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PubMed2006

Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy.

A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.

Genes, env↗
PubMed2005

Evolution of human immunodeficiency virus type 2 coreceptor usage, autologous neutralization, envelope sequence and glycosylation.

To investigate why human immunodeficiency virus type 2 (HIV-2) is less virulent than HIV-1, the evolution of coreceptor usage, autologous neutralization, envelope sequence and glycosylation was studied in sequentially obtained virus isolates and sera from four HIV-2-infected individuals. Neutralization of primary HIV-2 isolates was tested by a cell line-based assay and IgG purified from patients' sera. Significant autologous neutralization was observed for the majority (39 of 54) of the HIV-2 serum-virus combinations tested, indicating that neutralization escape is rare in HIV-2 infection. Furthermore, sera from 18 HIV-2 patients displayed extensive heterologous cross-neutralization when tested against a panel of six primary HIV-2 isolates. This indicates that HIV-2 is intrinsically more sensitive to antibody neutralization than HIV-1. In line with earlier reports, HIV-2 isolates could use several alternative receptors in addition to the major coreceptors CCR5 and CXCR4. Intrapatient evolution from CCR5 use to CXCR4 use was documented for the first time. Furthermore, CXCR4 use was linked to the immunological status of the patients. Thus, all CXCR4-using isolates, except one, were obtained from patients with CD4 counts below 200 cells microl(-1). Sequence analysis revealed an association between coreceptor usage and charge of the V3 loop of the HIV-2 envelope, as well as an association between the rate of disease progression and the glycosylation pattern of the envelope protein. Furthermore, HIV-2 isolates had fewer glycosylation sites in the V3 domain than HIV-1 (two to three versus four to five). It is proposed here that HIV-2 has a more open and accessible V3 domain than HIV-1, due to differences in glycan packing, and that this may explain its broader coreceptor usage and greater sensitivity to neutralizing antibodies.

Amino Acid Sequence↗
PubMed2002

The evolution of hepatitis B virus serological patterns and the clinical relevance of isolated antibodies to hepatitis B core antigen in HIV infected patients.

BACKGROUND/AIMS: The evolution of hepatitis B virus (HBV) serological patterns and the clinical relevance of isolated anti-HBc pattern are not well established in HIV infected patients. METHODS: A cohort of 240 patients was followed for 6.9+/-3.4 years, with iterative HBV serologic assays performed (mean interval of 2.2 years). RESULTS: Five patients without HBV markers at baseline subsequently developed positive anti-HBs (incidence 0.66/100 patient-year), as did two patients with chronic HBs antigenemia (incidence 1.66/100 patient-year). Only one patient with isolated anti-HBc pattern developed HBs chronic antigenemia. Persistent isolated anti-HBc pattern was observed in 37 patients (13 with detectable blood HBV DNA) and was strongly associated with positive hepatitis C virus (HCV) viremia (hazard ratio=9.5, confidence interval 95%: 4.5-20.0, P<0.0001). Hepatic lesions were more severe in HCV infected patients with persistent isolated anti-HBc pattern than in those without (Knodell score 9.2+/-4.6 versus 6.7+/-5.0, P=0.04). In time updated analysis, this pattern was not associated with an increased risk of hepatotoxicity, by contrast with HCV infection or positive HBs antigenemia. CONCLUSIONS: In HIV infected patients, HBV serological status must be systematically and regularly assessed, and systematic HBV vaccination must be proposed in those without HBV marker. Isolated anti-HBc pattern must be considered in the management of hepatitis C, but not for antiretroviral therapy.

Adult↗
PubMed1996

Evolution of tumor necrosis factor-alpha serum concentrations in HIV infected individuals treated with zidovudine.

We studied the evolution of Tumor Necrosis Factor-alpha serum concentration (TNF-alpha) and CD4+ lymphocyte counts (CD4+) in a pilot cohort study of HIV-infected patients during the first year of zidovudine therapy. Data on 17 patients remaining asymptomatic during the one-year follow-up period (non progressors) were analysed. Serum samples were obtained at entry and at each follow-up visit (1, 3, 6, 9 and 12 months). TNF-alpha was quantified in pg/ml using a very sensitive radioimmunoassay (Medgenix). All patients had increased TNF-alpha at entry (median: 26.4 pg/ml). TNF-alpha decreased significantly as soon as the first month of therapy (median: 16 pg/ml). A steady state was then observed until Month 6 (median: 17.5 pg/ml), from which a slow increase appeared, without reaching the initial level (median at Month 9: 21.3, at Month 12: 19.8). During the same time, less sustained changes in CD4+ lymphocytes count and beta-2 microglobulin level were observed. The results of this pilot study suggest that, during HIV infection treated course, TNF-alpha could potentially be an additional surrogate marker to CD4+ lymphocyte count.

Anti-HIV Agents↗
PubMed2001

Application of HIV-1 genotypic-resistance testing prevents the evolution of further resistance mutations in heavily pretreated patients.

BACKGROUND: Resistance-associated mutations in HIV-1 evolve even under highly active antiretroviral therapy. OBJECTIVE: To evaluate the clinical efficacy of genotypic-resistance testing (GRT), to estimate the potential of a given antiretroviral therapy for prevention of further resistance mutations. STUDY DESIGN: Ten patients were treated prospectively with drugs, according to the results of a GRT. Five patients were allocated to group I in which antiretroviral therapy could be switched to an effective regimen (consisting of at least three sensitive drugs, from at least two different classes of antiretroviral substances). Five patients (group II) had no option for effective therapy, and continued to be treated non-effectively (at least one applicated substance class only intermediately sensitive, or resistant). GRT and quantitative viral cultures were performed longitudinally for 8 months. Also, plasma HIV-1 RNA, total CD4+ cells, and rates of productively infected CD4+ cells were determined. RESULTS: All the patients in group I showed a significant decrease of HIV-RNA of >1 log/ml (mean, -1.35 log/ml, P=0.025). The mean increase of CD4+ cells was 46 (not significant). The rate of productively infected CD4+ cells decreased significantly (mean, -16 productively infected CD4+ cells per 10(6) total CD4+ cells, P=0.04). In this group no further resistance mutations were detected after 8 months. In group II, none of the patients showed a significant decrease of HIV-1 RNA (mean, +0.05 log/ml), total CD4+ cells decreased (mean, -35, not significant), the rate of productively infected CD4+ cells increased significantly (mean, +124 productively infected CD4+ cells per 10(6) total CD4+ cells, P=0.04), and 4 of 5 patients had additional mutations in the RT gene conferring multi-drug resistance within 8 months (P=0.048). CONCLUSIONS: GRT is predictive of the efficacy of a therapeutic regimen, in particular regarding evolution of further resistance mutations.

Adult↗
PubMed1996

Independent evolution of the env and pol genes of HIV-1 during zidovudine therapy.

OBJECTIVE: To determine the effect that selection for antiviral resistance in the HIV-1 pol gene has on the level of variation and pattern of evolution in the V3 region of env. DESIGN: Proviral genomes obtained from two patients before, during and after the termination of zidovudine (ZDV) therapy (approximately 2 years) were amplified and sequenced in pol and env, and the evolution of the V3 hypervariable region compared with that of the reverse transcriptase domain of pol. METHODS: Gene fragments were polymerase chain reaction-amplified from patients' peripheral blood mononuclear cells. Nucleotide sequencing was carried out using T7 DNA polymerase and dye-labelled terminators on an automated DNA sequencer. Sequences were analysed using maximum likelihood phylogenetic techniques. RESULTS: Both patients showed multiple resistance-associated mutations after 1 year of ZDV therapy. Sequence diversity in V3 showed no reduction during the period of treatment. Substantial change continued to occur in this region and multiple lineages were present in both patients, in contrast to the single lineage observed in the pol gene of one (patient 74), a difference confirmed by likelihood ratio tests. CONCLUSIONS: There is no evidence from this study that selection due to antivirals has any significant impact on the evolution of the env gene. The independence in the evolution of these genes implies that recombination was occurring between the two genes during the study period. Such independent evolution should be allowed for in developing strategies for HIV therapy involving multiple target genes.

Amino Acid Sequence↗
PubMed2000

Origin of HIV type 1 in colonial French Equatorial Africa?

Sociocultural factors during the postcolonial period have been implicated as paramount in generating conditions that promoted both the origin and subsequent epidemic spread of HIV-1 in Africa. We suggest, however, that the origin of the disease may lie in the interaction between colonial practices (e.g., labor camps, nonsterile vaccination campaigns) and traditional bushmeat hunting in French Equatorial Africa. Both the epidemiology of HIV-2 and the colonial history of West Africa appear more complex, but similar conditions existed there and may have contributed to the origin of HIV-2. Focusing the search for the origins of HIV-1 and HIV-2 on this earlier time period may contribute to understanding the evolution of the HIV viruses and the dynamics of emerging diseases.

Adaptation, Physiological↗
PubMed2004

Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy.

BACKGROUND AND OBJECTIVE: The optimal time for changing failing antiretroviral therapy (ART) is not known. It involves balancing the risk of exhausting future treatment options against the risk of developing increased drug resistance. The frequency with which new drug-resistance mutations (DRM) developed and their potential consequences in patients continuing unchanged treatment despite persistent viremia were assessed. DESIGN: A retrospective study of consecutive sequence samples from 106 patients at one institution with viral load (VL) of more than 400 copies/ml, with no change in ART for more than 2 months despite virologic failure. METHODS: Two consecutive pol sequences, CD4 cell counts and VL were analyzed to quantify the development of new DRM and to identify changes in immunologic and virologic parameters. Genotypic susceptibility scores (GSS) and viral drug susceptibilities were calculated by a computer program (HIVDB). Poisson log-linear regression models were used to predict the expected number of mutations at the second time point. RESULTS: : After a median of 14 months of continued ART, 75% (80 of 106) of patients acquired new DRM and were assigned a significantly lower GSS, potentially limiting the success of future ART. The development of new DRM was proportional to the time between the two sequences and inversely proportional to the number of DRM in the first sequence. However, the development of DRM was not associated with significant changes in CD4 or VL counts. CONCLUSIONS: Despite stable levels of CD4 and VL over time, maintaining a failing therapeutic regimen increases drug resistance and may limit future treatment options.

Adult↗
PubMed2005

Evolution of resistance mutations pattern in HIV-1-infected patients during intensification therapy with a boosted protease inhibitor.

Intensification therapy adding a boosted protease inhibitor (PI) to a failing regimen has the potential to worsen the resistance profile. Sixty-six patients included in four different boosted PI intensification studies were assessed and resistance mutations in the reverse transcriptase and protease genes were evaluated at baseline and 4 weeks after the initiation of the intensification strategy. Only one of the 66 patients developed changes in their pattern of mutations able to generate or increase resistance to new drugs.

Antiretroviral Therapy, Highly Active↗
PubMed2004

[Neurological and psychological evolution of adolescents with vertical transmission HIV infection].

AIM: Personal experience in a sample group of children with AIDS vertically transmitted followed from birth to adolescence (out of 56 cases with documented HIV infection, 9 who have reached the age of 13 have been studied) is presented. METHODS: The evaluation protocol includes: hematochemical, serological and virological tests to monitor the infectious status, as well as annual EEG, CT/MRI scan to detect anatomical alteration of CNS, neurological examination, intelligence test (WISC-R), interview and projective test (Blacky Pictures) to investigate emotional situation. RESULTS: As to the status of the disease, according to the CDC classification, 2 patients are asymptomatic, 2 paucisymptomatic, 2 with moderate symptoms, 2 severely symptomatic; 1 patient died due to progressive encephalopathy. Of the 2 severely symptomatic cases, 1 presents cortical atrophy and the other basal nuclei calcifications. No one of them has clinical signs of encephalopathy. All patients receive anti-retroviral medications. From tests and interviews emotional problem-emerge, future is seen as menacing and insidious, and defensive mechanisms are fragile and inconstant; denial can lead to a refusal of the pharmacological therapy; families themselves often refuse medical staff the consent to communicate the diagnosis fearing that this could induce unbearable anguish. CONCLUSIONS: It seems important that patients are informed, considering their capacity to make front to the communication, even if one must bear in mind that understanding and accepting the diagnosis may be a long and painful process requiring a long time.

Adolescent↗
PubMed2005

HIV-1-specific CD8+ T cell responses and viral evolution in women and infants.

CD8+ T lymphocyte responses play an important role in controlling HIV-1 replication but escape from CD8+ T cell surveillance may limit the effectiveness of these responses. Mother-to-child transmission of CD8+ T cell escape variants may particularly affect CD8+ T cell recognition of infant HIV-1 epitopes. In this study, amino acid sequence variation in HIV-1 gag and nef was examined in five untreated mother-infant pairs to evaluate the potential role of CD8+ T cell responses in the evolution of the viral quasispecies. Several CD8+ T cell escape variants were detected in maternal plasma. Evaluation of infant plasma viruses at 1-3 mo documented heterogeneity of gag and nef gene sequences and mother-to-child transmission of CD8+ T cell escape variants. Infant HLA haplotype and viral fitness appeared to determine the stability of the escape mutants in the infant over time. Changes in CD8+ T cell epitope sequences were detected in infants' sequential plasma specimens, suggesting that infants are capable of generating virus-specific CD8+ T cell responses that exert selective pressures in vivo. Altogether, these studies document that HIV-1-specific CD8+ T cell responses contribute to the evolution of the viral quasispecies in HIV-1-infected women and their infants and may have important implications for vaccine design.

Adult↗
PubMed2006

Physical theory of the competition that allows HIV to escape from the immune system.

Competition within the immune system may degrade immune control of viral infections. We formalize the evolution that occurs in both HIV-1 and the immune system quasispecies. Inclusion of competition in the immune system leads to a novel balance between the immune response and HIV-1, in which the eventual outcome is HIV-1 escape rather than control. The analytical model reproduces the three stages of HIV-1 infection. We propose a vaccine regimen that may be able to reduce competition between T cells, potentially eliminating the third stage of HIV-1.

Biological Evolution↗
PubMed2004

Perinatal transmission and viral evolution of hepatitis C virus quasispecies in infants coinfected with HIV.

OBJECTIVES: Three HIV/hepatitis C virus (HCV)-coinfected children and the mothers of 2 were studied to examine the nature of perinatal HCV infection in HIV-coinfected infants and to assess the evolution of viral quasispecies thereafter. Sequences of the hypervariable region in the N terminus of the E2/NS1 region (HVR-1) of the children and their mothers were compared. HCV quasispecies changes in the infants were tracked over several years. METHODS: Sequence similarity comparisons and phylogenetic trees were derived from cDNA of plasma isolates. Quantitation of plasma HCV and HIV was performed in the children, as well as CD4 T-cell percentage and liver transaminases. RESULTS: Phylogenetic analysis of the mother-child pairs suggested that transmission of multiple dominant and nondominant variants identified in the mother were seen. HCV diversification in the children was seen as early as 2 months of life. The child with the best immune status and HIV control demonstrated the most diversification throughout. CONCLUSION: Multiples HCV variants transmitted from mother to child and their early changes in the child may be related to maternal antibody. Variation after the 1st year of life may reflect immunologic pressure from the child. There was no trend suggesting that the presence or absence of selective immunologic pressure affected HCV load or liver transaminase values.

Amino Acid Sequence↗
PubMed2004

[Early ENT manifestations of HIV infection/AIDS. An analysis of 76 cases observed in Africa].

OBJECTIVE: The aim of this work is to describe the ENT clinical manifestations by which HIV positive patients inaugurate their AIDS-illness and to classify these manifestations in respect to the biological state of the infection. MATERIAL AND METHOD: It was a multicenter, prospective study carried out in the ENT services of Yaounde (Cameroon), between the period of September 2000 and June 2002. Included in this study were HIV patients who started their AIDS with an ENT illness. The stage of evolution of the HIV infection was evaluated using the CD4 and CD8 T lymphocyte counts. This was carried out using the Flux cytometric technique of Fascount/Becton. RESULTS: We thereafter recruited 76 patients. The incidence rate of ENT early manifestations in HIV positive patients was 11.5%. Pharyngeal and oral candidosis represented the most observed manifestation (30.60%), followed by peripheral facial paralysis (11.13%) and rhino-sinusitis (10.58%). Parotid gland hypertrophy represented 8.23% of the affections. Persistant cervical lymphadenopathy was observed in 7.05% of cases. Kaposi sarcoma and cervical lymph node tuberculosis represented each 3.53% of cases of the sample. The correlation of lymphocytic count and initial ENT manifestations showed that these manifestations were observed in all the biological states of the HIV/AIDS infection. CONCLUSION: The above mentioned ENT manifestations in the patient should motivate the request of the HIV screening tests.

CD4 Antigens↗
PubMed2005

Adaptive evolution of primate TRIM5alpha, a gene restricting HIV-1 infection.

Recent studies showed that nonhuman primate TRIM5alpha can efficiently block HIV-1 infection in human cell lines. It can also restrict other retroviruses, therefore, suggested as a general defender against retrovirus infection. Here, we present an evolutionary analysis of TRIM5alpha in primates. Our results demonstrated that TRIM5alpha has been evolving rapidly in primates, which is likely caused by Darwinian positive selection. The SPRY domain of TRIM5alpha, which may be responsible for recognition of incoming viral capsids showed higher nonsynonymous/synonymous substitution ratios than the non-SPRY domain, indicating that the adaptive evolution of TRIM5alpha in primates might be an innate strategy developed in defending retrovirus infection during primate evolution. In addition, the comparative protein sequence analysis suggested that the amino acid substitution pattern at a single site (344R/Q/P) located in the SPRY domain may explain the differences in susceptibilities of HIV-1 infection in diverse primate species.

Adaptation, Biological↗
PubMed2006

Sexually transmitted acute infection with a clustered genotype 4 hepatitis C virus in HIV-1-infected men and inefficacy of early antiviral therapy.

BACKGROUND: Recent studies have suggested an increased risk of acute hepatitis C (HCV) infection in homosexual HIV-infected men and that early treatment with standard or pegylated interferon-alfa, alone or associated with ribavirin, significantly reduces the risk of chronic evolution in HIV-infected patients. METHODS: A retrospective analysis of 12 HIV-infected patients who were consecutively diagnosed as developing acute HCV infection, defined by both seroconversion of anti-HCV antibodies and detection of serum HCV RNA in those with previous negative results. Ten of these patients received early antiviral treatment with standard or pegylated interferon-alfa, alone or associated with ribavirin. RESULTS: The only risk factor in these patients was unprotected sexual intercourse with men. Acute HCV infection was asymptomatic in 10 patients, and the HCV genotype was 4d in 10 patients. The 10 genotype 4d viruses formed a monophylogenetic group and clustered separately from other local sequences of HCV genotype 4d, suggesting a common source of infection. None of the 10 patients who were treated early with antiviral therapy had a sustained virological response, as defined by undetectable HCV RNA 6 months after therapy. CONCLUSIONS: There is a risk of sexual transmission of HCV in HIV-infected men who have sex with men; the cluster of HCV genotype 4d suggested a common source of infection and a failure in prevention counselling. Early treatment with standard interferon-alfa failed to prevent chronic evolution of HCV infection in this particular group of HIV-infected patients who had acquired this peculiar cluster of genotype 4 strains.

Acute Disease↗
PubMed1994

[Treatment of chronic hepatitis C virus infection with interferon in patients infected with the human immunodeficiency virus].

FOUNDATION: We assessed the effectivity of the treatment with interferon (IFN) in patients infected by the human immunodeficiency virus (HIV) with chronic hepatitis (CH) by the hepatitis C virus (HCV). METHODS: We studied 14 heterosexual males ex-parenterally drug consumers (PDC) and infected by the HIV (mean age 26 +/- 4.2 years), belonging to group A of CDC (1993); 10 had values of CD4 > 500 mmc and 4, between 200 and 500, the latter receiving treatment with zidovudine. In all these patients, the diagnosis of active chronic hepatitis was confirmed through histology. Three MUI of IFN-alpha 2b, 3 days/week during 24 weeks were administered. Sustained response to treatment was considered as the normalization of the aminotransferase levels until the end of the study; partial response, as the 50% decrease in the initial levels until the end of the treatment; relapse, as the response and latter increase in 1.5 of the ALT values at the end of the 24 weeks; and absence of response, as the lack of significant changes in the aminotransferase concentrations. RESULTS: Tolerance of the treatment was good, without severe side effects and just in one case, the medication had to be interrupted. In 5 patients, there was a response (all of them with more than 500 CD4). In 2 of these patients, the response was partial. In 3, there was a relapse and 3 other patients did not show any response (CD4 > 500). Three patients gave up the treatment. CONCLUSIONS: IFN-alpha 2b is well tolerated in a 24-week treatment in patients with HIV, CH and HCV. However, it was only effective for the control of this disease in patients with HIV infection with more than 500 lymphocytes CD4, without any significant effect in the evolution of the HIV infection.

HIV Infections↗