SEARCH · PubMed Health

Results for “HIV evolution”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,423 records · Page 79Linked to original sources

PubMed1988

Evolution of the structural proteins of human immunodeficiency virus: selective constraints on nucleotide substitution.

We have estimated the frequency of synonymous (KS) and amino acid replacement nucleotide substitutions (KA) among gag and env genes of published HIV sequences. The ratio of KS to KA can be used as an indicator of the intensity of the selective constraints on the amino acid sequence of a protein. By this approach we have shown that for both gp120 and gp41, the rate of change in amino acid sequence relative to the overall rate of change in nucleotide sequence is higher than for any other protein yet analyzed. The gag proteins p15 and p17 evolve slightly less rapidly, but p24 is relatively strongly conserved. We have compared the env gene of HIV with those of two other retroviruses for which appropriate data are available. In neither murine leukemia virus nor feline leukemia virus do the envelope glycoproteins evolve particularly rapidly. These results suggest that HIV is unusual among retroviruses in that both gp120 and gp41 are evolving under extremely weak selective constraints relative to the rest of the viral genome; accordingly, much of the observed variation may be selectively neutral.

Amino Acid Sequence↗

PubMed2001

Sequence-specific interaction between HIV-1 matrix protein and viral genomic RNA revealed by in vitro genetic selection.

The human immunodeficiency virus type-1 matrix protein (HIV-1 MA) is a multifunctional structural protein synthesized as part of the Pr55 gag polyprotein. We have used in vitro genetic selection to identify an RNA consensus sequence that specifically interacts with MA (Kd = 5 x 10(-7) M). This 13-nt MA binding consensus sequence bears a high degree of homology (77%) to a region (nt 1433-1446) within the POL open reading frame of the HIV-1 genome (consensus sequence from 38 HIV-1 strains). Chemical interference experiments identified the nucleotides within the MA binding consensus sequence involved in direct contact with MA. We further demonstrate that this RNA-protein interaction is mediated through a stretch of basic amino acids within MA. Mutations that disrupt the interaction between MA and its RNA binding site within the HIV-1 genome resulted in a measurable decrease in viral replication.

Base Sequence↗

PubMed1997

Adaptation to the fitness costs of antibiotic resistance in Escherichia coli.

Policies aimed at alleviating the growing problem of drug-resistant pathogens by restricting antimicrobial usage implicitly assume that resistance reduces the Darwinian fitness of pathogens in the absence of drugs. While fitness costs have been demonstrated for bacteria and viruses resistant to some chemotherapeutic agents, these costs are anticipated to decline during subsequent evolution. This has recently been observed in pathogens as diverse as HIV and Escherichia coli. Here we present evidence that these gentic adaptations to the costs of resistance can virtually preclude resistant lineages from reverting to sensitivity. We show that second site mutations which compensate for the substantial (14 and 18% per generation) fitness costs of streptomycin resistant (rpsL) mutations in E. coli create a genetic background in which streptomycin sensitive, rpsL+ alleles have a 4-30% per generation selective disadvantage relative to adapted, resistant strains. We also present evidence that similar compensatory mutations have been fixed in long-term streptomycin-resistant laboratory strains of E. coli and may account for the persistence of rpsL streptomycin resistance in populations maintained for more than 10,000 generations in the absence of the antibiotic. We discuss the public health implications of these and other experimental results that question whether the more prudent use of antimicrobial chemotherapy will lead to declines in the incidence of drug-resistant pathogenic microbes.

Adaptation, Physiological↗

PubMed1990

Steroid-responsive myeloneuropathy in a man dually infected with HIV-1 and HTLV-I.

Two human retroviruses, HIV-1 and HTLV-I, have been associated with myelopathies in addition to other neurologic disorders. We report an American dually infected with HIV-1 and HTLV-I who developed steroid-responsive myeloneuropathy. This 28-year-old bisexual man developed interstitial pneumonitis and a transient midthoracic sensory level followed by the evolution of a slowly progressive spastic paraparesis and sensorimotor neuropathy. Serologic studies demonstrated coinfection with both HIV-1 and HTLV-I. Peripheral blood absolute CD4 count was persistently within the normal range. Cranial MRI was normal and spinal MRI showed T3-T10 atrophy. Serial CSF analyses demonstrated marked intrathecal synthesis of anti-HTLV-I IgG, lymphocytic pleocytosis, elevated protein and immunoglobulin G, and oligoclonal bands. HIV-1 was isolated from CSF but not from peripheral nerve. Lymphoproliferative studies confirmed spontaneous proliferation in both blood and CSF. Soluble interleukin 2 receptor and soluble CD8 were greatly elevated in blood and CSF when compared with patients with HIV-related vacuolar myelopathy and seronegative patients with other causes of myelopathy. Nerve biopsy showed epi- and endoneurial CD8+ lymphocytic infiltration without vasculitis; muscle biopsy showed features of acute and chronic denervation. A 6-week course of prednisone produced sustained improvement in leg strength and walking times. We speculate that the myeloneuropathy was caused by HTLV-I in the setting of coinfection with HIV-1.

AIDS Dementia Complex↗

PubMed2005

Pain in hospitalized HIV-positive patients: clinical and therapeutical issues.

Pain is frequently reported by patients infected with Acquired Immunodeficiency Virus (HIV), and its causes and specific treatment should be appropriately investigated. We evaluated 197 hospitalized HIV-positive patients with serial interviews and analysis of prescriptions and clinical evolution charts. The main characteristics of pain reported by these patients were: high intensity (60.7%), high frequency (72.0%) and well-known causes (88.8%). Fifty-two per cent of the patients reported persistent or frequent pain during the two weeks before hospital admission. Parameters such as gender, educational level and Karnofsky Index showed no direct relation to the presence or absence of pain. The most commonly affected sites were the head (28.0%) and the abdomen (26.2%). The frequency of indications of pain in the clinical evolution charts (46.2%) was considerably lower than the frequency of complaints reported by patients during the interviews (76.3%). Pain was undertreated in 83.2% of patients, both due to poor efficacy of the prescribed medications and to the excessive and inefficient use of standing order ("if necessary") regimens. We observed that pain was better managed during the hospitalization period, although this cannot be explained by improvement of the analgesic treatment; it might be due to successful treatment of the underlying disease. We concluded that pain reported by hospitalized HIV-positive patients is often underestimated and inadequately treated by assisting doctors, in spite of its severity and frequency.

Adolescent↗

PubMed2006

Nef alleles from human immunodeficiency virus type 1-infected long-term-nonprogressor hemophiliacs with or without late disease progression are defective in enhancing virus replication and CD4 down-regulation.

Infection with human immunodeficiency virus (HIV)-encoding defective nef variants may contribute to a relatively benign course of disease in a minority of long-term nonprogressors (LTNP). We have examined the functions of nef alleles from six individuals belonging to the same cohort of hemophiliacs infected with HIV-1 prior to 1985 and classified as LTNP in 1995. Three out of six individuals have progressed to HIV disease (late progressors [LP]), whereas the three remainders have maintained their LTNP status at least up to 2003. The nef alleles were obtained from both plasma virus and peripheral blood mononuclear cells of all six individuals in 1995 and 1998. The proportion of sequences containing mutations not yielding Nef expression significantly diminished in 1998 versus that in 1995. Several previously defined functional regions of intact nef alleles were highly conserved. However, the major variant obtained in 1998 from plasma RNA of five out of six individuals significantly reduced HIV infectivity/replication and impaired Nef-mediated CD4 but not major histocompatibility complex class I antigen down-modulation from the cell surface. Thus, functional alterations of the nef gene are present in both LP and LTNP, suggesting that Nef defectiveness in vitro is not necessarily associated with the long-term maintenance of LTNP status. Of interest is the fact that isolates from three out of three LP showed a dual CCR5/CXCR4 coreceptor use (R5X4), in contrast to those from LTNP, which were exclusively R5. Thus, in vivo evolution of gp120 Env to CXCR4 use appears to be associated with HIV disease progression in individuals infected with nef-defective viruses.

Alleles↗

PubMedDate not supplied

Papular mucinosis with rapid spontaneous regression in an HIV-infected patient.

Papular mucinosis is a rare, papular eruption caused by the dermal deposition of mucin. Three clinical subtypes have been described. The evolution is usually chronic and no effective treatment is available. Papular mucinosis has recently been reported in patients with AIDS. We describe another case of papular mucinosis in an HIV patient with an uncommonly rapid, total regression.

Adult↗

PubMed2000

High rate of recombination throughout the human immunodeficiency virus type 1 genome.

The diploid nature of human immunodeficiency virus type 1 (HIV-1) indicates that recombination serves a central function in virus replication and evolution. Previously, while examining the nature of obligatory primer strand transfers during reverse transcription, a high rate of recombination was observed at the ends of the viral genome within the viral long terminal repeats, prompting the following question: does recombination occur at a high rate throughout the genome? To address this question, two vectors based upon different strains of HIV-1 were utilized. The vectors were comprised predominantly of autologous HIV-1 sequence and were approximately the same size as the parental genome. The proviral progeny of heterodimeric virions were analyzed after a single cycle of replication, and the sequence heterogeneity between the two strains allowed direct examination of recombination crossovers. The results obtained indicate that HIV-1 undergoes approximately two to three recombination events per genome per replication cycle. These results imply that both HIV-1 RNAs are typically utilized during reverse transcription and that recombination is an important aspect of HIV-1 replication.

Cell Line↗

PubMed2000

Emergence of new forms of human immunodeficiency virus type 1 intersubtype recombinants in central Myanmar.

We have previously shown that HIV-1 env subtypes B' (a Thai-B cluster within subtype B) and E (CRF01_AE) are distributed in Yangon, the capital city of Myanmar. However, HIV strains from the rest of country have not yet been genetically characterized. In the present study, we determined env (C2/V3) and gag (p17) subtypes of 25 specimens from central Myanmar (Mandalay). Phylogenetic analyses identified 5 subtype C (20%), in addition to 10 CRF01_AE (40%) and 4 subtype B' (16%). Interestingly, the remaining six specimens (24%) showed discordance between gag and env subtypes; three gag subtype B'/env subtype C, one gag subtype B'/env subtype E, one gag subtype C/env subtype B', and one gag subtype C/env subtype E. These discordant specimens were found frequently among injecting drug users (4 of 12, 33%) and female commercial sex workers (2 of 8, 25%) engaging in high-risk behaviors. The recombinant nature of these HIV-1 strains was verified in three specimens, indicating the presence of new forms of HIV-1 intersubtype C/B' and C/B'/E recombinants with different recombination breakpoints. The data suggest that multiple subtypes of B', C, and CRF01_AE are cocirculating in central Myanmar, leading to the evolution of new forms of intersubtype recombinants among the risk populations exhibiting one of the highest HIV infection rates in the region.

Adolescent↗

PubMed2006

Model based on a quantum algorithm to study the evolution of an epidemics.

A model based on a quantum algorithm is used to study the spread of HIV virus and to predict infection rates on individuals who are not aware of their particular condition. The model makes an analogy between quantum systems and individuals who are infected by the disease. Individuals are represented by two-level quantum systems (quantum "bit"), and the interactions among individuals who cause the infection are represented by unitary transformations. The population is divided into categories according to their behaviour, and the interactions among those individuals in the same category and those in different categories are simulated. The objective is to obtain statistical data on the number of infected individuals depending on the time for every category and for the entire population. Besides, we analyse the impact of the evolution of the disease on individuals who have not knowledge of their specific sanitary condition.

Algorithms↗

PubMed1999

The identification of a complex A/G/I/J recombinant HIV type 1 virus in various West African countries.

In this sequence note we describe the full-length genome sequence of an HIV-1 isolate originating from the west African country of Mali. The phylogenetic tree analysis from the near full-length genome shows that the 95ML84 strain forms a separate cluster, supported by 100% of the bootstrap values, with the previously described A/G/J/? mosaic virus BFP90 from Burkina Faso. Additional analysis showed that throughout the genome the lowest diversity was seen between the 95ML84 and the BFP90 viruses, and bootscan analysis showed a similar complex genomic structure. In addition to the initial report describing the BFP90 virus as an A/G/J/? recombinant, our data show that for the BFP90 and 95ML84 strains the unclassified region corresponds to subtype I. The A/G/I/J BFP90 and 95ML84 strains represent the fifth and most complex circulating recombinant form of HIV-1 detected so far, and our data show its presence in various West African countries. Subtype I and J sequences, initially considered rare, seem to have broadened their geographical spread by way of these recombinant forms.

Burkina Faso↗

PubMed2003

A longitudinal assessment of autologous neutralizing antibodies in children perinatally infected with human immunodeficiency virus type 1.

The evolution of autologous neutralizing antibodies to sequential human immunodeficiency virus type 1 (HIV-1) isolates was studied in a population of 16 children who were perinatally infected with human immunodeficiency virus type 1. The cohort included seven children with rapid disease progression (RP) and nine who had nonrapid disease progression (NRP). Four of the NRP after 6 months of age harbored viruses that could be neutralized by antibodies found in autologous contemporaneous plasma (titers up to 1:640) while the majority of longitudinally collected viruses from five NRP were resistant to neutralization with contemporaneous plasma. Because of their shorter survival, only five of the RP had studies after 6 months of age; three of the five had neutralizing antibodies to contemporaneous virus isolates and the highest titers were 1:20. The highest titers in RP (up to 1:160) occurred in specimens obtained prior to 6 months of age but these were most likely of maternal origin. Most isolates that were not neutralized by contemporaneous plasma could be neutralized using noncontemporaneous plasma obtained months to years after the virus isolates. These autologous noncontemporaneous neutralizing antibodies persisted for years, had titers that were higher to viruses isolated at younger ages, and were generally more potent in children with NRP than RP. Demonstration of neutralizing antibodies to viruses previously resistant to neutralization by contemporaneous plasma suggests a continuous evolution of virus variants in vivo that are able to escape the effect of neutralizing antibodies.

Antibody Specificity↗

PubMed2005

In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfection.

Human immunodeficiency virus type 1 (HIV-1) superinfection refers to the acquisition of another strain by an already infected individual. Here we report a comprehensive genetic analysis of an HIV-1 superinfection acquired heterosexually. The infected individual was in a high-risk cohort in Tanzania, was exposed to multiple subtypes, and was systematically evaluated every 3 months with a fluorescent multi-region genotyping assay. The subject was identified in the window period and was first infected with a complex ACD recombinant strain, became superinfected 6 to 9 months later with an AC recombinant, and was monitored for >2.5 years. The plasma viral load exceeded 400,000 copies/ml during the first 9 months of infection but resolved to the set point of 67,000 copies/ml by 3 months after superinfection; the CD4 cell count was 377 cells/mul at 30 months. Viral diversity was evaluated with techniques designed to fully sample the quasi-species, permitting direct observation of the evolution, temporal fluctuation, and intercompartment dynamics of the initial and superinfecting strains and recombinants derived from them. Within 3 months of superinfection, seven different molecular forms were detected in gag and six were detected in env. The proportions of forms fluctuated widely over time in plasma and peripheral blood mononuclear cells, illustrating how challenging the detection of dually infected individuals can be. Strain-specific nested PCR confirmed that the superinfecting strain was not present until the 9 month follow-up. This study further defines the parameters and dynamics of superinfection and will foster appropriate studies and approaches to gain a more complete understanding of risk factors for superinfection and its impact on clinical progression, epidemiology, and vaccine design.

Evolution, Molecular↗

PubMed1994

Anti-idiotypic antibodies to the third variable domain of gp120 induce an anti-HIV-1 antibody response in mice.

We tested the potential of anti-idiotypic antibodies to function as molecular mimics of a neutralizing epitope of the human immunodeficiency virus (HIV). Three monoclonal antibodies to the third variable domain (V3) of gp120 from the HIV-1LAI isolate were raised in a BALB/c mouse. They bound gp120LAI with high affinity (K congruent to 10(-11) M), immunoprecipitated viral gp120LAI, recognized HIVLAI-infected cells by immunofluorescence and neutralized HIVLAI infection in vitro. Mice and rabbits were immunized against each one of these antibodies, and one monoclonal and two polyclonal anti-idiotypic reagents were selected for further study. The three anti-idiotypes recognized binding site-related idiotopes that were not present on other V3-specific mouse sera or monoclonal antibodies. Groups of mice and rabbits were immunized against these anti-idiotypes presented in a homopolymerized form, conjugated to a protein carrier, or in an uncoupled form. In the absence of antigen, mice that received polyclonal anti-idiotypes mounted an antibody response to gp120LAI, but not to V3-deleted gp120LAI recombinant proteins. Unlike the three nominal mAbs, the induced antibodies also reacted with gp120 from the divergent HIV strain SF2. The isotypic distribution of the anti-idiotype-induced antibodies and their temporal evolution resemble the restricted pattern and the rapid rise of the antibody response obtained after administration of recombinant gp120LAI to mice. These data thus present evidence that anti-idiotypes raised against HIV-specific antibodies may substitute viral antigens for induction of a humoral immune response to HIV. They also suggest that the HIV epitope variability may be, in part, overcome with the use of anti-idiotypic reagents.

Animals↗

PubMed1999

Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: underrepresentation of X4 variants.

We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitutions. This observation is in contrast to that for subtype B HIV-1, where sequence variability is associated with such substitutions, and these substitutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated with the CD4 level in the infected person, while such a correlation was found with subtype B V3 sequences. Viruses were isolated from a subset of the subjects; all isolates used CCR5 and not CXCR4 as a coreceptor, and none was able to grow in MT-2 cells, a hallmark of the syncytium-inducing phenotype that is correlated with CXCR4 usage. The overall sequence variability of the subtype C V3 region was no greater than that of the conserved regions of gp120. This limited sequence variability was also a feature of subtype B V3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered coreceptor usage is rare in subtype C HIV-1 isolates in sub-Saharan Africa and that sequence variability is not a feature of the V3 region of env in the absence of altered coreceptor usage.

Base Sequence↗

PubMed2004

Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin.

Human and simian immunodeficiency viruses (HIV and SIV), influenza virus, and hepatitis C virus (HCV) have heavily glycosylated, highly variable surface proteins. Here we explore N-linked glycosylation site (sequon) variation at the population level in these viruses, using a new Web-based program developed to facilitate the sequon tracking and to define patterns (www.hiv.lanl.gov). This tool allowed rapid visualization of the two distinctive patterns of sequon variation found in HIV-1, HIV-2, and SIV CPZ. The first pattern (fixed) describes readily aligned sites that are either simply present or absent. These sites tend to be occupied by high-mannose glycans. The second pattern (shifting) refers to sites embedded in regions of extreme local length variation and is characterized by shifts in terms of the relative position and local density of sequons; these sites tend to be populated by complex carbohydrates. HIV, with its extreme variation in number and precise location of sequons, does not have a net increase in the number of sites over time at the population level. Primate lentiviral lineages have host species-dependent levels of sequon shifting, with HIV-1 in humans the most extreme. HCV E1 and E2 proteins, despite evolving extremely rapidly through point mutation, show limited sequon variation, although two shifting sites were identified. Human influenza A hemagglutinin H3 HA1 is accumulating sequons over time, but this trend is not evident in any other avian or human influenza A serotypes.

Animals↗

PubMed1991

An evolutionary view of viral regulatory genes.

It is my great honor to dedicate this article to Professor Ludwig C. Yen at the occasion of the Annual Meeting of the Chinese Society of Microbiology, commemorating his 101st Birthday. I have had the privilege of being one of the earliest students of Professor Yen, and as a staff member working for 16 years under him, I have been benefited enormously from his teachings. I am most grateful to Dr. Czausiung Yang and the executive board members of the Chinese Society of Microbiology for giving me this opportunity to present some of my research activities which would be relevant to Professor Yen's teachings. Introduction to the evolutionary view of host-parasite relationship was one of the many contributions Professor Yen made to enlighten students and colleagues as early as in 1940. As promulgated by Professor Yen, natural history of infectious diseases has witnessed the reality of Theobald Smith's premise, "pathogenicity of microorganisms is an accident in the evolutionary processes of host-parasite relationship, and the outcome of evolutionary forces is a modus vivendi (a feasible compromise) according to which the parasite and the host reach some sort of equilibrium which permits the survival of both"(1). These evolutionary concept has since become a common knowledge for modern students of infectious diseases. The natural history of recently discovered human retroviruses such as HTLVs (human T-lymphotropic viruses) and HIVs (human immunodeficiency viruses) has amply demonstrated the truth of the premise. I shall review some results of our research which would be of relevance to the evolution of viral quasispecies and variants, viral oncogenes, and the cellular as well as viral regulatory genes. I shall focus on the roles played by these genes in the delicate and complex balance of host-virus relationships, and on their association with cellular differentiation and oncogenesis.

Biological Evolution↗

PubMed2002

Progress in clinical neurosciences: The neuropathogenesis of HIV infection: host-virus interaction and the impact of therapy.

Despite the availability of highly active antiretroviral therapy (HAART), primary HIV-related neurological diseases remain major problems in HIV clinics. The present review examines the pathogenesis of HIV-related dementia and the less severe minor cognitive and motor deficit, together with distal sensory and drug-induced toxic polyneuropathies. Abnormal host immune responses within the nervous system and the role of viral expression and diversity are emphasized in relation to neurovirulence. Induction of innate immune responses within the central and peripheral nervous systems, largely mediated by cells of macrophage lineage, appear to be common to the development of primary HIV-related neurological disease. Activation of these cell types results in the release of a cascade of inflammatory molecules including cytokines, chemokines, matrix metalloproteinases, and arachidonic acid metabolites that influence neuronal survival. Individual viral proteins encoded by envelope and tat genes and discrete sequences within these genes influence the extent to which these pro-inflammatory molecules are induced. At the same time, systemic immune suppression may influence the occurrence and severity of HIV-related neurological diseases. Implementation of HAART and neuroprotective treatments improves neurological function although the evolution of drug-resistant viral strains limits the sustained benefits of HAART.

AIDS Dementia Complex↗