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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.

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.

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.

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.

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.

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.