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Ricardo Sobhie Diaz

Publications and source records attributed to Ricardo Sobhie Diaz.

15 recordsLinked to original sources
PubMed2006

Reactivation of ancestral strains of HIV-1 in the gp120 V3 env region in patients failing antiretroviral therapy and subjected to structured treatment interruption.

We analyzed gp120V3 HIV-1 env region genetic diversity of 27 patients failing antiretrovirals and subjected to 12-week structured treatment interruption (STI). Based on heteroduplex mobility assays, eight patients presented low pre- and post-STI genetic diversity (G1); five presented high pre-STI but low post-STI diversity (G2); five presented low pre-STI and high post-STI diversity (G3); and nine, high pre- and post-STI diversity (G4). One patient from G1, two from G2 and two from G3 were subjected to proviral DNA end-point PCR and sequencing. In three patients, the dramatic disturbance caused by STI resulted in ancestral viral progeny activation, which repopulated the cell reservoir. In two patients presenting highly homogeneous sequences and low immune selective pressure (dN/dS ratio <1), this phenomenon was not observed. The mechanisms involved in viral evolution, in which antiretroviral therapy also applies selective pressure, sometimes affects coreceptor usage of circulating viruses, leading to the suppression of x4 strains.

Amino Acid Sequence↗
PubMed2006

Analysis of the near full length genomes of HIV-1 subtypes B, F and BF recombinant from a cohort of 14 patients in São Paulo, Brazil.

The human immune deficiency virus (HIV) exhibits strikingly tremendous amount of genetic variability. Such feature is critically important for the virus to adapt to environmental changes by escaping the host immune system and by escaping candidate vaccine. Therefore, understanding of such diversity is fundamental for the design of successful drugs or vaccine, which is urgently needed to bring the HIV/AIDS epidemic under control. In this study, we investigated the magnitude of diversity of the HIV-1 near full-length genomes from patients previously assigned as infected with non-recombinant HIV-1 subtypes B and F1 variants based on small portion of viral genome. HIV-1 proviral DNA was extracted from 14 samples previously classified in our laboratory as six subtypes B and eight subtypes F on the basis of small amplicon sequencing. Reamplifications of DNA from these samples were carried out by an overlapping PCR followed by direct sequencing. The data were phylogenetically inferred. Sequence analysis revealed that two out of six partially identified subtype B and six out of eight partially identified subtype F were in fact BF recombinants throughout their full genomes. Two pairs BF recombinants had identical genomic recombination structure and distinct from the Argentinean CRF 12_BF strains, probably represents a novel circulating recombinant forms in Brazil. Our data provided new genetic material of some of the HIV-1 subtypes currently circulating in the country and points to the widespread of BF recombinants which are expected to change the epidemic nature by approaching the level of subtype B in Brazil.

Adult↗
PubMed2006

Identification of two HIV type 1 circulating recombinant forms in Brazil.

Recombination is an important way to generate genetic diversity. Accumulation of HIV-1 full-length genomes in databases demonstrated that recombination is pervasive in viral strains collected globally. Recombinant forms achieving epidemiological relevance are termed circulating recombinant forms (CRFs). CRF12_BF was up to now the only CRF described in South America. The objective was to identify the first CRF in Brazil conducting full genome analysis of samples sharing the same partial genome recombinant structure. Ten samples obtained from individuals residing in Santos, Brazil, sharing the same recombination pattern based on partial genome sequence data, were selected from a larger group to undergo full length genome analysis. Near full length genomes were assembled from overlapping fragments. Mosaic genomes were evaluated by Bootscan, alignment inspection, and phylogenetic analysis using neighbor joining and maximum likelihood. Full genomes were also analyzed by split decomposition. We were able to identify five mosaic genomes. Two of these structures were represented by at least three samples derived from epidemiologically unlinked individuals. These structures were named CRF28_BF and CRF29_BF and are the second and third CRFs composed exclusively by subtypes B and F as well as the second and third CRFs encountered in South America. Other recombinant forms studied here resembled CRF28_BF and CRF29_BF. Our results suggest that a diverse population of related recombinants, including CRFs may play an important part in the Brazilian and South American epidemic.

Adult↗
PubMed2006

Full-length genome analysis of human immunodeficiency virus type 1 subtype C in Brazil.

The most prevalent HIV-1 clade in the global epidemics is C, and this clade is also becoming important in the Brazilian epidemics. In this study, we characterized HIV-1 subtype C variants by sequencing their near full-length genomes. DNA was extracted from six samples previously classified in our laboratory as subtype C on the basis of partial genome sequencing. Amplification was carried out by overlapping PCR followed by direct sequencing. Phylogenetic analysis of full length genomes confirmed that all isolates belonged to subtype C, which formed a highly supported monophyletic cluster and showed a nucleotide distance of 5.4%. The core promoter of all isolates contained three NF-kappaB binding motifs. Our results suggest that subtype C viruses circulating in Brazil were likely introduced recently from a unique point source. The independent clustering of Brazilian subtype C on the phylogenetic tree suggests the profile of an ideal local candidate for the development of a single subtype vaccine.

Brazil↗
PubMed2005

Low accumulation of L90M in protease from subtype F HIV-1 with resistance to protease inhibitors is caused by the L89M polymorphism.

BACKGROUND: This work evaluates the role of subtype F human immunodeficiency virus type 1 (HIV-1) protease (PR) substitutions L89M and L90M in viral replication and resistance to PR inhibitors (PIs). METHODS: Subtype B and F PR genes were subjected to site-directed mutagenesis, to create and reverse the methionine at positions 89 and 90. Viruses were re-created in cell culture, and their replicative capacity was assessed by fitness assay. Generated viruses were also phenotyped for PI resistance. RESULTS: The subtype F clone (89M90L) showed a replicative capacity comparable to that of the PI-susceptible subtype B clone (89L90L) and was more fit than the L89M mutated subtype B clone (89M90L). Both 89M90M subtype B and F clones presented the lowest fitness s values. The L89M mutation impacted phenotypic resistance to all PIs in half of the subtype F isolates but not in the subtype B isolates. Subtype F isolates presented a phenotypic profile similar to that of subtype B isolates when the M89L mutation was introduced. CONCLUSION: The L89M mutation in subtype F viruses is a high genetic barrier to the accumulation of the L90M resistance mutation and can function as a resistance mutation, depending on the presence of other polymorphisms in the subtype F PR backbone.

Amino Acid Sequence↗
PubMed2005

HIV-1 superinfection is not a common event.

Evidence for human immunodeficiency virus type 1 (HIV-1) superinfection was investigated among a group of four previously HIV-1 infected transfusion recipients (and the four implicated HIV-1 infected donors) identified by the Transfusion Safety Study, and two groups of 4 and 5 Brazilian injection drug users, who consistently injected themselves using shared paraphernalia. To probe these cases for possible superinfection we used heteroduplex mobility analysis (HMA) of HIV-1 tat, a technique which is a reliable for establishing epidemiologic linkages and searching for minor strains in mixed infection settings. In all these cases with established, untreated HIV-1 infections, we were unable to detect HIV-1 superinfection, even though the involved individuals were at high risk for second strain acquisition. We therefore conclude that although superinfection can occur in a few cases, it is a rare event, and the vast majority of recombinant HIV-1s characterized to date resulted from acute coinfections, rather than superinfection.

Brazil↗
PubMed2005

Antiretroviral drug resistance among patients with human immunodeficiency virus who act as sources or potential sources in occupational accidents involving healthcare workers.

OBJECTIVE: To determine human immunodeficiency virus (HIV) type 1 genotypic antiretroviral drug resistance profiles of patients presenting a risk or potential risk for occupational exposure of healthcare workers. DESIGN: Observational survey involving HIV-infected patients. Blood samples collected from source-patients and potential source-patients underwent HIV-1 genotypic antiretroviral resistance testing and determination of CD4 counts and viral load. Affected healthcare workers were monitored for 6 months after exposure. SETTING: The survey was conducted in a tertiary-care hospital located in Sao Paulo, Brazil. Sao Paulo is considered the epicenter of the HIV-acquired immunodeficiency (AIDS) virus epidemic in Brazil. PARTICIPANTS: Source-patients, potential source-patients, and affected healthcare workers. RESULTS: A total of 371 occupational exposures to biological materials were reported, 46 (12.3%) of which were from HIV-seropositive source-patients. Samples from 18 source-patients and 26 patients considered "potential sources for accidents" were analyzed. Of these 44 samples, 18 (41%) presented resistance-related mutations in reverse transcriptase, protease, or both. Of these 18 samples, 16 (89%) had resistance to drugs included in the prophylactic schedule recommended by the Brazilian Ministry of Health. CONCLUSIONS: Use of the Centers for Disease Control and Prevention-Brazilian post-exposure prophylaxis regimen will result in the administration of antiretroviral agents to which the source HIV-1 isolate will often be resistant. Therefore, it would be advisable to carefully investigate the history of use of antiretroviral agents by source-patients and adjust the prophylactic therapy based on those data and, subsequently, the results of resistance testing.

Adult↗
PubMed2005

Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and f recombinants in São Paulo, Brazil.

Recombination is one of the major mechanisms contributing to human immunodeficiency virus type 1 (HIV-1) variability. Analysis of pol gene sequences of 215 HIV-1 samples from São Paulo, Brazil classified 189 sequences as subtype B (87.9%), 8 sequences as subtype F (3.7%), and 18 sequences (8.4%) as B/F recombinants. After the analysis of the pol gene, a subset of six recombinant samples composed of sequences with a related recombinant pol structure was selected for full-length genome analysis to identify a possible circulating recombinant form. According to full-length genome analysis, recombination was higher in gag, protease, reverse transcriptase, integrase, and vif. Identification of many distinct recombinant forms and the absence of an identifiable HIV-1 circulating recombinant form suggest that a high frequency of dual infections between HIV-1 subtypes B and F is occurring in São Paulo, Brazil.

Brazil↗
PubMed2005

Duplication of peri-kappaB and NF-kappab sites of the first human immunodeficiency virus type 2 (HIV-2) transmission in Brazil.

After the identification of HIV-2 in 1986, most of the cases reported have been concentrated in West Africa. We identified a case of HIV-2 infection in São Paulo, Brazil of a 45-year-old female who presented with Pneumocystis carinii pneumonia, with a CD4 count of 22 cells/ml. DNA samples from this patient were subjected to end-point PCR amplification of the LTR region. Clones were sequenced and subjected to phylogenetic analyses. All clones were subtype A related, and four presented an insertion, corresponding to an extra NF-kappaB site. This is the first confirmed case report of an HIV-2-infected subject identified in Brazil whose transmission occurred within the country. Furthermore, the NF-kappaB duplication would potentially be associated with an increase in viral cytopathogenicity. This raises concern for the need for permanent monitoring of the spread of HIV-2 in different areas of the world, even considering its lower rate of transmission and pathogenicity when compared to HIV-1.

Base Sequence↗
PubMed2004

Evidence for Selection of more Adapted Human Immunodeficiency Virus Type 1 Recombinant Strains in a Dually Infected Transfusion Recipient.

Human immunodeficiency virus type-1 (HIV-1) genetic diversity is one of the remarkable characteristics of these viruses, and the mechanisms involved in the selective forces driving HIV-1 evolution are of great interest. Samples from hosts infected with multiple distinct strains represent a valuable in vivo resource to investigate the role of recombination in the natural evolution of HIV-1. This work describes a detailed study regarding the evolution of the envelope gene (env) (C2-V5 region) in a dually infected child who received blood transfusions simultaneously from two distinct HIV-1 infected donors. In this study, we were able to directly compare the data obtained from the dually infected recipient with data obtained from two other singly HIV-1 infected children who had received blood transfusion from each of the two donors. Sequences from the singly infected children clustered into two distinct groups, each related to the respective donor-derived sequence by phylogenetic analysis, and hence were consistent with the epidemiological data. In the case of the dually infected child, a high degree of recombination between the two donor-derived sequences was observed at the C2-V3 region, whereas in the V4-V5 region selection of only one derived donor sequence was seen. Measurement of nonsynonymous versus synonymous substitution rates at each region revealed that negative selection was the main evolutionary force acting on the viral population of the dually infected child, regardless of the genetic mechanism by which each region evolved. Based on direct comparison with data obtained for the two singly infected children we propose that the higher amount of viral diversity observed in HIV-1 multi-infection events, as in the case of the dually infected patient, might contribute to maximizing selective advantage and possibly minimizing immune response. We conclude that recombination shaped by selective forces may increase the adaptive potential of HIV-1.

Adaptation, Physiological↗
PubMed2003

Frequency of polymorphisms of genes coding for HIV-1 co-receptors CCR5 and CCR2 in a Brazilian population.

Entry of human immunodeficiency type 1 virus (HIV-1) into target cells requires both CD(4)and one of the chemokine receptors. Viruses predominantly use one, or occasionally both, of the major co-receptors CCR5 and CXCR4, although other receptors, including CCR2B and CCR3, function as minor co-receptors. A 32-nucleotide deletion (D32) within the b-chemokine receptor 5 gene (CCR5) has been described in subjects who remain uninfected despite extensive exposition to HIV-1. The heterozygous genotype delays disease progression. This allele is common among Caucasians, but has not been found in people of African or Asian ancestry. A more common transition involving a valine to isoleucine switch in transmembrane domain I of CCR2B (64I), with unknown functional consequences, was found to delay disease progression but not to reduce infection risk. As the Brazilian population consists of a mixture of several ethnic groups, we decided to examine the genotype frequency of these polymorphisms in this country. There were 11.5% CCR5 heterozygotes among the HIV-1 infected population and 12.5% among uninfected individuals, similar to data from North America and Western Europe. The prevalence of CCR2-64I homozygotes and heterozygotes was 0.06 and 15.2%, respectively, also similar to what is known for North America and Western Europe.

Brazil↗
PubMed2002

Genetic diversity and HIV-1 incidence estimation among cocaine users in São Paulo, Brazil.

We describe HIV-1 incidence and the prevalence of genetic subtypes among cocaine users in São Paulo, Brazil. A cross-sectional HIV-1 survey was carried out among 839 current cocaine users attending seven drug treatment units in the São Paulo metropolitan area from 1997 to 1998. HIV-1 subtyping was performed among 41 positive individuals using the heteroduplex mobility assay and DNA sequencing. Participants were mainly male (95.7%) with a history of previous imprisonment (54%), and the mean age was 26.9 years (SD = 7.2). The majority (64.4%) were current crack cocaine users, and 82.1% of the total participants were noninjectors. HIV-1 seroprevalence was 4.9% (95% confidence interval [CI], 3.6%-6.6%), and the incidence (estimated by the sensitive/less-sensitive immunoassay testing strategy) was 0.71% per year (95% CI, 0.07-3.03). HIV-1 subtype B was predominant (90.3%), followed by subtype F. There was no statistically significant association between HIV-1 subtype and specific route of drug administration. Our incidence data show evidence of recent HIV-1 transmission among cocaine users, mainly among noninjectors. Detection of recently infected HIV-1 cases linked to genetic diversity analysis may provide baseline information for public health interventions in this sentinel group.

Adult↗