Biomedical subjects

Jan Albert

Publications and source records attributed to Jan Albert.

At least 19 recordsLinked to original sources

PubMed2025

HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data.

BACKGROUND: Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as recent or non-recent within a window of several months, and cannot assess the cumulative impact of an intervention. RESULTS: We developed a Random Forest Regression model, HIV-phyloTSI, which combines measures of within-host diversity and divergence to generate continuous TSI estimates directly from viral deep-sequencing data, with no need for additional variables. HIV-phyloTSI provides a continuous measure of TSI up to 9 years, with a mean absolute error of less than 12 months overall and less than 5 months for infections with a TSI of up to a year. It performs equally well for all major HIV subtypes based on data from African and European cohorts. CONCLUSIONS: We demonstrate how HIV-phyloTSI can be used for incidence estimates on a population level.

HIV Infections↗

PubMed2006

Antiretroviral treatment of HIV infection: Swedish recommendations 2005.

On 2 earlier occasions, in 2002 and 2003, the Swedish Medical Products Agency (MPA) and the Swedish Reference Group for Antiviral Therapy (RAV) have jointly publicized recommendations for the treatment of HIV infection. A working group from the same expert team that produced the 2002 report has now revised the text again. Since the publication of the last treatment recommendations, 4 new medicines have become available: emtricitabine, atazanavir, fosamprenavir, and enfuvirtid. The last-mentioned belongs to a new class of HIV medications called fusion inhibitors (Box 1). It is likely that tipranavir will also be on the market soon. Simultaneously, the drug zalcitabin has been deregistered. The following updated recommendations parallel the earlier ones, but increased knowledge allows us to be more specific in our recommendations. Thus, it is now suggested that the initial treatment for HIV infection consist of 2 nucleoside reverse transcriptase inhibitors (NRTIs) and 1 non-nucleoside reverse transcriptase inhibitor (NNRTI); or 2 NRTIs and 1 protease inhibitor (PI). In the group of the NRTIs, stavudine is no longer recommended for this purpose. In the NNRTI group, efavirenz should be preferred to nevirapine, except under special circumstances. Finally, PIs ought to be boosted with ritonavir (PI/r). Also new are recommendations regarding treatment choices for patients co-infected with hepatitis B virus (HBV) or tuberculosis (TB). As in the case of the previous publication, recommendations are evidence-graded in accordance with the Oxford Centre for Evidence Based Medicine, 2001 (see http://www.cebm.net/levels_of_evidence.asp#levels), and have been supplemented with references to newly-added sections and data not referred to in earlier background documentation.

Anti-Retroviral Agents↗

PubMed2006

Antiretroviral therapy does not induce HIV type 1-specific neutralizing activity against autologous HIV type 1 isolates.

To determine the ability of antiretroviral treatment (ART) to deter viral replication in the long term, we tested autologous neutralization of HIV-1 primary isolates in sera from six chronically HIV-1-infected patients before and during such treatment. For comparison, heterologous neutralization was tested in the same samples by using a panel of eight primary HIV-1 isolates. Preceding ART, none of the patients' samples contained neutralizing antibodies against autologous HIV-1 isolates. Subsequently, despite successful ART treatment during a 12- to 19-month period and a rise in CD4 T cell counts, the patients' viral neutralizing capacity did not increase significantly. Furthermore, the partial heterologous neutralizing response was not improved in these patients. This outcome signifies the failure of an HIV-1-specific humoral immune response to improve, despite successful ART. Therefore, our results emphasize the need for immunologic intervention before cessation of ART in chronically HIV-1-infected patients to achieve sustainable control of viral replication.

Adult↗

PubMed2006

Rapid viral decay in simian immunodeficiency virus-infected macaques receiving quadruple antiretroviral therapy.

The viral dynamics in human immunodeficiency virus type 1 (HIV-1) infection have been studied extensively using mathematical modeling, but data from other primate lentivirus systems are scarce. This study was initiated to increase the understanding of the differences and similarities between the different primate lentiviruses. Four cynomolgus macaques were infected with SIVmac251. Six months after infection the monkeys received a 7-day course of subcutaneous, quadruple antiretroviral therapy with zidovudine, lamivudine, tenofovir, and ritonavir-boosted lopinavir. Plasma virus levels were determined before therapy, daily during the first 10 days of therapy, and after 14 days using a sensitive commercial reverse transcriptase assay. All four monkeys showed a rapid and uniform decline in plasma virus load between day 1 and day 4 of treatment (first-phase decay). Two mathematical models, a piecewise linear regression analysis and a nonlinear model, were used to estimate the rate of viral decay in plasma and gave similar results. The mean half-life for plasma virus was 0.47 days (range, 0.37 to 0.50) and reflects the underlying decline of virus-producing CD4+ lymphocytes. This is the fastest primate lentivirus decay described hitherto. The rapid decay may be due to the high antiviral potency of the therapy or to intrinsic differences between simian immunodeficiency virus (SIV) infection in macaques and HIV-1 infection in humans.

Animals↗

PubMed2005

Coreceptor usage of primary HIV type 1 isolates obtained from different lymph node subsets.

Biological characteristics of virus quantitatively rescued from different cell types present in lymph nodes of HIV-1-infected individuals in various stages of their disease were determined, not including patients with AIDS defining illness. Viruses were obtained by cocultivation with donor monocyte-derived macrophages and T-lymphocytes and their biological phenotype compared to viruses obtained from the peripheral blood mononuclear cells of the same patient. The biological phenotype was determined on established cell lines (U937-2, CEM, and MT-2) and on the U87.CD4 coreceptor indicator cell lines and variable region 3 (V3) of the envelope was subjected to direct sequencing. All isolates obtained from lymph node subsets used CCR5 as coreceptor. Furthermore, these viruses were also sensitive to inhibition by beta-chemokines as analyzed for viruses of one patient. All 12 V3 regions showed a unique sequence indicating compartmentalization within each patient. The biological phenotype of CCR5-dependent (R5) HIV-1 isolates obtained from PBMC resembles the phenotype of viruses isolated from different lymph node cell subsets.

Amino Acid Sequence↗

PubMed2005

Short communication: HIV type 2 dynamics.

To gain a better understanding of why HIV-2 is less virulent than HIV-1 the viral dynamics of HIV-2 were studied in two Swedish HIV-2-infected patients after starting antiretroviral therapy. Linear regression analysis of log virus levels in plasma showed that virus decline during the first 2 weeks of therapy followed an exponential decay with half-lives of 2.2 and 2.0 days, respectively. These half-life measurements reflect the decline in the number of cells actively producing the virus, but may represent an underestimation of the true turnover of HIV-2. In one patient, preliminary estimates of the first and second phase of virus decline (halflife 1.3 and 15 days, respectively) were made. The viral dynamics of HIV-2 infection are strikingly similar to those for HIV-1. Thus, HIV-1 and HIV-2 appear to have similar rates of production and clearance in vivo. Consequently, the large differences in plasma virus levels, virulence, and natural course of the disease between the two infections are due to other factors that are yet to be identified.

Adult↗

PubMed2005

Selection of human immunodeficiency virus type 1 R5 variants with augmented replicative capacity and reduced sensitivity to entry inhibitors during severe immunodeficiency.

Early in human immunodeficiency virus 1 (HIV-1) infection CCR5-using (R5) viruses predominate. With disease progression, approximately 50% of infected individuals develop viruses able to use CXCR4. In the present work, the evolution of the biological properties of HIV-1 was studied in patients who retain viruses with an R5 phenotype despite AIDS onset. A panel of primary R5 HIV-1 isolates sequentially obtained at an asymptomatic stage and after AIDS diagnosis was examined. The viruses were selected based on our previous observation that R5 variants with reduced sensitivity to RANTES inhibition may appear during disease progression. Biological properties of the early and late R5 viruses, including infectivity, replicative capacity, impact of cationic polymer and sensitivity to inhibition by the entry inhibitors T-20 and TAK-779, were evaluated. R5 viruses isolated after AIDS onset displayed elevated replicative capacity and infectivity, and did not benefit from cationic polymer assistance during infection. Late R5 isolates also exhibited reduced sensitivity to inhibition by T-20 and TAK-779, even though the included patients were naïve to treatment with entry inhibitors and the isolates had not acquired mutations within the gp41 HR1 region. In addition, CD4+ T-cell counts at the time of R5 virus isolation correlated with infectivity, replicative capacity and sensitivity to inhibition by entry inhibitors. The results indicate that R5 HIV-1 variants with augmented replicative capacity and reduced sensitivity to entry inhibitors may be selected for during severe immunodeficiency. At a time when the clinical use of entry inhibitors is increasing, this observation could be of importance in the optimal design of such treatments.

Acquired Immunodeficiency Syndrome↗

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↗

PubMed2005

Differential pathogenesis of primary CCR5-using human immunodeficiency virus type 1 isolates in ex vivo human lymphoid tissue.

In the course of human immunodeficiency virus (HIV) disease, CCR5-utilizing HIV type 1 (HIV-1) variants (R5), which typically transmit infection and dominate its early stages, persist in approximately half of the infected individuals (nonswitch virus patients), while in the other half (switch virus patients), viruses using CXCR4 (X4 or R5X4) emerge, leading to rapid disease progression. Here, we used a system of ex vivo tonsillar tissue to compare the pathogeneses of sequential primary R5 HIV-1 isolates from patients in these two categories. The absolute replicative capacities of HIV-1 isolates seemed to be controlled by tissue factors. In contrast, the replication level hierarchy among sequential isolates and the levels of CCR5(+) CD4(+) T-cell depletion caused by the R5 isolates seemed to be controlled by viral factors. R5 viruses isolated from nonswitch virus patients depleted more target cells than R5 viruses isolated from switch virus patients. The high depletion of CCR5(+) cells by HIV-1 isolates from nonswitch virus patients may explain the steady decline of CD4(+) T cells in patients with continuous dominance of R5 HIV-1. The level of R5 pathogenicity, as measured in ex vivo lymphoid tissue, may have a predictive value reflecting whether, in an infected individual, X4 HIV-1 will eventually dominate.

Adult↗

PubMed2004

Modulation frequency response of a bistable system with noise.

We present a method to construct a modulation frequency response curve for bistable systems in the presence of noise. To this end, a small sinusoidal modulation is applied to the system such that it switches between its two stable states. The response curve we construct yields information on the nature of the physical mechanism underlying the switching process and is furthermore comparable to the standard response curves of linear systems. Our semianalytical approach, which only needs approximate Kramer rates, is in good agreement with numerical simulations. The concept is applicable to a wide range of systems.

Journal Article↗

PubMed2004

Cerebrospinal fluid viral load, virus isolation, and intrathecal immunoactivation in HIV type 2 infection.

Four patients with HIV-2 infection were followed longitudinally with cerebrospinal fluid (CSF) analyses. Two patients had positive CSF HIV-2 isolations. These two patients had CD4 cell count below 200 x 10(6)/liter and maximum CSF HIV-2 RNA viral loads above 4000 copies/ml. Intrathecal immune activation was demonstrated by elevated CSF neopterin concentrations (14-18 nmol/liter). No opportunistic infections were diagnosed. After antiretroviral treatment CSF viral counts decreased to below 125 copies/ml and CSF neopterin concentrations decreased. In two other patients who had CD4 counts within the normal range CSF virus isolations were repeatedly negative and viral CSF loads were below 125 copies/ml. However, a slightly elevated CSF neopterin concentration in one sample and pleocytosis in another might also be caused by HIV-2 in these patients. Before antiretroviral treatment HIV-2 isolations from blood were positive in all four patients. Maximum HIV-2 RNA viral loads were higher in blood than in CSF. Treatment failure in one patient with increasing viral loads in blood did not result in viral rebound in CSF.

Adult↗

PubMed2004

Pyrosequencing for detection of lamivudine-resistant hepatitis B virus.

Chronic hepatitis B virus (HBV) infection can cause severe liver disease, including cirrhosis and hepatocellular carcinoma. Lamivudine is a relatively recent alternative to alpha interferon for the treatment of HBV infection, but unfortunately, resistance to lamivudine commonly develops during monotherapy. Lamivudine-resistant HBV mutants display specific mutations in the YMDD (tyrosine, methionine, aspartate, aspartate) motif of the viral polymerase (reverse transcriptase [rt]), which is the catalytic site of the enzyme, i.e., methionine 204 to isoleucine (rtM204I) or valine (rtM204V). The latter mutation is often accompanied by a compensatory leucine-to-methionine change at codon 180 (rtL180M). In the present study, a novel sequencing method, pyrosequencing, was applied to the detection of lamivudine resistance mutations and was compared with direct Sanger sequencing. The new pyrosequencing method had advantages in terms of throughput. Experiments with mixtures of wild-type and resistant viruses indicated that pyrosequencing can detect minor sequence variants in heterogeneous virus populations. The new pyrosequencing method was evaluated with a small number of patient samples, and the results showed that the method could be a useful tool for the detection of lamivudine resistance in the clinical setting.

Base Sequence↗

PubMed2004

Coevolution of RANTES sensitivity and mode of CCR5 receptor use by human immunodeficiency virus type 1 of the R5 phenotype.

The evolution of human immunodeficiency virus type 1 (HIV-1) coreceptor use has been described as the acquisition of CXCR4 use linked to accelerated disease progression. However, CXCR4-using virus can be isolated only from approximately one-half of individuals with progressive HIV-1 disease. The other half continue to yield only CCR5-using viruses (R5 phenotype) throughout the course of disease. In the present work, the use of receptor chimeras between CCR5 and CXCR4 allowed us to study the evolution of HIV-1 with the R5 phenotype, which was not revealed by studies of wild-type coreceptor use. All together, 246 isolates (173 with the R5 phenotype) from 31 individuals were tested for their ability to infect cells through receptor chimeras. R5(narrow) virus was able to use only wild-type CCR5, whereas R5(broad(1)) to R5(broad(3)) viruses were able to use one to three chimeric receptors, respectively. Broad use of chimeric receptors was interpreted as an increased flexibility in the mode of receptor use. R5(broad) isolates showed higher infectivity in cells expressing wild-type CCR5 than R5(narrow) isolates. Also, the increased flexibility of R5(broad) isolates was concomitant with a lower sensitivity to inhibition by the CC chemokine RANTES. Our results indicate a close relationship between HIV-1 phenotypic changes and the pathogenic process, since the mode and efficiency of CCR5 use as well as the decrease in the RANTES sensitivities of isolated viruses are significantly correlated with CD4(+)-T-cell decline in a patient. One possible explanation is that ligand competition at the CCR5 receptor or changed CCR5 availability may shape the outcome of HIV-1 infection.

Cell Line, Tumor↗

PubMed2003

HIV biological variability unveiled: frequent isolations and chimeric receptors reveal unprecedented variation of coreceptor use.

OBJECTIVE: To follow the evolution of coreceptor use in HIV-1-infected individuals with varying rates of disease progression. METHODS: The coreceptor use of 278 sequential HIV-1 isolates from 23 individuals was tested by infection of two human cell lines, U87.CD4 and GHOST(3), expressing CD4 and CCR1, CCR2b, CCR3, CCR5, CXCR4, CXCR6 or BOB. Differences in coreceptor use were further dissected by testing chimeric coreceptors constructed by exchanging successively larger parts of CCR5 for corresponding regions of CXCR4. RESULTS: Three patterns of coreceptor use were distinguished: no evolution, evolution to CXCR4 use, and fluctuation. No evolution with stable CCR5 use (R5 phenotype) was linked to slow progression over 8-10 years in four patients. CXCR4-using virus was present from the onset (five patients) or appeared during clinical progression in all other patients, while taking zidovudine or didanosine monotherapy. The fluctuating pattern of coreceptor use, defined as reappearance of virus with R5 phenotype, was observed in five patients and, interestingly, followed initiation of highly active antiretroviral therapy in three of these. Monotropic R5 or X4 viruses were more selective in chimeric receptor use than R5X4 or multitropic viruses. Most importantly, the efficiency of chimeric receptor use increased over time. CONCLUSION: The increase in efficiency of chimeric receptor use allows a new interpretation of evolution of HIV-1 coreceptor use. Evolution could be a continuous process that may lead to changes in the way a coreceptor is used, with the potential of profound alteration in signalling at that receptor.

Adult↗

PubMed2003

Characterization of novel recombinant HIV-1 genomes using the branching index.

We have characterized six novel genomes of human immunodeficiency virus type 1 (HIV-1) sampled from individuals infected in Uganda and former Zaire. Four isolates (SE6954, SE8603, UG035, and UG266) had clear recombination patterns that included subtypes A1, D and C. The two remaining strains (SE8646 and SE9010) also appeared to be recombinant but had a more complex pattern. To facilitate the classification of these two genomes we developed a metric, the branching index, for characterization of "problematic" sequence fragments that associate to a subtype cluster with a high bootstrap value but are only distantly related to the reference sequences. The branching index is able to signal when parental representatives may be missing and a subtype classification thus is not meaningful. Several fragments of SE8646 and SE9010 had a branching index below the subtype defining cutoff value (0.55) and, therefore, these genomes could not be unequivocally classified. The branching index, with a cutoff value defined from analyses of HIV-1 reference sequences, may be a useful approach not only for more conservative classifications of HIV-1 subtypes but also for analyzing relationships among other types of sequences.

Evolution, Molecular↗

PubMed2003

A real-time TaqMan PCR for routine quantitation of cytomegalovirus DNA in crude leukocyte lysates from stem cell transplant patients.

A real-time TaqMan PCR based on the cytomegalovirus (CMV) polymerase (pol) gene was developed for quantitation of CMV DNA in crude peripheral blood leukocyte (PBL) lysate from stem cell transplantation (SCT) patients. The dynamic range of the assay was between 10 and 4x10(6) copies. Both intra- and inter-assay variability were well within +/-0.25 log10 S.D. Thus, a pooled PBL sample that was used as positive control in 57 consecutive TaqMan PCR runs over 7 months showed a stable CMV quantity (4.12+/-0.13, log10 mean+/-S.D.). The sensitivity of the pol TaqMan PCR was validated by parallel analysis of 177 PBL samples with a nested PCR. The use of crude PBL lysate as PCR input did not cause PCR inhibition. We demonstrated further the clinical utility of the newly developed TaqMan PCR by monitoring changes in CMV levels in eight patients receiving antiviral therapy. This TaqMan PCR was highly sensitive, reproducible, and stable and has served a useful tool for monitoring CMV DNA levels in large number of clinical samples in a routine diagnostic setting for over 1 year.

Cytomegalovirus↗

PubMed2003

A simple and sensitive 'in-house' method for determining genotypic drug resistance in HIV-1.

Antiretroviral combination therapy is a major advance in the treatment of HIV infection, but development of antiretroviral resistance is still an important cause of treatment failure. Therefore, resistance testing was recommended recently for follow-up of HIV-1 infected individuals. The aim of this study was to develop a new genotypic resistance assay because simple and affordable assays with sufficient sensitivity for different genetic subtypes and low copy number samples are still lacking. Different methods and primers for RNA extraction from plasma, cDNA synthesis, nested PCR and sequencing on an ABI310 automated sequencer were evaluated and optimised. The PCR was designed to amplify a fragment covering the protease and the first half of the reverse transcriptase (RT), which harbour most known resistance mutations to licensed antiretroviral drugs. Resistance mutations were identified using resistance analysis tools available over the Internet. The optimised assay had a sensitivity of approximately 200 RNA copies per ml. The method was evaluated on plasma samples from treated patients infected with different subtypes of HIV-1 and appeared to have similar sensitivity for all subtypes. Samples that had failed previously in routine testing were analysed successfully with the new assay. The new assay is more sensitive and robust than the current routine method.

Amino Acid Sequence↗

PubMed2003

pol gene sequence variation in Swedish HIV-2 patients failing antiretroviral therapy.

There is limited knowledge about how to treat and interpret results from genotypic resistance assays in HIV-2 infection. Here, genetic variation in HIV-2 pol gene was studied in 20 of 23 known HIV-2 cases in Sweden. Five patients with signs of virological treatment failure were longitudinally studied. Clinical, virological and immunological data were collected and the protease (PR) and first half of the reverse transcriptase (RT) was amplified and directly sequenced from plasma samples. Moderate to extensive genetic evolution was observed in four of the five patients who failed treatment. Some mutations occurred at positions known to confer resistance in HIV-1, but many occurred at other positions in PR and RT. All patients had been treated with zidovudine alone or in combination with other antiretroviral drugs, but none displayed a mutation at position 215, which is the primary zidovudine resistance site in HIV-1. Instead, a E219D mutation evolved in virus from two patients and a Q151M mutation evolved in two other patients. A M184V mutation indicative of lamivudine resistance was detected in three patients. The virus of one patient who had been treated with ritonavir, nelfinavir, and lopinavir successively acquired nine unusual mutations in the protease gene, most of which are not considered primary or secondary resistance mutations in HIV-1. Our data indicate that the evolutionary pathways that lead to antiretroviral resistance in HIV-2 and HIV-1 exhibit both similarities and differences. Genotypic HIV-2 resistance assays cannot be interpreted using algorithms developed for HIV-1, instead new algorithms specific for HIV-2 have to be developed.

Adolescent↗