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PubMed1992

Monoclonal immunoglobulins in patients with renal transplants: characterization, evolution and risk factors.

Gammopathies were found to be present in 25 (13%) of 192 HIV-negative renal transplant recipients with more than 30 months follow-up prospectively investigated for monoclonal or oligoclonal immunoglobulins (mIg) by agarose gel electrophoresis and immunofixation. Eleven patients had only one monoclonal band, whereas 14 had two or more bands. Of these bands, 60% were IgG kappa, 29% IgG lambda and 11% IgM lambda or kappa, and 90% did not exceed 2 g/l. Most gammopathies occurred early post-transplant (median 5 months) and they were always transient. Some predisposing factors for mIg emergence could be identified: 1. age, but only in women, 2. duration of dialysis, 3. occurrence of prior cytomegalovirus infection, and 4. immunosuppressive regimen including cyclosporine. Serological evidence for active EBV infection was obtained in ten patients, but in six cases infection occurred subsequent to the finding of mIg. In eight patients, the clinical course was characterised by severe infection or tumours (one Kaposi's sarcoma, one B-cell brain lymphoma). The present findings and experimental studies support the view that the development of mIg in renal transplant patients is associated with a failure of regulatory T-cell function. This T-B-cell imbalance requires a careful follow-up in these patients.

Antibodies, Monoclonal↗

PubMed2006

Sequential turnover of human immunodeficiency virus type 1 env throughout the course of infection.

We examined the rates of variant population turnover of the V1-V2 and V4-V5 hypervariable domains of the human immunodeficiency virus type 1 (HIV-1) gp120 molecule in longitudinal plasma samples from 14 men with chronic HIV-1 infection using heteroduplex tracking assays (HTA). Six men had high rates of CD4+ T-cell loss, and eight men had low rates of CD4+ T-cell loss over 2.5 to 8 years of infection. We found that V1-V2 and V4-V5 env populations changed dramatically over time in all 14 subjects; the changes in these regions were significantly correlated with each another over time. The subjects with rapid CD4 loss had significantly less change in their env populations than the subjects with slow CD4 loss. The two subjects with rapid CD4 loss and sustained low CD4 counts (<150/microl for at least 2 years) showed stabilization of their V1-V2 and V4-V5 populations as reflected by low levels of total change in HTA pattern and low HTA indices (a novel measure of the emergence of new bands and band distribution); this stabilization was not observed in other subjects. The stabilization of env variant populations at low CD4 counts following periods of rapid viral evolution suggests that selective pressure on env, likely from new immune responses, is minimal when CD4 counts drop dramatically and remain low for extended periods of time.

CD4 Lymphocyte Count↗

PubMed2003

Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method.

A new method for reconstructing phylogenetic relationships of within-host (patient) viral evolution from noncontemporaneous samples is presented. This method has two important features: noncontemporaneous viral samples can be dealt with by a simple computing algorithm, and both neutral and adaptive evolution patterns occurring during the process of viral evolution can be estimated. In our previous study, we proposed a preliminary formulation of this algorithm that was based on the maximum likelihood method. However, that preliminary formulation was difficult to use because the calculation of the likelihood required an extremely large amount of time and the number of possible tree topologies increased exponentially according to the increase in the number of viral variants. In this paper, we propose another new algorithm, referred to as a distance-based sequential-linking algorithm, in which the neighbor-joining method is employed for reconstruction of the longitudinal phylogenetic tree from serial viral samples. This algorithm is applied to a longitudinal data set of the env gene (V3 region) of human immunodeficiency virus type 1 (HIV-1) obtained over 7 years after the infection of a single patient. The results suggest that this method can successfully reconstruct a longitudinal phylogenetic tree from noncontemporaneous viral samples within a reasonable calculation time. This revised method proved to be a useful tool for estimating the dynamic process of within-host viral evolution.

Evolution, Molecular↗

PubMedDate not supplied

[Cutaneous leishmania in HIV patient in Ouagadougou: clinical and therapeutic aspects].

BACKGROUND: Immune suppression cause by HIV infection is a risk factor in the progression of leishmania diseases. In Burkina Faso atypical clinical presentations of leishmaniases have been observed among people living with HIV. The goal of this study was to describe clinical and evolutionary aspects of cutaneous leishmania and HIV co-infection among patients followed at Ouagadougou University Hospital. PATIENTS AND METHODS: This 16-month prospective study was carried out from January 2003 to April 2004 among HIV-seropositive patients with a diagnosed cutaneous leishmania infection. At baseline, infection and lesions were classified. Clinical diagnosis of cutaneous leishmania depended on finding parasites by microscopy in smears or tissue biopsies. Histological examinations were done if clinical and parasitological diagnosis were not concordant. Treatment consisted of three 21-day rounds of pentavalent antimonial, (Glucantime(R)). Clinical evolution was monitored at the end of each treatment round. RESULTS: Thirty-two HIV-1 positive patients (16 women and 16 men) were included. Mean age was 35.5 (10-67 years old). Leishmania lesions had been evolving, on average, for 12 weeks. Eleven patients were taking HAART and 21 patients were taking cotrimoxazole prophylaxis against opportunistic infections. Cutaneous lesions were found: in the face (15 cases), torso (18 cases), upperlimbs (26 cases) and lower-limbs (28 cases). Observed clinical forms were: papulo-nodular (9 cases), ulcerative (14 cases), infiltrative (12 cases), lepromatous and diffuse (15 cases), psoriasis-like (5 cases), cheloid, histioid or kaposi-like (1 case each). Some patients presented more than one clinical form. Prognosis was satisfactory in 24 patients after the first treatment. Twelve patients relapsed after the first treatment, among those 10 were only taking cotrimoxazole. At the end of the third treatment, 24 patients were cured, 3 died and 5 were lost to follow-up. CONCLUSION: Clinical polymorphism of cutaneous leishmania has been observed in HIV-patients, thereby increasing the risk of differential diagnosis.

AIDS-Related Opportunistic Infections↗

PubMed2002

A hierarchical model of HIV-1 protease drug resistance.

A hierarchical model of HIV-1 drug therapy may be used to evaluate new inhibitors and test new treatment strategies that address the problem of drug resistance. The model includes an atomic representation of drug-protease interaction, evaluation of viral fitness based on cleavage of polyprotein substrates during viral maturation, evolutionary modelling of drug resistance mutations in the face of selection pressures by drug and a mathematical description of viral population dynamics in infected individuals. These techniques have been used for the design of resistance-evading inhibitors by computational coevolution techniques and for the optimisation of existing protease inhibitors for improving their robustness in the face of resistance mutation.

Catalytic Domain↗

PubMed1998

Genetic differences between human immunodeficiency virus type 1 subpopulations in faeces and serum.

To study human immunodeficiency virus type 1 (HIV-1) compartmentalization between intestine and blood, paired faecal and serum samples were collected from 204 HIV-1-infected persons. Direct sequencing of the gp120 V3 region obtained from 33 persons showed that faecal and serum sequences could be nearly homologous (0.3% different) or very dissimilar (11.3% different). Individual clones were obtained and sequenced from the faecal and serum samples of 13 persons. In 6 persons the HIV-1 subpopulations in faeces and serum were similar, whereas in 7 persons, distribution of V3 genotypes showed a marked difference. Genetic characterization of the HIV-1 subpopulations showed less heterogeneity in faecal subpopulations than in serum subpopulations in 5 of the 7 subjects. Furthermore, faecal and serum subpopulations differed predominantly by nonsynonymous nucleotide substitutions (in 6 of 7 persons). Comparison of the HIV-1 subpopulations in faeces and serum of these 7 persons, using resampling techniques, revealed a significant difference between faecal and serum subpopulations at an N-linked glycosylation site, C-terminal of the V3 loop (amino acids 331-333). Sequences from faecal subpopulations of all 7 persons contained a glycosylation site at amino acid position 331-333. Four of these 7 harboured serum variants lacking a glycosylation site at this position. The faecal subpopulations in these 4 persons showed limited nonsynonymous substitutions compared to synonymous substitutions, indicating that purifying selection is operational on these subpopulations.

Acquired Immunodeficiency Syndrome↗

PubMed1999

[Diagnosis and virologic monitoring of HIV infection].

The new challenge of the diagnosis of HIV infection concerns the treatment since an early diagnosis permits to start antiretroviral therapy with the aim to block the evolution to aids. The virological diagnosis may be done easily using new sensitive and specific techniques. Using the test of detection of p24 antigenemia and HIV-RNA in plasma, it is easy to approach the diagnosis of primary infection. The tests for HIV viral load are now largely available and they must be systematically included in the follow-up of infected persons.

AIDS Serodiagnosis↗

PubMed1996

Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases.

Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.

Animals↗

PubMed1997

Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts.

Clonal diversifications of HIV virus were monitored by periodic samplings on each of the six patients with regard to 183- to 335-bp segments of the env gene, which invariably included the functionally critical V3 region. Subsequently, six individual phylogenetic trees of viral variants were constructed. It was found that at one time or another during the course of disease progression, viral variants were inexplicably released from a strong negative selection against nonsynonymous base substitutions, possibly indicating positive selection. This resulted in concentrated amino acid substitutions at five specific sites within the V3 region. It was noted that these sites were often involved as antigenic determinants that provoked the host immune response and that these sites were also involved in the determination of viral phenotypes as to their cell tropism, syncytium formation capability, and replication rates.

Amino Acid Sequence↗

PubMed1991

Evolution of human immunodeficiency virus type 1 nucleotide sequence diversity among close contacts.

The degree of change in the nucleotide sequence of human immunodeficiency virus type 1 (HIV-1) that occurs when it is transmitted sexually from one individual to another or vertically from mother to child is unknown. Previous studies have shown that most cultured HIV-1 isolates from the same individuals differed in the entire envelope gene nucleotide sequence by up to 2%, although most isolates from unrelated individuals differed by 6-22%. To examine diversity among HIV-1 isolates from close contacts, we determined the nucleotide sequences of viruses from a family with a known epidemiologic profile, in which a woman transmitted HIV-1 heterosexually to her partner and vertically to her daughter. Direct DNA sequence analysis of primary HIV-1 isolates amplified by PCR was used to distinguish the major and minor viral sequences, termed quasispecies, to rapidly determine the predominant sequences and their phylogenetic relationships. The nucleotide sequence diversity of a major portion of the HIV-1 envelope gene was 3.7% between isolates from the woman and her heterosexual partner and 8.5% between isolates from this woman and her daughter, who had been infected for a longer period than the partner. The configuration of the phylogenetic tree demonstrated that the daughter's predominant isolate evolved from a progenitor of her mother's current strain. This study provides evidence of a continuous spectrum of sequence diversity between any two isolates ranging from those derived from the same person to those from close contacts and, ultimately, those from unrelated individuals. These data and methods can be applied to epidemiologic investigations of possible HIV-1 transmission between health care workers and their patients.

Acquired Immunodeficiency Syndrome↗

PubMed1997

Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes.

The time of spread of human immunodeficiency virus type 1 (HIV-1) from lymphoid to nonlymphoid tissues in the course of infection was investigated by sequence comparisons of variants infecting a range of lymphoid and nonlymphoid tissues from three individuals with AIDS in the pl7gag gene and regions flanking the V1/V2 hypervariable regions. Phylogenetic analysis in both regions revealed several lineages in each individual that contained sequences from both lymphoid and nonlymphoid tissues such as the brain. This observation contrasts strongly with the previously described organ-specific sequences in the V3 region in this study population and other investigations. Although individual pairwise comparisons of relatively short sequences such as p17gag are subject to considerable stochastic error, we found that the diversity of gag sequences in variants from lymphoid tissue was consistently lower than that found among variants amplified from the brain. By estimating mean synonymous pairwise distances in the p17gag region, we were able to make an approximate calculation of the ages of populations in different tissues. Those from lymphoid tissue ranged from 2.65 to 5.6 years in the three study subjects, compared with 4.1 to 6.2 years for variants in the brain. Indeed, variants infecting the brain were no more closely related to each other than they were to variants infecting other tissues in the body. In two of the three individuals, these times of divergence indicate that infection of the brain may have occurred as an early event in the progression to disease, preceding the onset of AIDS by several years. This study is the first in which it was possible to estimate times of diversification in different tissues in vivo and is of importance in understanding the dynamics of the spread of HIV-1 into nonlymphoid tissues and its possible adaptation for replication in different cell types.

Acquired Immunodeficiency Syndrome↗

PubMed1997

pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D.

Naturally occurring mutations in the polymerase gene of human immunodeficiency virus type 1 (HIV-1) have important implications for therapy and the outcome of clinical studies. Using 42 virus isolates obtained from the UNAIDS sample collection, we analyzed the protease (99 amino acids [aa]) and the first 297 aa of reverse transcriptase (RT) coding regions. Based on the V3 sequence analysis, the collection includes subtype A (n = 5), subtype B (n = 12), subtype C (n = 1), subtype D (n = 11), and subtype E (n = 13) viruses. Of the 42 protease genes, 37 contained naturally occurring mutations at positions in the gene that contribute to resistance to protease inhibitors (indinavir, saquinavir, ritonavir, and nelfinavir) in clade B isolates. The phenotypic effect of these substitutions in non-B isolates is unclear. The The 5'half RT coding region of the 42 isolates was found to be less variable, although 19 of the 42 RT sequences contained amino acid substitutions known to contribute to nucleoside and/or nonnucleoside drug resistance. Since the virus isolates were obtained in 1992, it is unlikely that the infected subjects received protease inhibitors, but we found evidence that one subject acquired a zidovudine (AZT)-resistant HIV-1 strain from a contact who had received AZT. Phylogenetic analysis identified five subtype pol clusters: A, B, C, D, and A'. Comparison of env and pol sequences of the same viruses showed no more recombination events than were already identified on the basis of gag/env comparison (M. Cornelissen, G. Kampinga, F. Zorgdrager, J. Goudsmit, and the UNAIDS Network for HIV Isolation and Characterization, J. Virol. 70:8209-8212, 1996). In one of the known recombinants, a crossover site between subtypes A and C could be identified, and in another, a crossover site could not be identified due to lack of a reference subtype F pol sequence. We analyzed the ds/da ratio of gag, pol, and env sequences of 35 isolates, excluding the recombinants. Our analysis showed that gag and pol are subjected to purifying selection with an average ds/da ratio above 1, independent of the subtype and in contrast with V3 (ds/da approximately 1). Based on the low ds/da ratio of the intergroup analysis of A/E and B/D gag and pol sequences, we analyzed the evolutionary relation between subtypes B and D in more detail by constructing separate phylogenetic trees for synonymous and nonsynonymous substitutions. Our analysis suggests a common ancestry for subtypes B and D that is distinct from that of subtypes A and E.

Amino Acid Sequence↗

PubMed1997

[Perceptive deafness and AIDS].

We report a case of a 23 years old woman HIV positive for the past five years with a four year history of right perceptive hypoacusia evolution without tinitus, vertigo or any other otologic symptomatology. After reviewing her personal and family history and conducting imilar tonal audiometry, tympanometry bilateral, contralateral estapedial reflex, auditory evoked brain stem response and a bilateral nasal fiberendoscopy, we analyzed the evolution of her immunal deficiency and the treatments to which she has been submitted with the purpose of determining the risk factors that have coincided in this case to be able to establish some criteria to follow the auditive affect in HIV positive patients.

Acquired Immunodeficiency Syndrome↗

PubMed2001

Perinatal transmission of major, minor, and multiple maternal human immunodeficiency virus type 1 variants in utero and intrapartum.

Previous studies have provided conflicting data on the presence of selective pressures in the transmission of a homogeneous maternal viral subpopulation to the infant. Therefore, the purpose of this study was to definitively characterize the human immunodeficiency virus type 1 (HIV-1) quasispecies transmitted in utero and intrapartum. HIV-1 envelope gene diversity from peripheral blood mononuclear cells and plasma was measured during gestation and at delivery in mothers who did and did not transmit HIV perinatally by using a DNA heteroduplex mobility assay. Children were defined as infected in utero or intrapartum based on the timing of the first detection of HIV. Untreated transmitting mothers (n = 19) had significantly lower HIV-1 quasispecies diversity at delivery than untreated nontransmittting mothers (n = 18) (median Shannon entropy, 0.711 [0.642 to 0.816] versus 0.853 [0.762 to 0.925], P = 0.005). Eight mothers transmitted a single major env variant to their infants in utero, and one mother transmitted a single major env variant intrapartum. Four mothers transmitted multiple HIV-1 env variants to their infants in utero, and two mothers transmitted multiple env variants intrapartum. The remaining six intrapartum- and two in utero-infected infants had a homogeneous HIV-1 env quasispecies which did not comigrate with their mothers' bands at their first positive time point. In conclusion, in utero transmitters were more likely to transmit single or multiple major maternal viral variants. In contrast, intrapartum transmitters were more likely to transmit minor HIV-1 variants. These data indicate that different selective pressures, depending on the timing of transmission, may be involved in determining the pattern of maternal HIV-1 variant transmission.

Evolution, Molecular↗

PubMed1993

[Ulcerative colitis and HIV infection].

UNLABELLED: FUNDAMENTAL: The difficulties to raise to a correct diagnosis in patients with human immunodeficiency virus infection and diarrhea, and the few cases reported of ulcerative colitis in the context of HIV infection. OBJECTIVE: Description of 2 cases of ulcerative colitis in patients with HIV infection and the possibility of immunopathogenic relationship between them. MATERIAL AND METHODS: The clinic history of the patients, the anatomopathological diagnosis after the colon biopsy and the determination of CD4 cells. RESULTS: In case 1 the low level of CD4 cells didn't stop the aggressivity of ulcerative colitis. However, in both cases there was a good evolution of colitis after treatment although AIDS. CONCLUSION: It is necessary to study more cases of inflammatory bowel disease in patients with HIV infection to determine the influence of the level of CD4 cells in the enteropathy's evolution.

Adult↗

PubMed1997

Evolutionary variants of the human immunodeficiency virus type 1 V3 region characterized by using a heteroduplex tracking assay.

Syncytium-inducing (SI) variants of human immunodeficiency virus type 1 (HIV-1) are evolutionary variants that are associated with rapid CD4+ cell loss and rapid disease progression. The heteroduplex tracking assay (HTA) was used to detect evolutionary V3 variants by amplifying the V3 sequences from viral RNA derived from 50 samples of patient plasma. For this V3-specific HTA (V3-HTA), heteroduplexes were formed between the patient V3 sequences and a probe with the subtype B consensus V3 sequence. Evolution was then measured by divergence from the consensus. The presence of evolutionary variants was correlated with SI detection data on the same samples from the MT-2 cell culture assay. Evolutionary variants were correlated with the SI phenotype in 88% of the samples, and 96% of the SI samples contained evolutionary variants. In most cases the evolutionary V3 variants represented discrete clonal outgrowths of virus. Sequence analysis of the six discordant samples that did not show this correlation indicated that three non-syncytium-inducing (NSI) samples had V3 sequences that had evolved away from the consensus sequence but not toward an SI genotype. A fourth sample showed little evolution away from the consensus but was SI, which indicates that not all SI variants require basic substitutions in V3. The other two samples had SI-like genotypes and NSI phenotypes, suggesting that V3-HTA was able to detect SI emergence in these samples in the absence of their detection in vitro. V3-HTA was also used to confirm SI variant selection in MT-2 cells and to examine the possibility of variant selection during virus culture in peripheral blood cells.

Acquired Immunodeficiency Syndrome↗

PubMed2000

[Macaque immunization with virions purified from a primary isolate of the human immunodeficiency virus type 1 induced enhancement antibodies].

Six Rhesus macaques were hyperimmunized with either live infectious human immunodeficiency virus type 1 (HIV-1) or with beta-propiolactone--or formalin--inactivated HIV-1. The virus used was HIV-1 BX08, a primary virus isolate grown in human PBMC. Instead of eliciting virus-neutralizing antibodies, this regimen induced antibodies that enhanced HIV-1 infectivity for PBMC by 10 to 90 fold. Enhancement was also seen in a cell-to-cell fusion assay using a Semliki Forest virus replicon to express BX08 gp160 in CD4+, CCR5+ HeLa cell cultures. These observations raise the concern that whole virus particles-based HIV-1 vaccines might elicit enhancing antibodies that could play a facilitating role in the transmission and/or evolution of the disease.

Animals↗

PubMed2004

MAVID: constrained ancestral alignment of multiple sequences.

We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region, which consists of 1.8 Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments, an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat genomes.

Animals↗