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PubMedDate not supplied

Human immunodeficiency virus type 1 variability and long-term non-progression.

A high heterogeneity is found in the HIV-1 genome in vivo, not only between individuals, but also within a single individual. Different types of genetic heterogeneity of HIV-1 can be analyzed: the extension and the evolution of the viral quasispecies in blood, the variation between the virus obtained from different body compartment, the differences between isolates from diverse individuals and between HIV-1 subtypes. The virus population during primary HIV-1 infection is generally homogeneous and the intrahost viral evolution is thought to be forced (in absence of antiviral therapy) by the immune system pressure and is generally related to the length of the immunocompetent period. A group of 12 Italian and Swedish well characterized HIV-1 infected long-term nonprogressors (LNTP) have been analyzed for the viral heterogeneity, calculated in the nef gene and in the long terminal repeat (LTR). The intra-sample variations in LTNP were found comparable with those from 8 progressor patients, while a lower inter-individual diversity was observed in the former. In one LTNP the viral evolution during a four-years period was extremely low suggesting that other factors than the host immune pressure may be involved in modulating the intra- and inter-sample HIV-1 diversity.

Acquired Immunodeficiency Syndrome↗
PubMed2004

Role of minority populations of human immunodeficiency virus type 1 in the evolution of viral resistance to protease inhibitors.

Human immunodeficiency virus type 1 (HIV-1) drug resistance results from the accumulation of mutations in the viral genes targeted by the drugs. These genetic changes, however, are commonly detected and monitored by techniques that only take into account the dominant population of plasma virus. Because HIV-1-infected patients harbor a complex and diverse mixture of virus populations, the mechanisms underlying the emergence and the evolution of resistance are not fully elucidated. Using techniques that allow the quantification of resistance mutations in minority virus species, we have monitored the evolution of resistance in plasma virus populations from patients failing protease inhibitor treatment. Minority populations with distinct resistance genotypes were detected in all patients throughout the evolution of resistance. The emergence of new dominant genotypes followed two possible mechanisms: (i) emergence of a new mutation in a currently dominant genotype and (ii) emergence of a new genotype derived from a minority virus species. In most cases, these population changes were associated with an increase in resistance at the expense of a reduction in replication capacity. Our findings provide a preliminary indication that minority viral species, which evolve independently of the majority virus population, can eventually become dominant populations, thereby serving as a reservoir of diversity and possibly accelerating the development of drug resistance.

Base Sequence↗
PubMed2004

The phylogeography of human viruses.

Viruses, especially those with RNA genomes, represent ideal organisms to study the dynamics of microevolutionary change. In particular, their rapid rate of nucleotide substitution means that the epidemiological processes that shape their diversity act on the same time-scale as mutations are fixed in viral populations. Consequently, the branching structure of virus phylogenies provides a unique insight into spatial and temporal dynamics. Herein, I describe the key processes in virus phylogeography. These are generally associated with the relative rates of dispersal among populations and virus-host codivergence (vicariance), and the division between acute (short-term) and persistent (long-term) infections. These processes will be illustrated by important human viruses - HIV, dengue, rabies, polyomavirus JC and human papillomavirus - which display varying spatial and temporal structures and virus-host relationships. Key research questions for the future will also be established.

Dengue Virus↗
PubMed2002

Evaluation of methods for detecting recombination from DNA sequences: empirical data.

The performance of 14 different recombination detection methods was evaluated by analyzing several empirical data sets where the presence of recombination has been suggested or where recombination is assumed to be absent. In general, recombination methods seem to be more powerful with increasing levels of divergence, but different methods showed distinct performance. Substitution methods using summary statistics gave more accurate inferences than most phylogenetic methods. However, definitive conclusions about the presence of recombination should not be derived on the basis of a single method. Performance patterns observed from the analysis of real data sets coincided very well with previous computer simulation results. Previous recombination inferences from some of the data sets analyzed here should be reconsidered. In particular, recombination in HIV-1 seems to be much more widespread than previously thought. This finding might have serious implications on vaccine development and on the reliability of previous inferences of HIV-1 evolutionary history and dynamics.

DNA↗
PubMed2000

Unusual distribution of mutations associated with serial bottleneck passages of human immunodeficiency virus type 1.

Repeated bottleneck passages result in fitness losses of RNA viruses. In the case of human immunodeficiency virus type 1 (HIV-1), decreases in fitness after a limited number of plaque-to-plaque transfers in MT-4 cells were very drastic. Here we report an analysis of entire genomic nucleotide sequences of four HIV-1 clones derived from the same HIV-1 isolate and their low-fitness progeny following 7 to 15 plaque-to-plaque passages. Clones accumulated 4 to 28 mutations per genome, with dominance of A --> G and G --> A transitions (57% of all mutations) and 49% nonsynonymous replacements. One clone-but not three sibling clones-showed an overabundance of G --> A transitions, evidencing the highly stochastic nature of some types of mutational bias. The distribution of mutations along the genome was very unusual in that mutation frequencies in gag were threefold higher than in env. Particularly striking was the complete absence of replacements in the V3 loop of gp120, confirmed with partial nucleotide sequences of additional HIV-1 clones subjected to repeated bottleneck passages. The analyses revealed several amino acid replacements that have not been previously recorded among natural HIV-1 isolates and illustrate how evolution of an RNA virus genome, with regard to constant and variable regions, can be profoundly modified by alterations in population dynamics.

Base Sequence↗
PubMed1994

Fidelity of HIV-1 reverse transcriptase copying a hypervariable region of the HIV-1 env gene.

The unusually high mutation frequency exhibited by the human immunodeficiency virus (HIV) is a major impediment to developing effective vaccines against the virus and to designing analogs that inhibit viral replication. To investigate the molecular basis of HIV hypermutability, we established cell-free assays to measure the fidelity of HIV-1 reverse transcriptase (RT) in copying either DNA or both RNA and DNA templates that contain the hypervariable region 1 of the HIV-1 env gene (V-1). The fidelity of DNA synthesis was measured by repetitively copying the envelope gene (V-1) DNA by HIV-1 RT, followed by cloning and sequencing these newly synthesized DNA products. We found that the error rate of HIV RT copying either RNA or DNA of the env V-1 region is about one misincorporation per 5 kb polymerized. This rate is similar to that found with the M13mp2 forward mutation assay using the lacZ alpha gene as a template. This similarity suggests that the HIV env hypervariable sequence is not inherently hypermutable. The high error rate of HIV RT suggests that misincorporation by this enzyme is a major source of mutations throughout the viral genome and a determinant for rapid viral evolution. The spectrum of mutations produced by HIV RT in vitro partially correlates with the spectrum of HIV mutations observed in AIDS patients. The differences between these spectra highlight the contribution of phenotypic selection during HIV-1 infection. The overall uniformity of misincorporation of HIV-1 RT further suggests an alternative anti-HIV strategy based on increasing viral mutagenesis by nucleotide analogs.

Base Sequence↗
PubMed2004

Primate models for human immunodeficiency virus infection. Evolution of receptor use during pathogenesis.

Animal models greatly facilitate understanding of transmission, pathogenesis and immune responses in HIV and SIV infection and provide models for studies on the effect of candidate drugs or vaccines. However, there are several aspects that one should consider when drawing conclusions from results obtained from animal models. First, the genetic relationship of primate lentiviruses cannot be disregarded because it is known that HIV-1 is more closely related to SIV of chimpanzee origin (SIVcpz) than to SIV from sooty mangabey (SIVsm) origin. Nevertheless, SIVsm and SIVmac are the ones most often used as model systems. Second, there are differences in the biological properties, like CXCR4 use and CD4-independent coreceptor use, of HIV and SIV. These differences might be relevant in virus transmission, pathogenesis and in evoking immune responses. Third, in vivo and in vitro selection may influence the results. Neutralizing antibodies may play a role in selection of variant viruses since neutralization sensitive, CD4-independent SIVsm variants seemed to be suppressed in animals that mounted a neutralizing antibody response. It is tempting to speculate that neutralizing antibodies shape the SIV/HIV infection by selecting variants with a more "closed" envelope conformation with consequences for both receptor binding and neutralization sensitivity. The SIV/monkey model, although it has important advantages, may not answer all questions asked about HIV-1 infection in human.

Animals↗
PubMed1990

HIV-1 variability and progression to AIDS: a longitudinal study.

HIV-1 replicative activity and its relation to the clinical and immunological evolution of infection was studied in a group of 150 HIV-1 seropositive Italian i.v. drug abusers over a 1 year period. HIV-1 was isolated from 90 (60%) subjects; two groups of isolates were distinguished, according to replicative activity "in vitro" and ability to induce cytopathic effects in cell cultures, and were termed "rapid-high" and "slow-low" viruses, in agreement with other workers. Rapid-high viruses were recovered more frequently from patients with ARC/AIDS, while slow-low viruses seemed related to the asymptomatic period of infection. The replicative properties of HIV-1 seem to affect strongly the course of disease. In fact, an important CD4 cell decline occurred in asymptomatic subjects with rapid-high virus infection; asymptomatic subjects with negative viral cultures or with slow-low viruses showed no such decline. Asymptomatic subjects with negative viral cultures had no signs of disease during the observation period, while 9% with slow-low virus and 45% with rapid-high virus progressed to AIDS.

AIDS-Related Complex↗
PubMed1997

[Predictive factors of non-compliance with anti-tuberculosis treatment in patients infected with the human immunodeficiency virus].

A study was conducted to know the rate of non-compliance of antituberculosis therapy among HIV-infected patients, the factors associated with non-compliance and the evolution of these patients. The therapy compliance in 276 tuberculous HIV infected patients diagnosed in two Madrid hospitals was analyzed. Fifty-one patients (18%) were not included in the analysis (6 died without therapy, 6 were lost and 39 died during therapy). Out of the 225 evaluable patients, 36 (16%, 95% CI, 11.6-21.6) did not comply with therapy. The only factor associated with a higher therapy non-compliance was the antecedent of drug use (20% of non-compliance; relative risk: 10, 95% CI, 1.4-71). Patients using drugs at tuberculosis diagnosis had higher risk for non-compliance (31%; RR, 3.1; 95% CI, 1.6-6.3). The incidence of tuberculosis reactivation after leaving therapy was 78.8/100 patient-years. Therapy non-compliance increased death risk associated with tuberculosis (RR, 9.8; 95% CI, 4.6-21). Programs for controlling antituberculous therapy should give priority to active drug users, as this is the group with the highest risk for non-compliance.

Adult↗
PubMed2005

Immunologic pressure within class I-restricted cognate human immunodeficiency virus epitopes during highly active antiretroviral therapy.

Cytotoxic T lymphocytes (CTL) and highly active antiretroviral therapy (HAART) are known to exert strong evolutionary pressures on the virus population during human immunodeficiency virus (HIV) infection. However, it is not known whether CTL responses continue to substantially affect viral evolution during treatment. To study the effect of immunologic pressure on viral sequences during HAART, we identified 10 targeted HIV-specific CD8+-T-cell epitopes in five treatment-naive patients, sequenced each epitope in plasma-derived viruses, and then identified evidence of immunologic pressure at these epitopes by comparing the frequency of viral variants in plasma to the frequency of the CD8+-T-cell response for each variant identified. For one of the five patients, evidence of viral evolution was found during therapy. The sequence of the CTL-targeted epitope changed from an apparent escape variant prior to the initiation of therapy, to the sequence that is best recognized by the CTL response after the initiation of therapy, and then finally to a new escape variant during continued therapy. These data show that CTL-mediated pressure can continue to affect viral evolution after the initiation of HAART, even when treatment drives the viral load below detectable levels, and suggest that antiretroviral therapy may preferentially inhibit those virus variants that escape the CTL response.

Amino Acid Substitution↗
PubMed2005

The X4 phenotype of HIV type 1 evolves from R5 in two children of mothers, carrying X4, and is not linked to transmission.

Previously, we found that emergence of the X4 viral phenotype in HIV-1-infected children was related to the presence of X4 in their mothers (C.H. Casper et al., J Infect Dis 2002; 186:914-921). Here, we investigated the origin of the X4 phenotype in the child, analyzing two mother-child pairs (Ma-Ca, Mb-Cb) where the mothers carried X4 and their children developed X4 after an initial presence of R5. We used nested polymerase chain reaction of the env V3 region to generate 203 HIV-1 clones for sequencing (Ma, n = 44; Ca, n = 73; Mb, n = 61; Cb, n = 25) from DNA of peripheral blood mononuclear cell (PBMC) lysates, altogether 167 clones, or from cDNA of plasma RNA, 36 clones. PBMC and plasma isolate sequences from each time point enabled us to assign the probable phenotype to clone sequences in a phylogenetic tree. The transmission and evolution were reconstructed using the maximum likelihood method. In mother-child pair Ma-Ca, one maternal R5 isolate clustered with the child's R5 sequences, at the earliest time when R5 was isolated in the child, confirming this as a likely source of the transmitted R5 phenotype. At age 3, an X4 population was present in the child that had evolved from the child's own R5-associated population, clearly distinct from the maternal X4 sequences. The second mother-child pair (Mb-Cb) displayed a similar pattern. Amino acid substitution patterns corroborated the conclusions from the phylogenetic tree. Thus, in both children, the X4 virus developed from their own R5 population, and was not caused by transmission of X4.

Amino Acid Sequence↗
PubMed1992

[Human immunodeficiency virus infection and malignant lymphoma].

Infection by human immunodeficiency viruses (HIV) is associated with an increased incidence of non-Hodgkin's lymphomas (NHL) of B cell origin and of intermediate grade (diffuse large cell lymphomas according to the Working Formulation) or high grade (Kiel classification and Working Formulation). They may be either primary central nervous system lymphomas or systemic lymphomas and are considered as AIDS-defining events. Systemic lymphomas are usually disseminated with a high frequency of extranodal sites. Their overall prognosis is much worse than for NHL in the general population. Pathogenesis is still a matter of debate. An increased incidence of Hodgkin's diseases (HD) in HIV infection is being suspected but has not been proved yet. However, HIV-associated HD differ from usual HD by clinical presentation, histological type repartition, and evolution. Finally, low grade lymphomas have been described in HIV infection, the only peculiarity being the unusual age of occurrence.

HIV Infections↗
PubMed1997

Evolution of human immunodeficiency virus type 1 in perinatally infected infants with rapid and slow progression to disease.

We addressed the relationship between the origin and evolution of human immunodeficiency virus type 1 (HIV-1) variants and disease outcome in perinatally infected infants by studying the V3 regions of viral variants in samples obtained from five transmitting mothers at delivery and obtained sequentially over the first year of life from their infected infants, two of whom (rapid progressors) rapidly progressed to having AIDS. Phylogenetic analyses disclosed that the V3 sequences from each mother-infant pair clustered together and were clearly distinct from those of the other pairs. Within each pair, the child's sequences formed a monophyletic group, indicating that a single variant initiated the infection in both rapid and slow progressors. Plasma HIV-1 RNA levels increased in all five infants during their first months of life and then declined within the first semester of life only in the three slow progressors. V3 variability increased over time in all infants, but no differences in the pattern of V3 evolution in terms of potential viral phenotype were observed. The numbers of synonymous and nonsynonymous substitutions varied during the first semester of life regardless of viral load, CD4+-cell count, and disease progression. Conversely, during the second semester of life the rate of nonsynonymous substitutions was higher than that of synonymous substitutions in the slow progressors but not in the rapid progressors, thus suggesting a stronger host selective pressure in the former. In view of the proposal that V3 genetic evolution is driven mainly by host immune constraints, these findings suggest that while the immune response to V3 might contribute to regulating viral levels after the first semester of life, it is unlikely to play a determinant role in the initial viral decline soon after birth.

Amino Acid Sequence↗
PubMed1996

Enterocytozoon bieneusi as a cause of chronic diarrhea in a heart-lung transplant recipient who was seronegative for human immunodeficiency virus.

Enterocytozoon bieneusi is a major cause of chronic diarrhea and malabsorption in patients with AIDS. We report what we believe is the first case of intestinal infection due to E. bieneusi in a heart-lung transplant recipient who was seronegative for human immunodeficiency virus (HIV). The clinical presentation and the evolution of the disease were identical to those usually observed in patients with AIDS and included diarrhea, massive weight loss, and persistent infection despite treatment with albendazole. E. bieneusi was identified in the patient's duodenal mucosa by electron microscopy. No other etiologic agent was detected. We conclude that E. bieneusi may be responsible for serious intestinal infections in patients whose immunosuppression is not related to HIV.

Animals↗
PubMed2002

The pharmacoeconomic impact of generics: an evolutionary tale.

The very word generics stiffens sinews and tightens lips in the pharma industry. It has been proposed that large profits and much pride are now being lost through the creeping forces of intellectual piracy and generic plagiarism [1-3]. In this article, I will argue against this position. Using models from evolution and modern day complexity theory I will attempt to address some of the fears that surround generic pharmaceutical enterprise and to express my own concerns about some of the overly optimistic thinking that occurs with respect to developing world systems and the HIV virus.

Biological Evolution↗
PubMedDate not supplied

The role of CD8+ T-cell response in HIV infection.

CD8+ T-cells with cytotoxic (CTL) activity play a pivotal role in controlling viral infections. Although most patients chronically infected with HIV have CTL response against the virus, for reasons that are not well understood this response is not able to successfully control viral replication. The crucial role of this type of response has been clearly demonstrated in the setting of acute infection using the simian model of AIDS, in which a strong CTL response develops, supporting its role in humans. This approach has been possible due to the development of new assays to quantify CTL activity with great sensitivity and specificity. The interaction of CTL response and HIV during this acute stage of infection is crucial, since it most probably determines the viral set-point and thus the rate of HIV disease progression. In the setting of chronic HIV infection, the use of tetrameric complexes and IFN-gamma production assays have made it possible to investigate the different functional aspects of these cells and have also facilitated the evaluation of this response in large patient populations. Defects in cytokine production and in perforin expression have been found, as well as alterations in phenotypic maturation and a low proliferation of these cells. All these findings have been cited to explain the inability of CTLs to efficiently control virus replication. Nonetheless, accumulating evidence points toward an important role for CTL response in the partial containment of HIV replication in chronic infection. An especially strong support for this observation derives from studies analyzing the selective pressure exerted by the immune response over viral evolution. Very recently, longitudinal and cross-sectional studies in large populations of patients have demonstrated that viral evolution is in part driven by HIV-specific T-cell responses.

Animals↗
PubMed1990

Evolutionary origin of human and simian immunodeficiency viruses.

From what viruses the human immunodeficiency viruses (HIVs) originated is an extremely controversial question. To address this question, we have analyzed nucleotide sequences of simian immunodeficiency viruses (SIVs) and HIVs by using the techniques for understanding molecular evolution. In particular, we compared the nucleotide sequences of whole genomes, gene region by gene region, between a given pair of viruses, including four types of SIVs--isolated from mandrills (Papio sphinx), African green monkeys (Cercopithecus aethiops), sooty mangabeys (Cercocebus atys), and rhesus macaques (Macaca mulatta)--as well as HIVs. Phylogenetic trees for all gene regions examined showed that the present HIVs may have emerged as different variants of SIVs of Old World monkeys, possibly from recombination between viruses related to SIVs.

Biological Evolution↗