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PubMed2002

Inferring confidence sets of possibly misspecified gene trees.

The problem of inferring confidence sets of gene trees is discussed without assuming that the substitution model or the branching pattern of any of the investigated trees is correct. In this case, widely used methods to compare genealogies can give highly contradicting results. Here, three methods to infer confidence sets that are robust against model misspecification are compared, including a new approach based on estimating the confidence in a specific tree using expected-likelihood weights. The power of the investigated methods is studied by analysing HIV-1 and mtDNA sequence data as well as simulated sequences. Finally, guidelines for choosing an appropriate method to compare multiple gene trees are provided.

Animals↗

PubMedDate not supplied

[HTLV1 and coinfections].

After reminding the epidemiology of the HTLV1 infection the authors sum up the actually recommended diagnosis procedure. --Case finding by ELISA, confirmation by WESTERN-BLOT and/or RIPA (anti-gag and anti-env specificities), or even PCR which makes specific diagnosis of HTLV1/2. --Or if possible directly by PCR which has helped some authors to find provirus in seronegative people. Coinfections caused by HIV and by Strongyloides are the best documented. As a rule, HTLV1 seems to have rather a worsening effect on evolutiveness and on seriousness of the clinical picture caused by mixed infections, than the contrary (possibly for lack of experience and owing to slow evolution of HTLV1 pathology). Several mechanisms have been proposed concerning coinfections with HTLV1 and HIV (in vitro studies). --Immortalization of CD4 lymphocytes infected with HTLV1 by stimulating both IL2 and its receptor, and by activating lymphocytes with translocation of the replicating factor NF k B in the nucleus, on a promoting sequence of HIV-LTR by stimulating its replication. --The product of HTLV1 tax gene would also have a transactivating effect on the provirus HIV-LTR replication. And finally infection with HTLV1 may facilitate HIV by inducing CD4, molecule expression in non-expressing cells. In Strongyloides modulating effects of HTLV1 on the immune response would facilitate and predispose Strongyloides stercoralis multiplication. As far as other coinfections are concerned (caused by viruses, by parasites: such as malaria, filariasis, trypanosomiasis or by bacteria), epidemiological convergence (risk factors, and geographic distribution) on the one hand, and immunological dysregulation induced by the other, on the other hand, would be of varying importance. In conclusion, these data ask more questions than they answer. But it seems to be established that detection of HIV and Strongyloides should performed in every case HTLV1 carries and vice versa.

Blotting, Western↗

PubMedDate not supplied

[The molecular epidemiology of HIV-1 in Belarus in (1996-2004): a predominance of subtype A variants and circulation of subtype B variants].

To study the molecular epidemiology of HIV-1 in Belarus, the genetic sequences of HIV-1 variants were obtained from 50 infected persons, which represented the main stages, risk groups, and geographic areas of the epidemic. The env and gag sequences were studied for HIV-1 variants from 31 persons, the env sequences were for HIV-1 variants from 18 persons, and the gag sequence was for HIV-1 variant from 1 person. Phylogenetic analysis indicated that the sequences of HIV-1 variants from 46 persons were homogenic and evolutionally closely related to IDU-A strains specific for other epidemics in the former Soviet Union are dominating in the epidemic in Belarus. Circulation of epidemiologically unrelated subtype B viruses was also established.

Female↗

PubMed1991

Evolution of human immunodeficiency virus type 1 nef and long terminal repeat sequences over 4 years in vivo and in vitro.

The evolution of an 851-bp segment of the human immunodeficiency virus type 1 (HIV-1) genome encoding the nef open reading frame and U3/R elements of the long terminal repeat has been followed over a 4-year period in vivo and in vitro. The population of viral sequences at any given time was established by sequencing cloned polymerase chain reaction products. The samples studied were derived from the same man for whom a detailed analysis of the tat gene was previously described (A. Meyerhans, R. Cheynier, J. Albert, M. Seth, S. Kwok, J. Sninsky, L. Morfeldt-Manson, B. Asjö, and S. Wain-Hobson, Cell 58:901-910, 1989). Once again in vitro culture resulted in the selection of minor forms. Over a 4-year period in vivo, there was no obvious selection for, or outgrowth of, any particular nef or U3/R sequence. Few defective nef protein sequences were observed, which argues against nef acting as a negative regulatory factor. Although no functionally defective promoter/trans-activation-responsive elements were identified, the transactivation efficiencies varied between 0.2 and 2 times that of the control. The sequence encoding the most efficient trans-activation-responsive region did not outgrow others. The extreme genetic heterogeneity of the different samples of the locus, either in vivo or in vitro, indicates that there is no such thing as a single, distinct HIV sequence. It is suggested that different HIV-1 loci evolve independently, recombination being responsible for their uncoupling.

Base Sequence↗

PubMed1997

Recovery of replication-competent HIV despite prolonged suppression of plasma viremia.

In evaluating current combination drug regimens for treatment of human immunodeficiency virus (HIV) disease, it is important to determine the existence of viral reservoirs. After depletion of CD8 cells from the peripheral blood mononuclear cells (PBMCs) of both patients and normal donors, activation of patient CD4 lymphocytes with immobilized antibodies to CD3 and CD28 enabled the isolation of virus from PBMCs of six patients despite the suppression of their plasma HIV RNA to fewer than 50 copies per milliliter for up to 2 years. Partial sequencing of HIV pol revealed no new drug resistance mutations or discernible evolution, providing evidence for viral latency rather than drug failure.

Anti-HIV Agents↗

PubMed2005

Human immunodeficiency virus mutagenesis during antiviral therapy: impact of drug-resistant reverse transcriptase and nucleoside and nonnucleoside reverse transcriptase inhibitors on human immunodeficiency virus type 1 mutation frequencies.

The development of antiviral drug resistance is an important problem in the treatment of human immunodeficiency virus type 1 (HIV-1) infection. Potent antiretroviral therapy is currently used for treatment, and typically consists of at least two reverse transcriptase (RT) inhibitors. We have previously reported that both drugs and drug-resistant RT mutants can increase virus mutation frequencies. To further assess the contributions of nucleoside RT inhibitors (NRTIs), nonnucleoside RT inhibitors (NNRTIs), and drug-resistant RTs to HIV mutagenesis, a new high-throughput assay system was developed. This assay system was designed to specifically detect frameshift mutations in the luciferase gene in a single virus replication cycle. New drug-resistant RTs were identified that significantly altered virus mutation frequencies. Consistent with our previous observations of NRTIs, abacavir, stavudine, and zalcitabine increased HIV-1 mutation frequencies, supporting the general hypothesis that the NRTIs currently used in antiviral drug therapy increase virus mutation frequencies. Interestingly, similar observations were made with NNRTIs. This is the first report to show that NNRTIs can influence virus mutation frequencies. NNRTI combinations, NRTI-NNRTI combinations, and combinations of drug and drug-resistant RTs led to significant changes in the virus mutation frequencies compared to virus replication of drug-resistant virus in the absence of drug or wild-type virus in the presence of drug. This indicates that combinations of RT drugs or drugs and drug-resistant virus created during the evolution of drug resistance can act together to increase HIV-1 mutation frequencies, which would have important implications for drug therapy regimens. Finally, the influence of drug-resistant RT mutants from CRF01_AE viruses on HIV-1 mutation frequencies was analyzed and it was found that only a highly drug resistant RT led to altered virus mutation frequencies. The results further suggest that high-level drug-resistant RT can significantly influence virus mutation frequencies. A structural model that explains the mutation frequency data is discussed.

Anti-HIV Agents↗

PubMed1998

Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles.

Sequence variation displayed by the human immunodeficiency virus type 1 (HIV-1) has been proposed to be linked to the pathogenesis of acquired immunodeficiency syndrome (AIDS). To assess viral evolution during the course of infection, we evaluated sequence variability in the env variable domains in four HIV-1-infected individuals exhibiting differing profiles of CD4+ T cell decline when followed from seroconversion until the development of AIDS or loss of followup. Proviral sequences encoding the V3-V5 region of gp 120 were obtained following PCR amplification of peripheral blood mononuclear cell DNA and cloning. Virus in each patient was relatively homogeneous early in infection and then diverged with time, more consistently at its nonsynonymous sites. Just prior to or coincident with a rapid decline in CD4+ T cell numbers, sequences were found with basic amino acid substitutions clustered within and downstream of the gp 120 V3 domain. Within the constraints of the current data set, we conclude that the virus appears to continually accumulate changes in its amino acid sequences well into the time of marked CD4+ T cell decline.

Amino Acid Sequence↗

PubMed2002

HIV in Africa (Communication arising): chemokine-receptor genes and AIDS risk.

Schliekelman et al. have provided a model to quantify the speed at which HIV-resistance haplotypes can become enriched in a susceptible population through a delay in the onset of AIDS, permitting greater lifetime reproduction and the selection of AIDS-delaying haplotypes. But we question their conclusion that there could be a rapid evolution of resistance to AIDS onset in some African populations if the current HIV epidemic persists, as this depends on an untested assumption: that variant forms of the chemokine-receptor-5 (CCR5) gene impart selective advantages or disadvantages in Africa that are comparable to those reported for African Americans. Here we test this premise in a large Ugandan population, and find that CCR5 variants are not associated with HIV/AIDS disease risk in Africa--the origin and centre of the current AIDS pandemic. This gene may therefore not be subject to rapid evolutionary change as a result of the HIV epidemic in Africa.

Acquired Immunodeficiency Syndrome↗

PubMedDate not supplied

HIV-antibody detection in children by competitive and direct micro-ELISA techniques.

A comparative study was carried out on 110 sera from children or infants, suspected of HIV-antibody presence following several micro-ELISA assays, using four direct micro-ELISA (Wellcozyme HIV 1 + 2, Rapid Elavia Mixt, Ortho Diagnostics, RECVIH) and a competitive system--Wellcozyme-Recombinant. In three of the four direct systems, as well as in the competitive system, significantly higher mean values of sample/cut off, and cut off/sample ratios, respectively, as compared to the direct systems RECVIH, were present. High optimal levels of sensitivity and specificity (%), as related to Western Blot results, were found with Wellcozyme direct and competitive kits, as well as with Rapid Elavia Mixt kit, as compared to lower levels exhibited by the other two direct system kits (Ortho Diagnostics an especially RECVIH). As regards three Western Blot undetermined results, obtained in patients with a severe clinical state and evolution to exitus, by comparing some serological markers of HIV infection in two serum samples belonging to the same case (second sample collected 4 weeks after collection of the first homologous sample), the disappearance of gag-encoded-p24 band in Western Blot, associated with negativation of HIV-p24-antibody and with the presence of free virus antigen in all three second serum samples occurred, that would reflect a probable fall of immune anti-HIV "barriers" during final stages of illness. Although Western Blot confirmation cannot be excluded, it seems to be useful to assay comparatively HIV-antibody presence by means of direct and competitive micro-ELISA systems, in the same serum sample.

Blotting, Western↗

PubMed2003

Structural and functional evolution of human immunodeficiency virus type 1 long terminal repeat CCAAT/enhancer binding protein sites and their use as molecular markers for central nervous system disease progression.

The appearance and progression of human immunodeficiency virus type 1 (HIV-1)-associated pathogenesis in the immune and central nervous systems is dependent on the ability of the virus to replicate in these compartments, which is, in turn, controlled by numerous factors, including viral binding and entry, receptor and coreceptor usage, and regulation of viral expression by the long terminal repeat (LTR). The LTR promotes viral expression in conjunction with viral and cellular regulatory proteins, including members of the CCAAT/enhancer binding protein (C/EBP) family, which modulate LTR activity through at least two cis-acting binding sites. Previous studies have shown that these sites are necessary for HIV-1 replication in cells of the monocyte/macrophage lineage, but dispensable in T lymphocytes. To establish potential links between this important family of transcription factors and HIV-1-associated pathogenesis, C/EBP site I and II sequence variation in peripheral blood mononuclear cell (PBMC)-derived LTRs from HIV-1-infected patients with varying degrees of disease severity was examined. A high prevalence of C/EBP site variants 3T (site I) and consensus B (site II) within PBMC-derived HIV-1 LTRs was shown to correlate with late stage disease in HIV-1-infected patients. These results suggest that the increased prevalence in the PBMCs of HIV-1 LTRs containing the 3T C/EBP site I variant and the consensus B site II variant may serve as a molecular marker for disease progression within the immune system. The relative low or high binding affinity of C/EBP beta to sites I and II in electrophoretic mobility shift (EMS) analyses correlated with low or high LTR activity, respectively, in transient expression analyses during both early and late disease stages. The 3T C/EBP site I was the only variant examined that was not found in LTRs derived from PBMCs of patients at early stages of HIV-1 disease, but was found at increasing frequencies in patients with late stage disease. Furthermore, the 3T C/EBP site I was not found in brain-derived LTRs of patients without HIV-1-associated dementia (HIVD), but was found in increasing numbers in brain-derived LTRs from patients diagnosed with HIVD. The C/EBP site I 3T variant appears to be exclusive to patients progressing to increasingly severe HIV-1-associated immunologic and neurologic disease.

AIDS Dementia Complex↗

PubMed2005

Evolution of human immunodeficiency virus under selection and weak recombination.

To predict emergence of drug resistance in patients undergoing antiretroviral therapy, we study accumulation of preexisting beneficial alleles in a haploid population of N genomes. The factors included in the model are selection with the coefficient s and recombination with the small rate per genome r (r << s sqrt of k, where k is the average number of less-fit loci per genome). Mutation events are neglected. To describe evolution at a large number of linked loci, we generalize the analytic method we developed recently for an asexual population. We show that the distribution of genomes over the deleterious allele number moves in time as a "solitary wave" that is quasi-deterministic in the middle (on the average) but has stochastic edges. We arrive at a single-locus expression for the average accumulation rate, in which the effects of linkage, recombination, and random drift are all accounted for by the effective selection coefficient s lnNr/lnNs(2)k/r. At large N, the effective selection coefficient approaches the single-locus value s. Below the critical size N(c) approximately 1/r, a population eventually becomes a clone, recombination cannot produce new sequences, and virus evolution stops. Taking into account finite mutation rate predicts a small, finite rate of evolution at N < N(c). We verify the accuracy of the results analytically and by Monte Carlo simulation. On the basis of our findings, we predict that partial depletion of the HIV population by combined anti-retroviral therapy can suppress emergence of drug-resistant strains.

Computer Simulation↗

PubMed2006

Interactions between HIV infection and leprosy: a paradox.

Early in the HIV epidemic it was feared that the disease would undermine leprosy control, as has occurred with tuberculosis. It was predicted that patients with leprosy and HIV coinfection would have an increased risk of lepromatous disease and a faster clinical evolution, and that the leprosy would be more difficult to treat. None of these concerns have materialised and the interaction between HIV and Mycobacterium leprae seems to be far more subtle than that between HIV and tuberculosis. We review the epidemiological, clinical, and pathological data relating to leprosy/HIV coinfection. The published epidemiological data are limited in quality but show neither an increased HIV prevalence among leprosy cases nor an alteration in clinical spectrum of leprosy among coinfected patients. Some data suggest that immune-mediated reactions that complicate leprosy occur at a higher frequency in coinfected patients. Leprosy has now been reported presenting as immune reconstitution disease among patients commencing highly active antiretroviral treatment. Histopathological observations reveal a normal spectrum of appearances in biopsies of leprosy lesions from coinfected patients, even among those with advanced immunodeficiency. These observations suggest that cell-mediated immune responses to M leprae are preserved at the site of disease despite evidence that these responses are abrogated systemically, by contrast with tuberculosis, in which the host granulomatous response is impaired by HIV coinfection. We speculate that this paradox may relate to differences between the activation state and rates of cell turnover within leprosy and tuberculosis granulomas that differentially affect the susceptibility of the granulomas to HIV. The interactions between leprosy and HIV have been little studied and further research on the clinical, pathological, and management aspects of this coinfection is warranted.

Female↗

PubMed1988

[Human acquired immunodeficiency virus infection of the nervous system].

Neurological manifestations of HIV infection are recognised at different phases of the evolution of the disease. During the late stages opportunistic neuro-meningeal infections and tumors develop as a result of the immuno-suppression. There exist, however, various manifestations which evolve independently of the immune state, and seem to be directly related to the virus itself. One can distinguish central neuro-meningeal syndromes and peripheral syndromes at the onset, or at later stages. Their prognostic implications are uncertain, but often severe, for example in the case of the subacute dementias which, in this setting, may lead to death in several months. There are also other manifestations which may be self limited or slowly evolving in the central and peripheral nervous systems. The neuropathological changes are known for the dementias as mentioned above, though the characteristics lesions due to HIV infection per se remain controversial. The presence of the virus in the nervous system has been established by in situ hybridization techniques, immunohistochemistry and culture. Studies on CSF have also allowed virological (cultures) and immunological studies to be carried out. The physiopathological mechanisms for the apparent neurological effects of this virus remain hypothetical. A better understanding of these mechanisms should lead to a rationalisation of therapeutic strategies, in a disorder which would seem to be an early and persisting viral infection of the nervous system.

Acquired Immunodeficiency Syndrome↗

PubMed1994

[AIDS in childhood].

HIV infection in infants is transmitted through the placenta. Antibodies reduce and annul in nearly 18 months: HIV + subjects older than 18 months are considered as infected and divided into two classes--i.e., P1: infected and P2: AIDS. The most interesting clinical and diagnostic imaging findings are reported relative to 209 babies who were born HIV + and followed-up with clinical and laboratory tests plus chest films, brain and abdomen US to assess the presence of changes and their evolution features. The following conclusions have been drawn: 1) in their early life, HIV + subjects are especially liable to the action of bacteria, viruses and protozoa: their respiratory system is easily affected with acute, recurring and/or chronic inflammations which are frequently associated with heart enlargement from dilatative cardiomyopathy. Bacterial inflammations are characterized by single or multiple opacities, with blurred and irregular patterns, which are frequently confluent in areas of inhomogeneous opacity. The diagnosis of virus and protozoa infections is more difficult because of their radiologic patterns--i.e., linear fan-like opacities, small shadow areas, enlarged hila. In some cases radiology demonstrates only or mostly lung hyperexpansion, with no opaque images, which however does not exclude the presence of severe and diffuse bronchioloalveolar and interstitial compromission with high-grade pulmonary insufficiency. The common association of cytomegalovirus and Pneumocystis carinii infections with slow-evolution changes and frequent recurrences appears on radiologic images as diffuse and blurred shadows and irregular cotton-like opacities. 2) Brain and abdomen US scans in the newborn show no particular changes, while in the following months both US and CT demonstrate hydrocephalic, atrophic and hemorrhagic changes. 3) In both early and late infancy, lung infections are mostly caused by pneumocystis and cytomegalovirus. Chronic interstitial lymphocyte pneumonia is a peculiar finding with punctiform images in the bases of lung and spreading craniocaudally with similar features to miliary tuberculosis. Different than in the adult, in our series of 209 infants no tubercular abnormalities were observed: in one patient only an active primary complex was demonstrated with broncholavage. Candida infections were observed in 3 patients in their late infancy. Hepatopancreatic and lymph node changes suggesting probably evolving inflammation were uncommon in our series; this condition must be followed-up and checked over time.

Acquired Immunodeficiency Syndrome↗

PubMed2002

Increased sensitivity of T lymphocytes to tumor necrosis factor receptor 1 (TNFR1)- and TNFR2-mediated apoptosis in HIV infection: relation to expression of Bcl-2 and active caspase-8 and caspase-3.

The destruction of CD4 T cells in human immunodeficiency virus (HIV) infection is associated with activation of apoptotic programs, partly mediated by death receptors. The role of CD95L/CD95 in depletion of patients' CD4 T cells is well documented, but the possible contribution of the tumor necrosis factor/tumor necrosis factor receptor (TNF/TNFR) pathway has not been examined. In this study, we found that both TNFR1 and TNFR2 induced marked apoptosis in peripheral T cells from HIV-infected persons, involving both CD4 and CD8 T cells. Longitudinal follow-up of HIV(+) patients suggests an association between the in vivo evolution of CD4 T-cell numbers and variations in susceptibility to TNFR-induced apoptosis. Analysis of molecular mechanisms involved showed that it was not related to altered ex vivo expression of TNFR1-associated death domain, receptor interacting protein, or TNFR-associated factor 2. Susceptibility to TNFR-mediated apoptosis was rather related to Bcl-2 expression, because patients' T cells expressing high levels of Bcl-2 were completely protected from TNFR1- and TNFR2-induced cell death, whereas T cells expressing normal levels of Bcl-2 were not protected in patients in contrast to controls. Early recruitment of caspase-8 and caspase-3 is needed to transduce the apoptotic signals, and expression of both caspases in their active form was detected in blood T cells from HIV(+) patients, whereas it was hardly detected in controls. Moreover, ligation of TNFRs induced increased activation of both caspases in patients' T cells. Together these data demonstrate that exacerbated TNFR-mediated cell death of T cells from HIV-infected individuals is associated with both alteration of Bcl-2 expression and activation of caspase-8 and caspase-3 and may contribute to the pathogenesis of acquired immunodeficiency syndrome.

Adult↗

PubMed1995

Different patterns of HIV-1-specific cytotoxic T-lymphocyte activity after primary infection.

OBJECTIVE: To analyse the HIV-1-specific cytotoxic T-lymphocyte (CTL) responses of nine HIV-seropositive subjects in relation with primary infection. METHODS: Anti-HIV CTL were generated by in vitro stimulation of peripheral mononuclear cells obtained from HIV-seropositive donors at various times after primary infection. They were tested against several structural or regulatory HIV-1 proteins, using autologous target cells infected with recombinant vaccinia viruses expressing one of the HIV-1LAI proteins. RESULTS: An important CTL activity was found during the first month following seroconversion only in those donors who showed clinical symptoms during primary infection. The temporal evolution of this response differed for each subject; one remained a non-responder even 30 months after seroconversion. The structural proteins were recognized particularly early, while the antigenicity of regulatory proteins appeared later. CONCLUSION: Different patterns of HIV-specific CTL response can be observed after primary infection. The evolution of infection in these different HIV-seropositive subjects will be particularly interesting to analyse.

Adult↗

PubMed1995

The evolution of virulence in sexually transmitted HIV/AIDS.

A mathematical model is used to examine the effects of host population demography and transmission behavior on the evolution of virulence of a sexually transmitted pathogen such as HIV. The effect of the rate at which hosts acquire new partners is shown to depend critically on the details of the host population's growth pattern, sexual contact rate, and level of infection. At density-limited equilibrium, new partner acquisition rates have no effect on virulence. In an exponentially growing host population, higher partner acquisition rates favor the less virulent strain, as do lower rates of host population growth. In contrast, in uninfected populations, faster new partner acquisition rates encourage epidemics of the more virulent strain. Two extensions of the model--one including vertical transmission and another including within-host evolution--confirm the robustness of the predictions.

Acquired Immunodeficiency Syndrome↗

PubMed2004

In vivo evolution of X4 human immunodeficiency virus type 1 variants in the natural course of infection coincides with decreasing sensitivity to CXCR4 antagonists.

CXCR4-using (X4) human immunodeficiency virus type 1 (HIV-1) variants evolve from CCR5-restricted (R5) HIV-1 variants. Early after their first appearance in vivo, X4 HIV-1 variants additionally use CCR5. The ability to use CCR5 in addition to CXCR4 is generally lost late in infection. Here we studied whether this evolution of the coreceptor repertoire is also reflected in a changing sensitivity of X4 variants to CXCR4 antagonists such as peptide T22 and the synthetic compound AMD3100. We observed differences in the concentrations of CXCR4 antagonists needed to suppress replication of X4 HIV variants from different patients. In general, late X4 HIV variants were less sensitive to AMD3100 than were early R5X4 HIV variants. The differences between early R5X4 HIV variants and late X4 variants were less pronounced for T22-mediated inhibition. These results suggest an ongoing evolution of X4 virus variants toward more efficient usage of the cellular entry complex.

Anti-HIV Agents↗