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PubMed2003

Clinically relevant interpretation of genotype for resistance to abacavir.

OBJECTIVE: To develop a stepwise methodology for the development and validation of clinically relevant genotypic score for resistance to antiretroviral drugs and to apply this approach to the genotypic resistance to abacavir. METHODS: All patients having received abacavir during the Narval trial were included in this study. The impact of each nucleoside analogue resistance mutation on the virologic response to abacavir was studied in a univariate analysis. Mutations with a P value < 0.20 and those selected by abacavir were retained. According to the number of mutations three levels of resistance were defined. A multivariate analysis accounting for confonding variables assessed whether the genotypic score was an independent predictor of the response. The robustness of the score was analysed using the bootstrap resampling method. RESULTS: In the 175 patients exposed to abacavir, the strongest association between the decrease in viral load and the number of mutations was observed with a set of six mutations at codons 41, 67, 210, 215, 74 and 184 of the reverse transcriptase gene. In patients with fewer than four mutations (no evidence of resistance) the median decrease in viral load was -1.64 log(10) copies/ml while it was -0.69 log(10) and -0.19 log(10) in those with four (possible resistance) and five or six (resistance) mutations respectively. In the multivariate analysis this score was an independent predictor of the response. The bootstrap analysis showed the robustness of the score. CONCLUSIONS: We developed a new strategy for the analysis of correlation between genotype profile at baseline and virologic response.

Algorithms↗
PubMed2006

A novel dnaC mutation that suppresses priB rep mutant phenotypes in Escherichia coli K-12.

The loading of a replisome in prokaryotic and eukaryotic cells at an origin of DNA replication and during replication restart is a highly ordered and regulated process. During replication restart in Escherichia coli, the PriA, PriB, PriC, DnaT and Rep proteins form multiple pathways that bind to repaired replication forks. These complexes are then recognized by DnaC as sites to load DnaB, the replicative helicase. Several dnaC mutations have been isolated that suppress phenotypes of some replication restart mutants. A new dnaC mutation (dnaC824) is reported here that efficiently suppresses priB rep mutant phenotypes. Furthermore, it is shown that dnaC824 will suppress phenotypes of priB priA300, rep priA300 and priB priC strains. Unlike other dnaC suppressors, it can only weakly suppress the absence of priA. Others have reported a different type of dnaC mutation, dnaC1331, is able to mimic priB mutant phenotypes. This is supported herein by showing that like dnaC1331, a priB mutation is synthetically lethal with a dam mutation and this can be rescued by a mutH mutation. Furthermore, priB dam lethality can also be suppressed by dnaC824. Like a priB mutation, a dnaC1331 mutation causes a priA2::kan-like phenotype when combined with priA300. Lastly, we show that dnaC824 is dominant to wild type and that dnaC1331 is recessive to wild type. Several models are discussed for the action of these mutant dnaC proteins in replication restart.

DNA Replication↗
PubMed2004

Evaluation of the genotypic pattern of HIV-1 resistance in AIDS patients failing antiretroviral therapy.

We analyzed the first 96 patients tested for HIV resistance to antiretroviral therapy in three Brazilian states. The HIV-1 reverse transcriptase (RT) and protease (PR) were sequenced by using the ABI ViroSeq system. The drugs previously used for each patient were recorded and correlated with the mutations found in the samples. Viral load (VL) and CD4 count were also recorded. Only one patient had the wild type sequence. The most prevalent mutations were: 184V (59%), 41L (47.9%), 63P (53%), 215Y (50%), 36I (46%), 10I (35%), 67N (42%), 77I (37%), 90M (36%) and 210W (33%). A positive correlation between the number of previously used ARVs and the number of mutations was observed (p<0.05). Associations between mutations and ARV drugs were identified at positions 69, 118, 184 and 215 with previous exposure to NRTI, mutations at positions 98, 100, 103, 181 and 190 with previous NNRTI use and at positions 10, 20, 30, 46, 53, 54, 71, 73, 82, 84, 88 and 90 with previous PI therapy (p<0.05). Previous exposure to ARV drugs was associated with previous genotypic resistance to specific drugs, leading to treatment failure in HIV patients. Genotypic resistance was clearly associated with virological and immunological failure.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

HIV treatment strategies utilizing virologic and immunologic markers as criteria for changing treatments.

Currently available antiviral drugs used in the treatment of AIDS patients are effective for a limited time. Therapy consisting of different drugs given in sequence thus has the potential to yield the greatest possible benefit to patients, yet it is not known in what order the drugs should be administered, or for how long. Can patient-specific information, such as viral load or determination of mutation status, be used to make these decisions on a patient by patient basis? We propose a general model for the relationship between treatment, virologic or immunologic markers, and clinical disease progression that can provide answers to these questions. We develop guidelines for optimizing progression under several settings. Optimal survival is derived for full, partial, or no interim information.

Acquired Immunodeficiency Syndrome↗
PubMed2005

High replicative full-length lamivudine-resistant hepatitis B virus isolated during acute exacerbations.

During chronic HBV infections, exacerbations of disease usually occur without clearly understood mechanisms. In this study, full-length HBV genomes were analyzed from four chronic hepatitis B patients who developed resistance to lamivudine [-2'-deoxy-3'-thiacytidine, LMV] accompanied by acute exacerbation of disease. Paired full-length HBV isolates were cloned from the sera of patients prior to LMV treatment and after drug resistant breakthrough isolates emerged with exacerbation. Compared to the isolates before treatment, isolates from all four patients during exacerbation showed marked increase in replicative competence by cell transfection study. Viral genome amplification and direct sequencing was used further to study the sequence differences between the dominant species and the clones used for functional analysis. Apart from mutations at the YMDD motif, no shared mutations were shown between all isolates. The isolates from the one patient who recovered from the exacerbation showed a lower number of mutations, and in particular, lacked basal core promoter (BCP) mutations at 1762/1764. In contrast, BCP mutations were found in isolates from the other three patients. Thus, in patients with acute exacerbation, high replicative strains might be selected from the total HBV quasispecies during treatment, and amongst these strains, those with core promoter mutations were most likely to be associated with severe clinical exacerbations.

Amino Acid Substitution↗
PubMed1997

Prediction of effect of interferon on chronic hepatitis C.

Clinical, pathological, and virological analysis including hypervariable region-1 of hepatitis C virus (HCV) was performed to predict the effect of interferon (IFN) on 41 patients with chronic hepatitis type C. The low virus load, low frequency of the mutation in the hypervariable region-1 as the change of amino acid and high level of serum aminotransferase make one estimate the good effect of IFN on patients with HCV. Mutation in the hypervariable region-1 of HCV measured by fast assay fluorescence single-stranded conformational polymorphism was more frequent in nonresponders to IFN than responders. The most frequently mutated position was amino acid number 406. This indicates that the specific mutation site might affect the response of IFN.

Amino Acid Sequence↗
PubMed2005

Delay of HIV-1 rebound after cessation of antiretroviral therapy through passive transfer of human neutralizing antibodies.

To determine the protective potential of the humoral immune response against HIV-1 in vivo we evaluated the potency of three neutralizing antibodies (2G12, 2F5 and 4E10) in suppressing viral rebound in six acutely and eight chronically HIV-1-infected individuals undergoing interruption of antiretroviral treatment (ART). Only two of eight chronically infected individuals showed evidence of a delay in viral rebound during the passive immunization. Rebound in antibody-treated acutely infected individuals upon cessation of ART was substantially later than in a control group of 12 individuals with acute infection. Escape mutant analysis showed that the activity of 2G12 was crucial for the in vivo effect of the neutralizing antibody cocktail. By providing further direct evidence of the potency, breadth and titers of neutralizing antibodies that are required for in vivo activity, these data underline both the potential and the limits of humoral immunity in controlling HIV-1 infection.

Acute Disease↗
PubMed1999

Development of an Epstein-Barr virus type 2 (EBV-2)-associated hepatic B cell non-Hodgkin's lymphoma in an HIV-1-infected patient following a change in the EBV dominant type.

From the longitudinal study of a cohort of HIV-positive patients, we report the case of a patient who initially harbored the Epstein-Barr virus (EBV) type 1 and subsequently developed an EBV-2-associated non-Hodgkin's B lymphoma a few years after an EBV-2 reactivation, or an exogenous reactivation, in the blood. At the time of diagnosis of hepatic lymphoma, the blood and the throat harbored high levels of the EBV-1 dominant strain. Sequence analysis of EBNA-2 gene revealed that: (1) type 2 EBV detected during reactivation and then in hepatic tumor was very likely to be the same strain and was mostly identical to the EBV prototype AG876; (2) type 1 virus conserved the same mutations during all the follow-up. These results suggest that EBV-2 might be associated with lymphomatogenesis and that a transient reactivation could lead to the development of an EBV-associated disease.

Genotype↗
PubMed1996

New strategies to combat HIV drug resistance.

Recent insights into HIV dynamics argue strongly for early intervention with antiretroviral combinations designed to block resistant mutations. By using more potent agents and taking advantage of drug selective pressure to force the emergence of strains with reduced evolutionary fitness, investigators are attempting to bring HIV replication to a halt. And in many cases, they appear to be succeeding.

Anti-HIV Agents↗
PubMed2002

Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach.

Using pseudomaximum-likelihood approaches to phylogenetic inference and coalescent theory, we develop a computationally tractable method of estimating effective population size from serially sampled viral data. We show that the variance of the maximum-likelihood estimator of effective population size depends on the serial sampling design only because internal node times on a coalescent genealogy can be better estimated with some designs than with others. Given the internal node times and the number of sequences sampled, the variance of the maximum-likelihood estimator is independent of the serial sampling design. We then estimate the effective size of the HIV-1 population within nine hosts. If we assume that the mutation rate is 2.5 x 10(-5) substitutions/generation and is the same in all patients, estimated generation lengths vary from 0.73 to 2.43 days/generation and the mean (1.47) is similar to the generation lengths estimated by other researchers. If we assume that generation length is 1.47 days and is the same in all patients, mutation rate estimates vary from 1.52 x 10(-5) to 5.02 x 10(-5). Our results indicate that effective viral population size and evolutionary rate per year are negatively correlated among HIV-1 patients.

Bayes Theorem↗
PubMed2004

A robust measure of HIV-1 population turnover within chronically infected individuals.

A simple nonparameteric test for population structure was applied to temporally spaced samples of HIV-1 sequences from the gag-pol region within two chronically infected individuals. The results show that temporal structure can be detected for samples separated by about 22 months or more. The performance of the method, which was originally proposed to detect geographic structure, was tested for temporally spaced samples using neutral coalescent simulations. Simulations showed that the method is robust to variation in samples sizes and mutation rates, to the presence/absence of recombination, and that the power to detect temporal structure is high. By comparing levels of temporal structure in simulations to the levels observed in real data, we estimate the effective intra-individual population size of HIV-1 to be between 10(3) and 10(4) viruses, which is in agreement with some previous estimates. Using this estimate and a simple measure of sequence diversity, we estimate an effective neutral mutation rate of about 5 x 10(-6) per site per generation in the gag-pol region. The definition and interpretation of estimates of such "effective" population parameters are discussed.

Evolution, Molecular↗
PubMed2004

Mitochondrial and nuclear DNA base excision repair are affected differently by caloric restriction.

Aging is strongly correlated with the accumulation of oxidative damage in DNA, particularly in mitochondria. Oxidative damage to both mitochondrial and nuclear DNA is repaired by the base excision repair (BER) pathway. The "mitochondrial theory of aging" suggests that aging results from declining mitochondrial function, due to high loads of damage and mutation in mitochondrial DNA (mtDNA). Restriction of caloric intake is the only intervention so far proven to slow the aging rate. However, the molecular mechanisms underlying such effects are still unclear. We used caloric-restricted (CR) mice to investigate whether lifespan extension is associated with changes in mitochondrial BER activities. Mice were divided into two groups, receiving 100% (PF) or 60% (CR) of normal caloric intake, a regime that extends mean lifespan by approximately 40% in CR mice. Mitochondria isolated from CR mice had slightly higher uracil (UDG) and oxoguanine DNA glycosylase (OGG1) activities but marginally lower abasic endonuclease and polymerase gamma gap-filling activities, although these differences were tissue-specific. Uracil-initiated BER synthesis incorporation activities were significantly lower in brain and kidney from CR mice but marginally enhanced in liver. However, nuclear repair synthesis activities were increased by CR, indicating differential regulation of BER in the two compartments. The results indicate that a general up-regulation of mitochondrial BER does not occur in CR.

Aging↗
PubMed1998

The frequency of resistant mutant virus before antiviral therapy.

OBJECTIVE: To calculate the expected prevalence of resistant HIV mutants before antiviral therapy. DESIGN: HIV replication generates virus mutants. The prevalence of these mutants is determined by mutation and selection/fitness. Some mutations will confer drug resistance and it is crucial for the success of antiviral drug therapy to determine whether these resistant viruses are present before the initiation of therapy. METHODS: A quasispecies equation was used to calculate the expected frequency of drug-resistant virus prior to therapy. RESULTS AND CONCLUSIONS: We show how the pretreatment frequency of resistant virus depends on the number of point mutations between wild-type and mutant virus, the selective disadvantage of the resistant mutant and the intermediate mutants, and the mutation rate.

Anti-HIV Agents↗
PubMed2002

Discordant response to antiretroviral therapy: HIV isolation, genotypic mutations, T-cell proliferation and cytokine production.

OBJECTIVE: To study virologic and immunologic factors associated with discordant treatment response in HIV-infected patients receiving highly active antiretroviral therapy (HAART). DESIGN: Study participants included a total of 27 patients: (a) 10 discordant patients (mean CD4+ cell count, 396.1 x 10 cells/l; mean HIV-RNA, 5.4 log copies/ml); (b) seven responder patients (mean CD4+ cell count, 997.5 x 10 cells/l); and (c) 10 failing patients (mean CD4+ cell count 66.5 x 10 cells/l; mean HIV-RNA, 5.4 log copies/ml).(10) (10) METHODS: The HIV-1 isolation rate and biological phenotype, drug resistance genotypic mutations of HIV-1 strains, recall and HIV-1-specific antigen lymphocyte proliferation (LP), and interleukin (IL)-15 production were studied. RESULTS: Virus isolation was obtained in 30% of discordant patients, and in 100% of failing patients. A higher replication constant was reported in discordant patients. No difference in the number of drug resistance mutations and biological phenotypes of HIV-1 was found in discordant patients with respect to failing patients. Discordant patients developed positive LP responses to and HIV-1 p24. LP in response to, HIV-1 p24 and gp160 was positive in responder patients. No significant LP was found in failing patients. Increased levels of IL-15 after stimulation with lipopolysaccaride (LPS) and were found in both discordant patients and responder patients. Conversely, a strong reduction of IL-15 levels was observed in failing patients. CONCLUSION: The present results suggest that decreased virus isolation rate, restoration of both lymphocyte proliferation and IL-15 production are factors involved in the discordant antiretroviral therapy response of HIV-infected patients.

Adult↗