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.

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.

In Brazil, where three distinct HIV-1 subtypes (B, F, and C) cocirculate, a significant portion of the HIV-infected population has been exposed to antiretroviral drugs. This study analyzes the antiretroviral resistance profiles of HIV-1-infected individuals failing antiretroviral therapy. Genotypic resistance profiles of 2474 patients presenting virologic failure to antiretroviral therapy in the city of Sã o Paulo, Brazil, were generated and analyzed. Resistance mutations to protease inhibitors and nucleoside reverse transcriptase inhibitors were less common in subtype C viruses, whereas nonnucleoside reverse transcriptase inhibitor resistance mutations were less common in subtype F viruses. The thymidine analog mutation pathway known as pathway 1 was more prevalent in subtype B viruses than in subtype C viruses, whereas pathway 2 was more prevalent in subtype C viruses. Selected resistance mutations varied according to subtype for all three classes of antiretrovirals. We describe two distinct pathways of nonnucleoside reverse transcriptase inhibitor resistance (to nevirapine and efavirenz). Although cross-resistance to etravirine should occur more frequently among individuals failing nevirapine treatment, the prevalence of cross-resistance to etravirine, darunavir, and tipranavir was found to be low. We found that increases in the number of resistance mutations will be related to increases in the viral load. Special attention should be given to resistance profiles in non-B subtype viruses. The accumulation of knowledge regarding such profiles in the developing world is desirable.

Entry of human immunodeficiency type 1 virus (HIV-1) into target cells requires both CD

Quinolones (nalidixic acid--NAL, norfloxacin--NOR, ciprofloxacin--CIP and gatifloxacin--GAT) were tested against Escherichia coli isolated from urine (385 patient samples) by disk diffusion (DD) and agar dilution (AD) methods. Fifty-three samples (13.8%) were classified as resistant to at least one of the quinolones tested. CIP and NOR susceptibilities were the same (91.4%) and they were similar to GAT (92.7%). Susceptibility to NAL, detected by the disk diffusion method, was used to predict susceptibility to NOR, CIP and GAT by the agar dilution method. The sensitivity and specificity of NAL were 100% and 95%, respectively. Twelve samples were analyzed for mutations in the quinolone resistance-determining region (QRDR) of the gyrA and parC genes. Sequencing of these genes failed to find any mutations in the quinolone-sensitive isolates. However, three mutations were observed in the isolates resistant to all the quinolones tested--two in gyrA and one in parC. A single mutation in gyrA was found in the strains that were resistant to nalidixic acid but fluoroquinolone-sensitive. These findings support the suggestion that NAL could be used as a marker for susceptibility to fluoroquinolones in routine microbiology laboratories. The overall resistance rate to quinolones in the present study was 13.8%, which is higher than that observed in other studies carried out in developed countries. Our findings serve as a warning that resistance to this group of antimicrobial agents is increasing.