Human immunodeficiency virus type 1 (HIV-1) genotyping in Rio de Janeiro, Brazil: assessing subtype and drug-resistance associated mutations in HIV-1 infected individuals failing highly active antiretroviral therapy

HIV Reverse Transcriptase and Protease Genes Variability Can Be a Biomarker Associated with HIV and Hepatitis B or C Coinfection

Variability of the HIV reverse transcriptase (RT) and protease (PR) genes has been used as indicators of drug resistance and as a mean to evaluate phylogenetic relationships among circulating virus. However, these studies have been carried in HIV mono-infected populations. The goal of this study was to evaluate, for the first time, the HIV PR and RT sequences from HIV/HBV and HIV/HCV co-infected patients. HIV PR and RT genes were amplificated and sequenced to resistance analysis. The bioinformatics analysis was performed to infer about sequences clustering and molecular evolution. The results showed that the most frequent amino acid substitutions in RT were L214F (67.6%), I135T (55.9%), and in PR was V15I (41.2%). The molecular clock analysis showed that the HIV circulating in co-infected patients were separated in two clusters in the years 1999-2000. Some patients included as HIV mono-infected according patients' medical records and inside the co-infected cluster were, in fact, co-infected by PCR analysis. Analysis of the decision trees showed susceptibility to lamivudine and emtricitabine were important attribute to characterize co-infected patients. In conclusion, the results obtained in this study suggest, for the first time, that HIV RT and PR genes variability could be a genetic biomarker to coinfection.

An overview of the molecular and epidemiological features of HIV-1 infection in two major cities of Bahia state, Brazil

BACKGROUND

The high mutation rate of the human immunodeficiency virus (HIV) has created a public health challenge because the use of antiretroviral drugs can generate selective pressure that drives resistance in these viruses.

OBJECTIVE

The aim of this work was to characterise the molecular and epidemiological profile of HIV in Bahia, Brazil.

METHODS

DNA sequences from regions of HIV gag, pol, and env genes were obtained from previous studies performed in this area between 2002 and 2012. Their genotype and drug-resistance mutations were identified using bioinformatics tools. Clinical and epidemiological data were analysed.

FINDINGS

Among 263 individuals (46.4% male), 97.5% were asymptomatic and 49.1% were receiving treatment. Most of the individuals were 31 to 40 years old (36.9%) and infected through heterosexual contact (40.7%). The predominant genotype was B (68.1%) followed by BF recombinants (18.6%). Among the individuals infected with either F or BF genotypes, 68.4% were women and 76.8% were infected through heterosexual transmission. The prevalence of associated mutations conferring antiretroviral resistance was 14.2%, with 3.8% of all mutations conferring resistance to protease inhibitors, 9.43% to nucleoside reverse transcriptase inhibitors, and 8.5% to non-nucleoside reverse transcriptase inhibitors. Drug resistance was higher in individuals receiving treatment (26.1%) than in the drug-naïve (4.3%) individuals.

MAIN CONCLUSIONS

This study will contribute to the understanding and monitoring of HIV epidemic in this Brazilian region.

HIV-1 genetic diversity and antiretroviral drug resistance among individuals from Roraima state, northern Brazil

The HIV-1 epidemic in Brazil has spread towards the Northern country region, but little is known about HIV-1 subtypes and prevalence of HIV strains with resistance mutations to antiretrovirals in some of the Northern states. HIV-1 protease (PR) and reverse transcriptase (RT) sequences were obtained from 73 treatment-naive and -experienced subjects followed between 2013 and 2014 at a public health reference unit from Roraima, the northernmost Brazilian state. The most prevalent HIV-1 clade observed in the study population was the subtype B (91%), followed by subtype C (9%). Among 12 HIV-1 strains from treatment-naïve patients, only one had a transmitted drug resistance mutation for NNRTI. Among 59 treatment-experienced patients, 12 (20%) harbored HIV-1 strains with acquired drug resistance mutations (ADRM) that reduce the susceptibility to two classes of antiretroviral drugs (NRTI and NNRTI or NRTI and PI), and five (8%) harbored HIV-1 strains with ADRM that reduced susceptibility to only one class of antiretroviral drugs (NNRTI or PI). No patients harboring HIV strains with reduced susceptibility to all three classes of antiretroviral drugs were detected. A substantial fraction of treatment-experienced patients with (63%) and without (70%) ADRM had undetectable plasma viral loads (<40 copies/ml) at the time of sampling. Among treatment-experienced with plasma viral loads above 2,000 copies/ml, 44% displayed no ADRM. This data showed that the HIV-1 epidemic in Roraima displayed a much lower level of genetic diversity and a lower prevalence of ADRM than that described in other Brazilian states.

Impact of HIV-1 Subtypes on AIDS Progression in a Brazilian Cohort

Viral and host factors are known to play a role in the different patterns of AIDS progression. The cocirculation of HIV-1 subtypes B, F1, B_BR, and BF1; the occasional detection of HIV-1 subtype D; and an increasing prevalence of subtype C and other recombinant forms have been described in Rio de Janeiro, Brazil. The aim of this study was to evaluate the potential association of HIV-1 subtypes circulating among HIV-1+ individuals in Rio de Janeiro with AIDS disease progression. For this purpose, 246 HIV-1 individuals under clinical and laboratory follow-up from 1986 to 2011 were classified according to their progression to AIDS in typical progressors (n = 133), rapid progressors (n = 95), and long-term nonprogressors (n = 18). The env-gp120 region was amplified and sequenced. Neighbor-joining phylogenetic inferences were performed in Mega 6 and bootscan analysis was performed in Simplot 3.5.1. The Kaplan-Meier method and Cox modeling were performed to determine the time until an AIDS-defining event based on the HIV-1 subtypes/variants. Similar AIDS progression rates were observed among individuals infected with HIV-1 subtype B and variant B_BR. However, a direct association between more rapid AIDS progression and HIV-1 subtypes, D and BF1, was confirmed in the multivariate analysis, corroborating previous results. Our findings contribute to the investigation of the possible influence of HIV-1 subtypes in AIDS outcome.

Single Nucleotide Polymorphisms in Cellular Drug Transporters Are Associated with Intolerance to Antiretroviral Therapy in Brazilian HIV-1 Positive Individuals

Adverse reactions are the main cause of treatment discontinuation among HIV+ individuals. Genes related to drug absorption, distribution, metabolism and excretion (ADME) influence drug bioavailability and treatment response. We have investigated the association between single nucleotide polymorphisms (SNPs) in 29 ADME genes and intolerance to therapy in a case-control study including 764 individuals. Results showed that 15 SNPs were associated with intolerance to nucleoside and 11 to non-nucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs), and 8 to protease inhibitors (PIs) containing regimens under alpha = 0.05. After Bonferroni adjustment, two associations remained statistically significant. SNP rs2712816, at SLCO2B1 was associated to intolerance to NRTIs (OR_GA/AA = 2.37; p = 0.0001), while rs4148396, at ABCC2, conferred risk of intolerance to PIs containing regimens (OR_CT/TT = 2.64; p = 0.00009). Accordingly, haplotypes carrying rs2712816A and rs4148396T alleles were also associated to risk of intolerance to NRTIs and PIs, respectively. Our data reinforce the role of drug transporters in response to HIV therapy and may contribute to a future development of personalized therapies.

Extensive variation in drug-resistance mutational profile of Brazilian patients failing antiretroviral therapy in five large Brazilian cities

Background

Development of drug-resistance mutations is the main cause of failure in antiretroviral therapy. In Brazil, there is scarce information on resistance pattern for patients failing antiretroviral therapy.

Objectives

To define the HIV mutational profile associated with drug resistance in Brazilian patients from 5 large cities, after first, second or further failures to antiretroviral therapy.

Methods

We reviewed genotyping results of 1520 patients failing therapy in five Brazilian cities. Frequency of mutations, mean number of active drugs, viral susceptibility to each antiretrovirals drug, and regional differences were assessed.

Results

Mean time of antiretrovirals use was 22.7 ± 41.1 months. Mean pre-genotyping viral load was 4.2 ± 0.8 log (2.1 ± 2.0 after switching antiretrovirals). Mean number of remaining active drugs was 9.4, 9.0, and 7.9 after 1st, 2nd, and 3rd failure, respectively. We detected regional variations in drug susceptibility: while BA and RS showed the highest (∼40%) resistance level to ATV/r, FPV/r and LPV/r, in the remaining cities it was around half of this rate. We detected 90% efavirenz/nevirapine resistance in SP, only 45% in RS, and levels between 25% and 30% in the other cities. Regarding NRTI, we found a similar pattern, with RJ presenting the highest, and CE the lowest susceptibility rates for all NRTI. Zidovudine resistance was detected in only 3% of patients in RJ, against 45–65% in the other cities. RJ and RS showed 3% resistance to tenofovir, while in CE it reached 55%. DRV/r (89–97%) and etravirine (61–85%) were the most active drugs, but again, with a wide variation across cities.

Conclusions

The resistance mutational profile of Brazilian patients failing antiretroviral therapy is quite variable, depending on the city where patients were tested. This variation likely reflects distinctive choice of antiretrovirals drugs to initiate therapy, adherence to specific drugs, or circulating HIV-1 strains. Overall, etravirine and DRV/r remain as the most active drugs.

Short Communication: Reassessing the Origin of the HIV-1 CRF02_AG Lineages Circulating in Brazil

HIV-1 CRF02_AG is responsible for at least 8% of the HIV-1 infections worldwide and is distributed mainly in West Africa. CRF02_AG has recently been reported in countries where it is not native, including Brazil. In a previous study including 10 CRF02_AG Brazilian samples, we found at least four independent introductions and two autochthonous transmission networks of this clade in Brazil. As more CRF02_AG samples have been identified in Brazil, we performed a new phylogeographic analysis using a larger dataset than before. A total of 20 Brazilian (18 from Rio de Janeiro and two from São Paulo) and 1,485 African HIV-1 CRF02_AG pol sequences were analyzed using maximum likelihood (ML). The ML tree showed that the Brazilian sequences were distributed in five different lineages. The Bayesian phylogeographic analysis of the Brazilian and their most closely related African sequences (n = 212) placed the origin of all Brazilian lineages in West Africa, probably Ghana, Senegal, and Nigeria. Two monophyletic clades were identified, comprising only sequences from Rio de Janeiro, and their date of origin was estimated at around 1985 (95% highest posterior density: 1979-1992). These results support the existence of at least five independent introductions of the CRF02_AG lineage from West Africa into Brazil and further indicate that at least two of these lineages have been locally disseminated in the Rio de Janeiro state over the past 30 years.

The Evolving Genotypic Profile of HIV-1 Mutations Related to Antiretroviral Treatment in the North Region of Brazil

HIV related mutations can be associated with decreased susceptibility to antiretrovirals and treatment failures. There is scarce information about HIV mutations in persons failing HIV treatment in North of Brazil. Our aim was to evaluate evolution of HIV subtypes and mutations patterns related to antiretroviral therapy in this region. We investigated HIV resistance profile in adults failing antiretroviral regimen in Northern Brazil from January, 2004, through December, 2013. Genotype data was evaluated through Stanford University algorithm. There were 377 genotypes from different individuals to evaluate. Resistance mutations were similar to worldwide reports and related to antiretroviral exposure. Most prevalent mutations in the reverse transcriptase gene were M184V (80.1%) and K130N (40.6%). Thymidine associated mutations were more frequent in multiexperienced patients. Most common protease mutations were M46I, V82A, I54V, L90M, I84V, M46L, and L76V. Subtype B was the most prevalent (90.7%). There were differences between subtypes B and non-B mutations. We documented for the first time subtypes and patterns of HIV associated mutations in Northern Brazil. A1 subtype was identified for the first time in this area. Depending on drug regimen and how experienced the patient is, an empirical switch of a failing antiretroviral treatment could be a reasonable option.

Multifaceted roles of cysteinyl leukotrienes in eliciting eosinophil granule protein secretion

Cysteinyl leukotrienes (cysLTs) are cell membrane-impermeant lipid mediators that play major roles in the pathogenesis of eosinophilic inflammation and are recognized to act via at least 2 receptors, namely, cysLT1 receptor (cysLT1R) and cysLT2 receptor (cysLT2R). Eosinophils, which are granulocytes classically associated with host defense against parasitic helminthes and allergic conditions, are distinguished from leukocytes by their dominant population of cytoplasmic crystalloid (also termed secretory, specific, or secondary) granules that contain robust stores of diverse preformed proteins. Human eosinophils are the main source of cysLTs and are recognized to express both cysLTs receptors (cysLTRs) on their surface, at the plasma membrane. More recently, we identified the expression of cysLTRs in eosinophil granule membranes and demonstrated that cysLTs, acting via their granule membrane-expressed receptors, elicit secretion from cell-free human eosinophil granules. Herein, we review the multifaceted roles of cysLTs in eliciting eosinophil granule protein secretion. We discuss the intracrine and autocrine/paracrine secretory responses evoked by cysLTs in eosinophils and in cell-free extracellular eosinophil crystalloid granules. We also discuss the importance of this finding in eosinophil immunobiology and speculate on its potential role(s) in eosinophilic diseases.

Temporal trends and molecular epidemiology of HIV type 1 infection in Rio de Janeiro, Brazil

HIV-1 molecular epidemiology studies carried out in Rio de Janeiro, Brazil have identified the prevalence of subtypes B, F1 and BF1 recombinants. A high percentage of HIV-1 subtype B isolates in Rio de Janeiro harbor the GWG motif at the V3 tip (B'' variant) instead of the canonical GPG motif (B variant). To trace the dynamics of the HIV-1 variants over time in different exposure categories in Rio de Janeiro, the HIV-1 proviral DNA from heterosexual men (HET) and men who have sex with men (MSM) from two distinct time periods (1990-1992 and 2008-2010) were extracted, and the env-gp120 region was amplified. Neighbor-joining phylogenetic analysis was performed to determine the viral subtype, and Bayesian analysis was used to trace the HIV-1 transmission networks. A predominance of subtype B was observed in both study periods, independent of the exposure risk category. An increase of non-B subtypes was observed in the HET group, but these subtypes were maintained among the MSM group. The distribution of HIV-1 subtype B signatures in the first and second periods studied were, respectively, HET (GPG) [44.8-51.5%], (GWG) [13.8-33.3%], and (GXG) [41.4-15.2%] and MSM (GPG) [34-50%], (GWG) [55.3-30.6%], and (GXG) [10.7-19.4%]. In the first period, an association between GWG and MSM was verified while a significant reduction of this association was observed during the second period. The phylogenetic tree and the BaTS program detected the clustering of isolates only according to the B signatures but not by exposure risk category. Our findings indicate a stable prevalence of HIV-1 subtypes B and F over time in Rio de Janeiro and further suggest that the B'' subclade of subtype B was possibly introduced into the MSM group in this area of Brazil.

Tracing the origin and northward dissemination dynamics of HIV-1 subtype C in Brazil

Previous studies indicate that the HIV-1 subtype C epidemic in southern Brazil was initiated by the introduction of a single founder strain probably originating from east Africa. However, the exact country of origin of such a founder strain as well as the origin of the subtype C viruses detected outside the Brazilian southern region remains unknown. HIV-1 subtype C pol sequences isolated in the southern, southeastern and central-western Brazilian regions (n = 209) were compared with a large number (n ~ 2,000) of subtype C pol sequences of African origin. Maximum-likelihood analyses revealed that most HIV-1 subtype C Brazilian sequences branched in a single monophyletic clade (CBR-I), nested within a larger monophyletic lineage characteristic of east Africa. Bayesian analyses indicate that the CBR-I clade most probably originated in Burundi and was introduced into the Paraná state (southern region) around the middle 1970s, after which it rapidly disseminated to neighboring regions. The states of Paraná and Santa Catarina have been the most important hubs of subtype C dissemination, and routine travel and spatial accessibility seems to have been the major driving forces of this process. Five additional introductions of HIV-1 subtype C strains probably originated in eastern (n = 2), southern (n = 2) and central (n = 1) African countries were detected in the Rio de Janeiro state (southeastern region). These results indicate a continuous influx of HIV-1 subtype C strains of African origin into Brazil and also unveil the existence of unrecognized transmission networks linking this country to east Africa.

HIV type 1 virological response and prevalence of HIV type 1 drug resistance among patients receiving antiretroviral therapy, Shandong, China

Shandong province has been providing antiretroviral therapy (ART) to eligible HIV/AIDS patients since 2003 using first-line regimens. We conducted a cross-sectional study to assess virological response and resistance development from ART patients. Between 2006 and 2008, blood was collected from 143 ART patients. Viral load (VL) was determined with a detection limit of 50 copies/ml; those with detectable VL were genotyped with dried plasma spots using a broadly sensitive genotyping assay. Resistance mutations were identified using the Stanford HIV drug resistance database. Of the 143 patients, 72% [95% confidence interval (CI): 65.9-78.2] suppressed their VL to <50 copies/ml. Genotyping analysis of the remaining 40 patients revealed that 21 (53%, CI: 37.0-68.0) harbored one or more mutations. The most common mutations were thymidine-analog mutations (22.5%) and M184V (10%) to nucleoside reverse transcriptase inhibitors (NRTIs), and V106I/A /M (17.5%), Y181C (15%), and H221Y (12.5%) to non-NRTIs (NNRTIs); 13 patients had mutations to both NRTIs and NNRTIs. Patients with VL >1000 copies/ml appear to harbor more mutations than those with VL between 50 and 1000 (62.1% vs. 27.3%, p>0.05). Resistance mutations were intensified among 10 patients for whom two sequential specimens were obtained and accumulation of resistance mutations predicted compromised treatment outcomes and future drug selections. This study provides a snapshot of the virological responses and resistance profiles for patients on first-line regimens, indicating that patient monitoring is a critical component in preventing the accumulation of resistance mutations among patients failing their regimens and thus maintaining the effectiveness of the first-line regimens.

Evidence of multiple introductions and autochthonous transmission of the HIV type 1 CRF02_AG clade in Brazil

HIV-1 CRF02_AG is the most prevalent intersubtype recombinant form worldwide. Six HIV-1 samples from patients living in Rio de Janeiro, Brazil, were subtyped as CRF02_AG at the pol gene between 2004 and 2011. To trace the origin of these viruses, they were compared with 793 CRF02_AG pol sequences of African origin and another four Brazilian CRF02_AG pol sequences previously described. Phylogenetic analysis reveals that there have been at least four introductions of the CRF02_AG clade in Brazil, as signified by the presence of four phylogenetically distinct lineages, probably originated from western African countries (Benin, Ghana, and Guinea-Bissau). At least two CRF02_AG Brazilian lineages were successful in getting established and disseminated throughout the Rio de Janeiro state, with evidence of both horizontal and vertical transmission. Continuous epidemiological surveillance of HIV-1 strains circulating in Brazil is of paramount importance to the early detection of newly emerging viral lineages.

Drug resistance mutations in HIV type 1 isolates from patients failing antiretroviral therapy in Morocco

The emergence of viral-resistant strains is a major problem for the medical management of HIV-infected individuals. The aim of this study was to characterize viral subtypes and drug-resistance mutations (DRMs) in HIV-1 isolates from patients failing antiretroviral therapy (ART). A total of 45 HIV-1-infected patients failing ART were enrolled. The viral RT and Prot genes were amplified and sequenced to determine subtypes and potential DRMs. The subtype distribution was 74% subtype B, 11% subtype A, 9% CRF02-AG, 4% subtype G, and 2% subtype C. Virus samples from 34% of the patients had no DRM while 53%, 27%, and 2% of samples carried at least one DRM conferring resistance to drugs of one, two, or three classes, respectively. DRMs were observed in 50% of the patients infected with non-B strains. The prevalence of nucleoside transcriptase inhibitor (NRTI) mutations was 48%, M184V being largely predominant. The prevalence of nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations was 13%, with K103N present in 57% of samples from NNRTIs-exposed patients. The prevalence of protease inhibitor (PI) mutations was 22%, with major mutations V82A and M46I seen in 16% and 11% of viruses from PI-exposed individuals, respectively. Our study shows the emergence of DRMs in HIV-1 isolates from Moroccan patients failing ART. Although not surprising, the data plead for longitudinal surveys of the dynamics of emergence of DRMs (with a focus on multidrug resistance) in treated patients and circulation of resistant HIV-1 strains in this country.

Phylogeographic analysis of HIV-1 subtype C dissemination in Southern Brazil

The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Paraná). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianópolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Paraná state). This analysis further suggested that Florianópolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r² = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades.

Detection of distinct human immunodeficiency virus type 1 circulating recombinant forms in northeast Brazil

The extraordinary genetic diversity and immune evasion of human immunodeficiency virus (HIV) pose significant challenges for vaccine development and antiretroviral therapy efficacy. The objective of this study was to characterize the molecular profile of HIV-1 epidemic in Salvador, Bahia, Brazil, determining the genetic subtypes and the presence of antiretroviral resistance mutations. HIV-1 pol DNA sequences from 57 individuals infected with HIV were obtained by PCR, followed by sequencing. The subtypes were determined by phylogenetic analyses and the intersubtype recombination was investigated by bootscanning. The pol subtypes were compared with gag and env subtypes. Antiretroviral susceptibility was evaluated through the Stanford HIV resistance Database. The subtypes frequencies were: 77.2% of subtype B, 1.8% of subtype F1, and 21.0% of BF recombinant forms. Two intergenic and three intragenic BF recombinant patterns were observed. Six (10.5%) viruses were related to CRF28/CRF29, two were related to CRF12 (3.5%), and one (1.8%) was CRF39. Fourteen (24.6%) strains carried one or more mutations associated with at least intermediate resistance: 24.6% had resistance to nucleoside reverse transcriptase inhibitors, 21.0% to non-nucleoside reverse transcriptase inhibitors, and 7% to protease inhibitors. The substitutions I54V (7.0%), M184V (14.0%), and K103N (10.5%) were the most frequent within each class of drugs. The results show a high diversity of BF genotypes and a lower prevalence of major reverse transcriptase and protease drug resistance mutations in Salvador, compared with other regions of Brazil. These findings may contribute to improve treatment strategies of patients infected with HIV-1 from this Brazilian region.

Distribution of human immunodeficiency virus type 1 subtypes in the State of Amazonas, Brazil, and subtype C identification

Few studies have reported the molecular epidemiological characterization of HIV-1 in the Northern region of Brazil. The present study reports the molecular and epidemiological characterization of 31 HIV-1 isolates from blood donors from the State of Amazonas who donated blood between April 2006 and March 2007. Serum/plasma samples from all donors were screened for HIV antibodies by ELISA and the results confirmed by Western blot analysis. Genomic DNA was extracted from the buffy coat using the Super Quik-Gene-DNA Isolation kit. Nested PCR was performed on the env, gag, and pol regions of HIV-1 using the Gene Amp PCR System 9700. Sequencing reactions were performed using the inner PCR primers and the DYEnamic™ ET Dye Terminator Kit, and phylogenetic analysis was performed using the gag, pol, and env gene sequences. We collected samples from 31 blood donors who tested positive for HIV-1 in confirmatory experiments. The male:female ratio of blood donors was 3.4:1, and the mean age was 32.4 years (range: 19 to 61 years). Phylogenetic analysis showed that subtype B is the most prevalent among Northern Brazilian HIV-1-seropositive blood donors. One HIV-1 subtype C and one circulating recombinant form (CRF_BF) of HIV-1 were identified in the State of Amazonas. This is the first study showing the occurrence of a possible “homogenous” subtype C in this region of Brazil. This finding could contribute to a better characterization of the HIV-1 strains that circulate in the country. Key words: HIV-1; Subtypes; Phylogenetic analysis; Blood donors; Molecular and epidemiological characterization

Resistance-associated mutation prevalence according to subtypes B and non-B of HIV type 1 in antiretroviral-experienced patients in Minas Gerais, Brazil

The emergence of resistance-associated mutations to the antiretroviral agents and the genetic variability of HIV-1 impose challenges to therapeutic success. We report the results of genotype testing assays performed between 2002 and 2006 in 240 antiretroviral-experienced patients followed up in an HIV reference center in Brazil. Drug resistance mutations and viral subtypes were assessed through the algorithms from the Brazilian Genotyping Network (RENAGENO-Brazil) and from Stanford University. Mutation 184VI was the most prevalent (70%) and the thymidine analogue mutations that appeared most frequently were 215FY, 41L, 67N, and 210W, in this order. Among nonnucleoside reverse transcriptase inhibitor mutations, 103NS (32.5%) stood out. HIV subtype B was identified in 184 patients (76.7%). A significant increasing trend in the prevalence of non-B subtypes was observed during the study period (p=0.004). The main differences in prevalence of mutations among HIV-1 subtypes were related to viral protease, with 20MRI, 36I, and 89IMT more prevalent among non-B subtypes, and 84V, 10FR, 63P, 71LTV, and 77I more common in subtype B (p<0.05). Most mutations to etravirine had a prevalence lower than 10%, but at least one mutation to this drug was observed in 45% of the patients. In only 11 patients (4.6%) three mutations to etravirine were verified. Regional surveillance of the resistance profile and HIV-1 subtypes is crucial in the context of public health, to prevent the transmission of resistant strains and to guide the introduction of new drugs in a specific population.

Concurrent partnerships and HIV: an inconvenient truth

The strength of the evidence linking concurrency to HIV epidemic severity in southern and eastern Africa led the Joint United Nations Programme on HIV/AIDS and the Southern African Development Community in 2006 to conclude that high rates of concurrent sexual partnerships, combined with low rates of male circumcision and infrequent condom use, are major drivers of the AIDS epidemic in southern Africa. In a recent article in the Journal of the International AIDS Society, Larry Sawers and Eileen Stillwaggon attempt to challenge the evidence for the importance of concurrency and call for an end to research on the topic. However, their "systematic review of the evidence" is not an accurate summary of the research on concurrent partnerships and HIV, and it contains factual errors concerning the measurement and mathematical modelling of concurrency.Practical prevention-oriented research on concurrency is only just beginning. Most interventions to raise awareness about the risks of concurrency are less than two years old; few evaluations and no randomized-controlled trials of these programmes have been conducted. Determining whether these interventions can help people better assess their own risks and take steps to reduce them remains an important task for research. This kind of research is indeed the only way to obtain conclusive evidence on the role of concurrency, the programmes needed for effective prevention, the willingness of people to change behaviour, and the obstacles to change.

Analysis of HIV-1 BF pr/rt recombinant strains from Rio de Janeiro/Brazil reveals multiple unrelated mosaic structures

Due to the co-circulation of HIV-1 subtypes B and F1 in Brazil, a large variety of unique BF1 recombinant forms (URFs_BF1) and four circulating BF1 recombinant forms (CRF28, CRF29, CRF39 and CRF40) have been described. The aim of this study was to investigate mosaic structure and phylogenetic relationship among several BF1 (protease-reverse transcriptase, pr/rt) recombinant sequences obtained from a group of patients from Rio de Janeiro, Brazil, from 1994 to 2005. Phylogenetic relationships were estimated by Bayesian and SplitsTree methods. Recombination breakpoints were analyzed by Bootscan. Those samples presenting the same recombinant pattern in the pr/rt region were investigated in the integrase (int) and envelope (env) regions as a screening method for the detection of potential new CRFs candidates. Third out of 61 pr/rt HIV-1 BF1 recombinant sequences analyzed depicted unique recombinant structures and were classified URFs_BF1. The other 31 samples segregated in eight well-supported phylogenetic clusters composed of at least three samples sharing the same recombination pattern. Analyses of the int and env regions from these 31 samples revealed that 11 samples were URFs_BF1. Three and four sequences corresponded, respectively, to the previously described CRF39 and CRF40. Three samples displayed a CRF28-like mosaic structure, and one sample a CRF29-like mosaic pattern. The other nine BF1 samples segregate in three distinct clusters with the same recombination profile and could represent good candidates for new CRFs_BF profiles. The HIV-1 BF1 epidemic in Rio de Janeiro is characterized by a high prevalence (67%) of URFs_BF1 and a low prevalence (4.9-6.6%) of each CRFs_BF previously identified in Brazil.

Assessing subtype and drug-resistance-associated mutations among antiretroviral-treated HIV-infected patients

BACKGROUND

Several studies have reported an increasing number of therapeutic failures with antiretroviral drugs in HIV-infected patients. The emergence of viral-resistant strains is a major problem for the medical management of infected individuals. The aim of this study is to determine viral subtypes and drug-resistance mutations among antiretroviral-treated HIV-infected patients.

METHODS

A total of 42 antiretroviral-treated but still viremic HIV-infected patients were enrolled. The HIV pol regions were amplified and sequenced to determine subtypes and antiretroviral-resistant mutations.

RESULTS

The subtype distribution was 48% A/D recombinants, 43% subtype B, 5% subtype A and 5% CRF01-AE recombinants. Drug-resistant mutations were most common in subtype B (53%) and A/D recombinant strains (44%). Virus samples from 19% of participants had no drug-resistant mutations; 2, 2 and 76% of samples carried one, two and at least three drug-resistant mutations, respectively. The prevalence of nucleoside transcriptase inhibitor mutations was 76%, with M184V and L74V present in 60 and 38% of samples, respectively. The prevalence of nonnucleoside transcriptase inhibitor mutations was 74%, with P225H present in 55% of study specimens. The prevalence of protease inhibitor mutations was 45%, with major mutation L90M seen in 33% and minor mutation A71V in 36% of samples. Of note, the P225H and A71V are 'minor' drug-resistance mutations conferring only minimal drug-resistance phenotypes in the absence of major mutations.

CONCLUSION

Our study found a high prevalence of drug-resistant mutations in Iranian HIV-infected patients. Our data support the need for continued surveillance of resistance patterns to help guide therapeutic approaches and limit transmission of these variants.

Cross-talk between macrophage migration inhibitory factor and eotaxin in allergic eosinophil activation forms leukotriene C₄-synthesizing lipid bodies

Recent studies have demonstrated an essential and nonredundant role for macrophage migration inhibitory factor (MIF) in asthma pathogenesis. Here we investigate the mechanisms involved in MIF-induced eosinophil activation. By using a model of allergic pulmonary inflammation, we observed that allergen challenge-elicited eosinophil influx, lipid body (also known as lipid droplets) biogenesis, and leukotriene (LT) C₄ synthesis are markedly reduced in Mif(-/-) compared with wild-type mice. Likewise, in vivo administration of MIF induced formation of new lipid bodies within eosinophils recruited to the inflammatory reaction site that corresponded to the intracellular compartment of increased LTC₄ synthesis. MIF-mediated eosinophil activation was at least in part due to a direct effect on eosinophils, because MIF was able to elicit lipid body assembly within human eosinophils in vitro, a phenomenon that was blocked by neutralization of the MIF receptor, CD74. MIF-induced eosinophil lipid body biogenesis, both in vivo and in vitro, was dependent on the cooperation of MIF and eotaxin acting in a positive-feedback loop, because anti-eotaxin and anti-CCR3 antibodies inhibit MIF-elicited lipid body formation, whereas eotaxin-induced lipid body formation is affected by anti-CD74 and MIF expression deficiency. Therefore, allergy-elicited inflammatory MIF acts in concert with eotaxin as a key activator of eosinophils to form LTC₄-synthesizing lipid bodies via cross-talk between CD74 and CCR3. Due to the effect of MIF on eosinophils, strategies that inhibit MIF activity might be of therapeutic value in controlling allergic inflammation.

HIV type 1 antiretroviral resistance mutations in subtypes B, C, and F in the City of São Paulo, Brazil

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 São 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.

Prevalence of antiretroviral drug resistance among treatment-naive and treated HIV-infected patients in Venezuela

An in-house, low-cost method was developed to determine the genotypic resistance of immunodeficiency virus type 1 (HIV-1) isolates. All 179 Venezuelan isolates analysed belonged to subtype B. Primary drug resistance mutations were found in 11% of 63 treatment-naïve patients. The prevalence of resistance in isolates from 116 HIV-positive patients under antiretroviral treatment was 47% to protease inhibitors, 65% to nucleoside inhibitors and 38% to non-nucleoside inhibitors, respectively. Around 50% of patients in the study harboured viruses with highly reduced susceptibility to the three classical types of drugs after only five years from their initial diagnoses.

Differences in resistance mutations among HIV-1 non-subtype B infections: a systematic review of evidence (1996-2008)

Ninety percent of HIV-1-infected people worldwide harbour non-subtype B variants of HIV-1. Yet knowledge of resistance mutations in non-B HIV-1 and their clinical relevance is limited. Although a few reviews, editorials and perspectives have been published alluding to this lack of data among non-B subtypes, no systematic review has been performed to date.With this in mind, we conducted a systematic review (1996-2008) of all published studies performed on the basis of non-subtype B HIV-1 infections treated with antiretroviral drugs that reported genotype resistance tests. Using an established search string, 50 studies were deemed relevant for this review.These studies reported genotyping data from non-B HIV-1 infections that had been treated with either reverse transcriptase inhibitors or protease inhibitors. While most major resistance mutations in subtype B were also found in non-B subtypes, a few novel mutations in non-B subtypes were recognized. The main differences are reflected in the discoveries that: (i) the non-nucleoside reverse transcriptase inhibitor resistance mutation, V106M, has been seen in subtype C and CRF01_AE, but not in subtype B, (ii) the protease inhibitor mutations L89I/V have been reported in C, F and G subtypes, but not in B, (iii) a nelfinavir selected non-D30N containing pathway predominated in CRF01_AE and CRF02_AG, while the emergence of D30N is favoured in subtypes B and D, (iv) studies on thymidine analog-treated subtype C infections from South Africa, Botswana and Malawi have reported a higher frequency of the K65R resistance mutation than that typically seen with subtype B.Additionally, some substitutions that seem to impact non-B viruses differentially are: reverse transcriptase mutations G196E, A98G/S, and V75M; and protease mutations M89I/V and I93L.Polymorphisms that were common in non-B subtypes and that may contribute to resistance tended to persist or become more frequent after drug exposure. Some, but not all, are recognized as minor resistance mutations in B subtypes. These observed differences in resistance pathways may impact cross-resistance and the selection of second-line regimens with protease inhibitors. Attention to newer drug combinations, as well as baseline genotyping of non-B isolates, in well-designed longitudinal studies with long duration of follow up are needed.

Genetic variability of human immunodeficiency virus-1 in Bahia state, Northeast, Brazil: high diversity of HIV genotypes

The HIV-1 genetic variability in Bahia state, Brazil, was investigated. DNA samples from 229 and 213 HIV-1-infected individuals were analyzed using the heteroduplex mobility assay (HMA) in gag and env fragments, respectively. One hundred seventy-five samples were characterized in both genes. Thirty-two subtype F and BF recombinant viruses were sequenced and analyzed by phylogenetic methods. The combination of HMA and sequencing results showed that seven different HIV-1 genotypes comprised this sample: 147 (84%) B/B, 4 (2.3%) F/F, 3 (1.7%) B/F, 1 (0.6%) F/B, 1 (0.6%) F/D, 1 (0.6%) BF/F, and 18 (10.3%) BF/B. A significant divergence was observed between these two techniques results (84.4%). This is explained by the low accuracy of the HMA for detecting recombinant viruses. These recombinants were unrelated to CRF12, while two sequences were related to CRF28 and CRF29. Nineteen BF mosaics shared the same gag breakpoint. In conclusion, the use of HMA may be inappropriate in regions where different subtypes are co-circulating. Subtype B is the most common genotype, however, an increased prevalence (13.1%) of different BF variants and a potentially new CRF suggest that recombination is occurring frequently in Bahia. These viruses were associated with women infected heterosexually. Finally, this study identified the presence of an F/D recombinant HIV-1 in Brazil.

Origin and evolutionary history of HIV-1 subtype C in Brazil

OBJECTIVE

To investigate the origin and to reconstruct the onset date of the HIV-1 subtype C epidemic in Brazil.

DESIGN

Three independent datasets of subtype C sequences isolated from HIV-1-positive patients from southern Brazil over a period of 15 years (1991-2006) were analyzed: 82 env V3 sequences (213 nt), 40 env C2-C5 sequences (559 nt), and 72 pol sequences (960 nt).

METHODS

Brazilian sequences were compared with other subtype C reference strains from the database using basic local alignment search tool, phylogenetic analyses, and searching of specific amino acid signature patterns. Evolutionary parameters were estimated using a Bayesian coalescent-based method under either strict or relaxed molecular clock models.

RESULTS

HIV-1 subtype C sequences from Brazil and Burundi formed a monophyletic cluster at both env and pol regions and shared specific amino acid signatures in the protease region when compared with other viruses of the same subtype from around the world. All Brazilian strains arose as a monophyletic subcluster within the Burundi-Brazilian lineage, whereas isolates from Burundi appeared at the origin of the clade. Evolutionary analyses of both env and pol genomic regions indicate that the age of the most recent common ancestor of the Brazilian subtype C clade dates back to the early 1980s.

CONCLUSION

The subtype C epidemic in the southern Brazilian region was initiated by the introduction of a single founder strain closely related to subtype C strains from Burundi. Our results suggest that this founder event probably took place around the early 1980s, roughly a decade before the previous estimates.

Antiretroviral resistance in individuals presenting therapeutic failure and subtypes of the human immunodeficiency virus type 1 in the Northeast Region of Brazil

This study aimed to analyze human immunodeficiency virus (HIV) mutation profiles related to antiretroviral resistance following therapeutic failure, and the distribution of hiv subtypes in the Northeast Region of Brazil. A total of 576 blood samples from AIDS patients presenting therapeutic failure between 2002 and 2004 were analyzed. The genotyping kit viroSeq was used to perform viral amplification in order to identify mutations related to hiv pol gene resistance. An index of 91.1% of the patients presented mutations for nucleoside reverse transcriptase inhibitors (nrti), 58.7% for non-nucleoside reverse transcriptase inhibitors (nnrti), and 94.8% for protease inhibitors (pi). The most prevalent mutations were 184V and 215E for nrti, 103N and 190A for nnrti. Most mutations associated with PIs were secondary, but significant frequencies were observed in codons 90 (25.2%), 82 (21.1%), and 30 (16.2%). The resistance index to one class of antiretrovirals was 14%, to two classes of antiretrovirals 61%, and to three classes 18.9%. Subtype B was the most prevalent (82.4%) followed by subtype F (11.8%). The prevalence of mutations related to nrti and nnrti was the same in the two subtypes, but codon analysis related to PI showed a higher frequency of mutations in codon 63 in subtype B and in codon 36 in subtype F. The present study showed that there was a high frequency of primary mutations, which offered resistance to nrti and nnrti. Monitoring patients with treatment failure is an important tool for aiding physicians in rescue therapy.

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

As part of an ongoing study on the features of AIDS spread towards small cities and rural areas, we present a molecular survey of human immunodeficiency virus type 1 (HIV-1) polymerase sequences recovered between 2004 and 2006 from 71 patients receiving care in the city of Saquarema, inner state of Rio de Janeiro. Phylogenetic reconstructions found the two prevalent lineages in the state (subtypes B [59 strains, 83.1%], F1 [6 strains; 8.4%], and BF1 recombinants [four strains; 5.6%]), as well as two (2.8%) CRF02_AG strains, which seems to be an emerging lineage in the capital. These CRF02_AG sequences were recovered from a married heterosexual couple who never traveled abroad, thus providing the first molecular evidence of autochthonous horizontal transmission of this lineage of major global importance. Also, three phylogenetic clusters of strains recovered from a total of 18.3% of the cohort were uncovered. Their close genetic relatedness suggests they were recovered from patients who probably took part in the same chain of viral spread. In conjunction with our previous surveys from inner Rio de Janeiro, these results suggest that although small cities harbor unique molecular features of HIV-1 infection, they also clearly reflect and may rapidly absorb the diversity recorded in large urban centers.

HIV genotyping among female sex workers in the State of Santa Catarina

The objective of this study was to investigate the frequency of HIV infection among female sex workers in the port area of Imbituba (State of Santa Catarina), and to identify the viral subtype and its susceptibility to antiretroviral medications. Ninety women were interviewed between December 2003 and February 2004. Six (6.7%) were HIV-positive. Genotyping for HIV, performed on four samples, detected subtype C in three of them, which is predominant in Africa and Asia, and subtype B in one of them, which is prevalent in Brazil, USA and Europe. The results suggest that the Port of Imbituba may be one of the gateways for HIV-1 subtype C to enter Brazil, and for its dissemination to the rest of the country and the Mercosul area, along the highway BR-101. This points towards the need for preventive work to reduce the introduction and dissemination of HIV subtype C in Brazil.

Human immunodeficiency virus type-1 subtypes of infected patients in Espírito Santo, Brazil

Genetic variability of human immunodeficiency virus type-1(HIV-1) is a potential threat for both diagnosis and treatment of HIV/AIDS, as well as the development of effective vaccines. Up to now, HIV subtypes circulating among HIV-positive patients in the state of Espírito Santo were not known. In the present study, blood samples from 100 therapy-naïve HIV-1 infected patients were collected and the HIV subtype was determined through the Heteroduplex Mobility Assay (HMA). Ninety-seven out of 100 studied samples were subtyped by HMA, 73 samples (75.2%) were from subtype B, 9 (9.3%) from subtype F, 3 (3.1%) from subtype C, 6 (6.2%) Benv/Fgag, and another 6 (6.2%) Fenv/Bgag, what suggests that recombinant viruses were present in the studied samples. Twenty-eight percent of the subtype B samples were represented by the Brazilian B" subtype, which were identified by RFLP with Fok I. Data presented here demonstrate that the epidemiological characteristics of the HIV epidemic in the state of Espírito Santo are similar to those from the other Southeastern states and helped to better understand the genetic polymorphism of HIV in Brazil.

Safety and efficacy of the HIV-1 integrase inhibitor raltegravir (MK-0518) in treatment-experienced patients with multidrug-resistant virus: a phase II randomised controlled trial

BACKGROUND

Raltegravir (MK-0518) is an HIV-1 integrase inhibitor with potent in-vitro activity against HIV-1 strains including those resistant to currently available antiretroviral drugs. The aim of this study was to assess the safety and efficacy of raltegravir when added to optimised background regimens in HIV-infected patients.

METHODS

HIV-infected patients with HIV-1 RNA viral load over 5000 copies per mL, CD4 cell counts over 50 cells per muL, and documented genotypic and phenotypic resistance to at least one nucleoside reverse transcriptase inhibitor, one non-nucleoside reverse transcriptase inhibitor, and one protease inhibitor were randomly assigned to receive raltegravir (200 mg, 400 mg, or 600 mg) or placebo orally twice daily in this multicentre, triple-blind, dose-ranging, randomised study. The primary endpoints were change in viral load from baseline at week 24 and safety. Analyses were done on a modified intention-to-treat basis. This trial is registered with ClinicalTrials.gov, with the number NCT00105157.

FINDINGS

179 patients were eligible for randomisation. 44 patients were randomly assigned to receive 200 mg raltegravir, 45 to receive 400 mg raltegravir, and 45 to receive 600 mg raltegravir; 45 patients were randomly assigned to receive placebo. One patient in the 200 mg group did not receive treatment and was therefore excluded from the analyses. For all groups, the median duration of previous antiretroviral therapy was 9.9 years (range 0.4-17.3 years) and the mean baseline viral load was 4.7 (SD 0.5) log10 copies per mL. Four patients discontinued due to adverse experiences, three (2%) of the 133 patients across all raltegravir groups and one (2%) of the 45 patients on placebo. 41 patients discontinued due to lack of efficacy: 14 (11%) of the 133 patients across all raltegravir groups and 27 (60%) of the 45 patients on placebo. At week 24, mean change in viral load from baseline was -1.80 (95% CI -2.10 to -1.50) log10 copies per mL in the 200 mg group, -1.87 (-2.16 to -1.58) log10 copies per mL in the 400 mg group, -1.84 (-2.10 to -1.58) log10 copies per mL in the 600 mg group, and -0.35 (-0.61 to -0.09) log(10) copies per mL for the placebo group. Raltegravir at all doses showed a safety profile much the same as placebo; there were no dose-related toxicities.

INTERPRETATION

In patients with few remaining treatment options, raltegravir at all doses studied provided better viral suppression than placebo when added to an optimised background regimen. The safety profile of raltegravir is comparable with that of placebo at all doses studied.

Molecular epidemiology of HIV type 1 in inner Rio De Janeiro State, Brazil

In the State of Rio de Janeiro, Brazil, HIV-1 diversity surveys have been performed mainly in the capital, and little is known about HIV-1 molecular epidemiology in small, inner cities. We studied 87 polymerase sequences recovered from 2 different studies conducted in inner cities of Rio de Janeiro State: a cross-sectional survey of patients receiving care in the small city of Santo Antonio de Pádua, and a case series of patients who were failing HAART in 26 additional inner cities throughout the State. Subtypes B (83.9%), F1 (8%), D (2.3%), and unique BF1 recombinants (5.7%) were demonstrated. The cross-sectional study found that 41.6% of the patients harbored genetically related strains that fell within clusters and probably took part in the same chain of viral spread. These clusters were phylogenetically unrelated to previously reported clusters from a neighboring city, suggesting that each small city harbors its own set of microepidemic lineages.

Human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns among treatment-naive patients in different stages of infection in Rio de Janeiro, Brazil

The presence of genetic mutations in HIV-1-positive untreated individuals and its contribution to treatment failure, either in an individual or on a population basis, remains an important concern. The goal was to analyze and compare HIV-1 reverse transcriptase (RT) and protease (PR) genes of untreated individuals with chronic and recent infections. Fifty-one chronic infected individuals for whom initiation of antiretroviral treatment had been recommended and 20 individuals with recent documented HIV-1 seroconversion had their plasma viral RNA extracted and the PR and RT genes sequenced in order to determine subtype, presence of genetic polymorphisms and mutations associated with resistance to antiretroviral drugs. All 20 recent seroconvertors were infected with subtype B viruses. Of the 51 chronically infected patients, 40 (78.4%), 7 (13.7%), and 2 (3.9%) were infected with subtypes B, F, and C, respectively. Two (3.9%) hybrid forms were also observed in two individuals with chronic infection: D/B and D/F. Despite seroconversion stage, type and quantity of mutations were similar to both groups (P = 0.961). This group also presented the only (1.4%) drug-resistance mutation (M184V) among all samples investigated. In summary, the present study shows a high occurrence of equivalent polymorphisms unrelated to drug resistance in samples collected from untreated HIV-1- infected individuals in different seroconversion status, and suggests low primary resistance mutations. Results also indicate that non-B subtypes circulating in Rio de Janeiro have specific Brazilian non-synonymous mutations.

Human immunodeficiency virus-1 subtypes and antiretroviral drug resistance profiles among drug-naïve Brazilian blood donors

BACKGROUND

Human immunodeficiency virus-1 (HIV-1) genetic variability and its implication on the development of new reagents were investigated by correlating time of infection and resistance to antiretroviral drugs.

STUDY DESIGN AND METHODS

Seventy-four plasma samples from Brazilian drug-naïve blood donors were assayed to further develop a panel of biologic reagents to be used in serology and molecular tests. After viral RNA extraction, cDNA was generated and used in nested polymerase chain reaction protocols with primers for the ENV (C2-V3 and gp41), protease (PR), and reverse transcriptase (RT) of HIV-1. Genomic sequencing was conducted to define HIV-1 subtypes and drug resistance mutations.

RESULTS

Subtype B was found in 83.8 percent of all samples, subtype F in 2.7 percent, and BF mosaics in 11 percent of the cases. B and F different genetic profiles were evidenced: B(PR)B(RT)B(gp120)B(gp41), F(PR)F(RT)F(gp120)F(gp41), F(PR)F(RT)B(gp120)B(gp41), F(PR)B(RT)B(gp120)B(gp41), and B(PR)B(RT)F(gp120)B(gp41). A single sample (1.4%) was characterized as a BC mosaic (B(PR)C(RT)U(gp120)C(gp41)) and an AGH mosaic (AG(PR)G(RT)H(gp120)H(gp41)) was first observed in the country. Antiretroviral resistance to nucleoside RT inhibitor was observed in one sample (1.35%) showing M41L and T215S mutations. Nonnucleoside RT inhibitor and major PR inhibitor resistance mutations were not observed. Previously unseen patterns of resistance to T20 were found among HIV-1-infected drug-naïve individuals in Brazil. Recent infections were characterized in 21.6 percent of the blood donor samples included in this study.

CONCLUSIONS

The availability of characterized plasma samples and HIV isolates will allow the development of biologic reagents necessary to implement quality control programs and to develop, validate, and evaluate the performance of diagnostic kits, considering all HIV-1-circulating variants in the country.

Impact of HIV-1 pol diversity on drug resistance and its clinical implications

PURPOSE OF REVIEW

HIV knowledge is based on subtype B, common in resource-rich settings, whereas globally non-B subtypes predominate. Inter-subtype pol diversity encompasses multiple genotypic differences among HIV variants, the consequence of which is unknown. This review summarizes publications from the past year relevant to the impact of HIV diversity on drug resistance evolution and its potential clinical implications.

RECENT FINDINGS

The benefit of antiretroviral therapy in non-B infected patients is ongoing, though subtype heterogeneity in rates of disease progression is observed. Pol inter-subtype diversity is high, and known subtype B drug resistance mutations occur in non-B subtypes. New mutations and subtype-specific mutation rates are identified, however, unexplained drug susceptibilities are seen, and additional insight is offered on structural pathogenic mechanisms of resistance in non-B subtypes. These differences may affect genotypic interpretation and our ability to apply drug resistance to patient care.

SUMMARY

Current evidence suggests good treatment response and comparable drug resistance evolution in HIV-1 B and non-B infected patients, with increasingly emerging differences. Impact of inter-subtype diversity on drug susceptibility and on evolution of drug resistance should continue to be a major research focus to increase our understanding and ability to improve global patient care.

Differential secretion of cytokines

Eosinophil granules store a vast array of cytokines and chemokines, many of which possess opposing activities. Specific stimuli can induce the release of entire granules or selective mediators through a process termed piecemeal degranulation. Until recently, the mechanisms that governed the decision to opt for either of these processes were unknown. Recent research has identified a mechanism through which differential secretion occurs during piecemeal degranulation. Eotaxin stimulation of eosinophils induces the selective mobilization of the granule-stored alpha chain of the interleukin-4 (IL-4) receptor into secretory vesicles. This process selectively recruits IL-4 to these vesicles and facilitates its differential secretion. There is also recent evidence for a mechanism of differential mobilization and membrane fusion of secretory vesicles versus granules. These two compartments possess a different set of SNARE and Rab molecules as vesicle fusion and transport-docking proteins, respectively. This presumably allows differential regulation of the processes of mobilization and plasma membrane fusion. These findings provide a model to explain the mechanism by which eosinophils, and likely many other cell types, differentially secrete cytokines and chemokines.

Pesquisas brasileiras biomédicas e epidemiológicas face às metas da UNGASS

O foco do estudo é a resposta brasileira em Ciência, Tecnologia e Inovação às metas formuladas no documento da UNGASS. Foram analisados os itens 70-73 que integram o documento Draft Declaration of Commitment for the UNGASS on HIV/AIDS, 2001, que definem metas para a Ciência, Tecnologia e Inovação em HIV/Aids. Os principais tópicos listados nesses itens foram operacionalizados sob a forma de "palavras-chave", de modo a orientar buscas sistemáticas nos bancos de dados padrão em biomedicina, incluindo ainda o Web of Science, nas suas subdivisões referentes às ciências naturais e sociais. O sucesso da pesquisa brasileira no âmbito da caracterização e isolamento do HIV-1 é inegável. Estudos vacinais fases II/III têm sido desenvolvidos no Rio de Janeiro, Belo Horizonte e São Paulo. O monitoramento da resistência primária teve estudos empíricos desenvolvidos em populações específicas, por meio da "Rede Brasileira em Monitoramento da Resistência do HIV". No âmbito do monitoramento da resistência secundária, destacaram-se iniciativas como a Rede Nacional de Genotipagem. Dois sistemas nacionais, o Sistema de Informações de Mortalidade e o Sistema de Informações de Agravos de Notificação - Aids e alguns estudos de maior abrangência têm dado origem a trabalhos sobre tendências da epidemia. A produção de medicamentos genéricos de qualidade e sua distribuição gratuita aos pacientes foram destacadas. O Brasil tem implementado uma resposta consistente e diversificada no âmbito do HIV/Aids, com estudos referentes ao desenvolvimento de vacinas, novos medicamentos e monitoramento da epidemia.

Phylogenetic analysis of Brazilian HIV type 1 subtype D strains: tracing the origin of this subtype in Brazil

HIV-1 Subtype D occurs mainly in East and Central African countries, especially Uganda, where the prevalence of HIV-1 infection is among the highest in the world. We present the phylogenetic analysis of one nonautochthonous and four autochthonous (including a near full-length genome) Brazilian HIV-1 subtype D strains identified in Rio de Janeiro State, where subtypes B, F1, and BF1 recombinants predominate. Phylogenetic inferences using maximum likelihood were applied on a near-full length genome and on concatenated gag, protease, reverse transcriptase, integrase, C2V3/env, gp41, and nef segments. Sequences from an Angolan immigrant showed close genetic similarity with a strain described in Finland, from an HIV patient of African origin, whereas all four autochthonous Brazilian sequences clustered with South African strains, where subtype D occurs only in isolated cases. Our results suggest the successful introduction and circulation in Brazil of closely related HIV-1 subtype D strains, possibly of South African origin.

A genotyping study of human immunodeficiency virus type-1 drug resistance in a small Brazilian municipality

In Brazil, surveillance studies on antiretroviral drug resistance among drug-naïve and treatment-experienced patients have focused primarily on patients living in large urban centers. As the epidemic spreads towards small municipalities and the innermost parts of the country, it will be essential to monitor the prevalence of antiretroviral drug resistance in these areas. We report the first survey on the prevalence of antiretroviral drug resistance in a small Brazilian municipality. Between July 1999 and March 2005, 72 adult human immunodeficiency virus type-1(HIV-1)-infected patients received care at the Municipal HIV/AIDS Program of the small, southeastern municipality of Miracema, state of Rio de Janeiro. A genotyping study of antiretroviral drug resistance was performed in 54 patients. Among 27 samples from treatment-experienced patients, 9 (33.3%) harbored strains with reduced drug susceptibility. Among these, 6 had reduced susceptibility to reverse transcriptase (RT) inhibitors and 3 to both RT and protease inhibitors. No primary antiretroviral drug resistance was recorded among 27 drug-naïve subjects. The relatively low prevalence of resistance mutations in the Miracema cohort argues against the concern that resource-poor settings should not implement widespread accessibility to standard of care antiretroviral combinations due to the possibility of sub-optimal adherence leading to the emergence and spread of drug-resistant strains.