences from HCV-4 harboured L31M. The double mutant L31M+Y93H was found in 7% of HCV-1b and 13% of HCV-4. Finally, all NS5A sequences from HCV-1b and HCV-4 harboured changes at codon 28 (M28L) and 30 (L30R), which are of unknown significance. The rate of all these NS5A polymorphisms did not differ significantly when comparing HIV-HCV-coinfected patients and sequences from HCV-monoinfected subjects deposited at Los Alamos HCV database. CONCLUSIONS: Primary resistance mutations to daclatasvir, an investigational HCV NS5A inhibitor, are not seen in HCV-1a or in HCV-3 as natural polymorphisms. By contrast, they can be recognized in most HCV-1b and HCV-4 strains, regardless HIV coinfection.

Nuclear insertions of mitochondrial origin: Database updating and usefulness in cancer studies.

Nuclear insertions of mitochondrial origin (NUMTs) can be useful tools in evolution and population studies. However, due to their similarity to mitochondrial DNA (mtDNA), NUMTs may also be a source of contamination in mtDNA studies. The main goal of this work is to present a database of NUMTs, based on the latest version of the human genome-GRCh37 draft. A total of 755 insertions were identified. There are 33 paralogous sequences with over 80% sequence similarity and of a greater length than 500bp. The non-identical positions between paralogous sequences are listed for the first time. As an application example, the described database is used to evaluate the impact of NUMT contamination in cancer studies. The evaluation reveals that 220 positions from 256 with zero hits in the current mtDNA phylogeny could in fact be traced to one or more nuclear insertions of mtDNA. This is due to they are located in non-identical positions between mtDNA and nuclear DNA (nDNA). After in silico primer validation of each revised cancer study, risk of co-amplification between mtDNA and nDNA was detected in some cases, whereas in others no risk of amplification was identified. This approach to cancer studies clearly proves the potential of our NUMT database as a valuable new tool to validate mtDNA mutations described in different contexts. Moreover, due to the amount of information provided for each nuclear insertion, this database should play an important role in designing evolutionary, phylogenetic and epidemiological studies.

Short communication: severe immune suppression in patients infected with R5-tropic HIV-1 strains is associated with increased gp120 net charge at variable regions.

CXCR4-tropic viruses have been associated with advanced immune suppression. However, 50% of patients with AIDS exclusively harbor CCR5-tropic viruses. The net charge at HIV-1 envelope gp120 variable regions was examined in 66 HIV-1-infected individuals with CCR5-tropic viruses, of whom 30 had less than 200 cells/mm(3). A positive net charge at gp120 variable regions was significantly associated with lower CD4 counts. Thus, the net charge at gp120 variable regions could influence HIV-1 disease progression in subjects with CCR5-tropic viruses.

Dynamics of HIV tropism under suppressive antiretroviral therapy: implications for tropism testing in subjects with undetectable viraemia.

OBJECTIVES: The use of maraviroc as part of a simplification of antiretroviral therapy (ART) is hampered by the difficulty of assessing viral tropism in patients with undetectable viraemia. In this context, information on tropism might be obtained from testing either older stored viraemic sera collected before initiation of ART or current proviral DNA in peripheral blood cells. METHODS: HIV-1-infected individuals who had initiated ART and had undetectable viraemia for >2 years were identified. V3 genotyping was performed in parallel from plasma HIV-RNA and proviral DNA before starting ART and from proviral DNA while on suppressive ART. Viral tropism was interpreted using geno2pheno (false positive rate = 10%) and an optimized version of position specific scoring matrices (PSSM) with a greater sensitivity to detect X4 variants (PSSM(X4/R5-8)). RESULTS: A total of 78 HIV-1 infected individuals were examined. Mean time under suppressive ART was 3.5 years (interquartile range: 2.3-4.4). The rate of X4 variants in plasma and proviral DNA samples at baseline was 32.8% and 34.0%, respectively. It was 33.9% after >2 years of suppressive ART in DNA samples. Paired RNA/DNA tropism results at baseline could be obtained for 38 patients, with an overall 82% concordance. After >2 years of suppressed plasma viraemia, HIV tropism was re-assessed in proviral DNA; tropism switches were uncommon, especially comparing baseline and most recent DNA longitudinal specimens (12%). CONCLUSIONS: HIV tropism switches over time under suppressive ART are rare. There is a relatively good correlation between RNA and DNA tropism estimations using genotypic tests. Thus, HIV-1 tropism might confidently be examined either in older stored viraemic plasma specimens or in current proviral DNA samples.

Impact of antiretroviral therapy on viral tropism in HIV-infected patients followed longitudinally for over 5 years.

BACKGROUND: Viral tropism plays a major role in HIV pathogenesis and may influence the activity of entry inhibitors. The impact of antiretroviral therapy use on the dynamics of viral tropism over time is still poorly understood. PATIENTS AND METHODS: HIV co-receptor usage was determined longitudinally for over 5 years in 237 plasma specimens collected from 73 distinct HIV-1-infected drug-naive individuals, 42 of whom initiated antiretroviral therapy thereafter and 31 who remained untreated. Viral tropism was estimated genotypically using the phenotype predictor software webPSSM, considering as X4 virus populations those with pure X4 and dual/mixed X4/R5 variants. RESULTS: At baseline, the prevalence of X4 viruses was 3.2% and 14.6% in patients who remained untreated and in those who initiated antiretroviral therapy, respectively (P = 0.112). Mean plasma HIV-RNA was lower in the former compared with the latter (3.8 +/- 0.9 versus 4.5 +/- 0.9 log; P < 0.004), while conversely the mean CD4 count was greater in untreated than in those who had begun therapy (536 +/- 191 versus 278 +/- 192 cells/mm3; P < 0.001). During follow-up, switch in co-receptor use occurred overall in 26% of the study population, with no significant differences between the groups. Emergence of X4 viruses was significantly associated with lower CD4 counts regardless of antiretroviral treatment exposure. CONCLUSIONS: The use of antiretroviral therapy does not seem to influence the selection of X4 viruses, which mainly occur in patients with low CD4 counts.

Correlation between a phenotypic assay and three bioinformatic tools for determining HIV co-receptor use.

The predictive value of three genotypic methods to determine HIV-1 co-receptor usage was assessed in 83 plasma specimens taking as reference the results obtained using a recombinant phenotypic assay (Phenoscript). The best concordance was found for webPSSM, followed by geno2pheno and wetcat (85.9, 71.8 and 70.5%, respectively). Less than 5.1% of phenotypic X4 viruses were missed by genotypic tools. The genotypic prediction of HIV-1 co-receptor usage can thus assist therapeutic decisions for using CCR5 antagonists.

Effect of C-reactive protein on Fcgamma receptor II in cultured bovine endothelial cells.

The major CRP (C-reactive protein) receptor on leucocytes has been identified as the low-affinity IgG receptor Fcgamma receptor II (CD32). Our aim was to assess whether inflammation may modify the presence of the CD32 receptor in BAEC (bovine aortic endothelial cells). Confocal microscopy experiments showed a weak expression of the CD32 receptor in control BAEC that was slightly increased by 10 microg/ml CRP. Incubation of BAEC with TNF-alpha (tumour necrosis factor-alpha) did not modify the fluorescence signal of CD32. Addition of CRP to TNF-alpha-incubated BAEC enhanced the fluorescence signal of the CD32 receptors. The CD32 receptors showed a perinuclear cytoplasmic localization in BAEC. An alteration of the NO (nitric oxide)-dependent vasorelaxation has been defined as endothelial dysfunction. Endothelial dysfunction has been associated with the presence of superoxide anion and with a reduction in the expression of the eNOS (endothelial NO synthase). A concentration of CRP similar to that detected in patients with cardiovascular risk (10 microg/ml) failed to modify the generation of superoxide anion stimulated by TNF-alpha. Western blot experiments showed that TNF-alpha decreased the expression of the eNOS protein, which was partially protected by treatment with 10 microg/ml CRP. The protective effect of 10 microg/ml CRP on eNOS expression in TNF-alpha-incubated BAEC was prevented by an antibody against CD32 receptors. In conclusion, the present results suggest that, although CRP has been associated with inflammation, CRP may protect the expression of eNOS protein against pro-inflammatory mediators such as TNF-alpha.

Phenotypic characterization of a Candida albicans strain deficient in its major exoglucanase.

Both alleles of the XOG1 gene of Candida albicans, which encodes a protein with exoglucanase activity, were sequentially disrupted. Enzymic analysis of either cell extracts or culture supernatants of disrupted strains revealed that this gene is responsible for the major exoglucanase activity in C. albicans, although residual exoglucanase activity could still be detected. xog1 null mutants showed similar growth rates in both rich and minimal liquid medium as compared to the wild-type strain, indicating that the enzyme is not essential for C. albicans growth. In addition, no differences were observed between wild-type and xog1 null mutants with respect to their ability to undergo dimorphic transition. However, small but repeatable differences were found between the wild-type and the null mutant with respect to susceptibility to chitin and glucan synthesis inhibitors. Using a murine model of experimental infection, no significant differences in virulence were observed. The xog1 null strain is thus a suitable recipient for studying Candida gene expression using the exoglucanase as a reporter gene.