HIV-1 polymorphism: a challenge for vaccine development - a review

Moderate prevalence of HIV-1 transmitted drug resistance mutations in southern Brazil

Background

Despite the advances in therapy, the occurrence of drug-resistant human immunodeficiency virus type 1 (HIV-1) is a major obstacle to successful treatment. This study aimed to characterize the genetic diversity and to determine the prevalence of transmitted drug resistance mutations (TDRM) between individuals recently or chronically diagnosed with HIV-1 from Paraná, Brazil.

Methods

A total of 260 HIV-1 positive antiretroviral therapy-naïve patients were recruited to participate on the study, of which 39 were recently diagnosed. HIV-1 genotyping was performed using sequencing reaction followed by phylogenetic analyses to determine the HIV-1 subtype. TDRM were defined using the Calibrated Population Resistance Tool program.

Results

The HIV-1 subtypes frequency found in the studied population were 54.0% of subtype B, 26.7% subtype C, 6.7% subtype F1 and 12.7% recombinant forms. The overall prevalence of TDRM was 6.7%, including 13.3% for recently diagnosed subjects and 5.9% for the chronic group.

Conclusions

The prevalence of resistance mutations found in this study is considered moderate, thus to perform genotyping tests before the initiation of antiretroviral therapy may be important to define the first line therapy and contribute for the improvement of regional prevention strategies for epidemic control.

Electronic supplementary material

The online version of this article (10.1186/s12981-019-0219-1) contains supplementary material, which is available to authorized users.

Profile of the HIV epidemic in Cape Verde: molecular epidemiology and drug resistance mutations among HIV-1 and HIV-2 infected patients from distinct islands of the archipelago

HIV-1 and HIV-2 have been detected in Cape Verde since 1987, but little is known regarding the genetic diversity of these viruses in this archipelago, located near the West African coast. In this study, we characterized the molecular epidemiology of HIV-1 and HIV-2 and described the occurrence of drug resistance mutations (DRM) among antiretroviral therapy naïve (ARTn) patients and patients under treatment (ARTexp) from different Cape Verde islands. Blood samples, socio-demographic and clinical-laboratory data were obtained from 221 HIV-positive individuals during 2010–2011. Phylogenetic and bootscan analyses of the pol region (1300 bp) were performed for viral subtyping. HIV-1 and HIV-2 DRM were evaluated for ARTn and ARTexp patients using the Stanford HIV Database and HIV-GRADE e.V. Algorithm Homepage, respectively. Among the 221 patients (169 [76.5%] HIV-1, 43 [19.5%] HIV-2 and 9 [4.1%] HIV-1/HIV-2 co-infections), 67% were female. The median ages were 34 (IQR = 1–75) and 47 (IQR = 12–84) for HIV-1 and HIV-2, respectively. HIV-1 infections were due to subtypes G (36.6%), CRF02_AG (30.6%), F1 (9.7%), URFs (10.4%), B (5.2%), CRF05_DF (3.0%), C (2.2%), CRF06_cpx (0.7%), CRF25_cpx (0.7%) and CRF49_cpx (0.7%), whereas all HIV-2 infections belonged to group A. Transmitted DRM (TDRM) was observed in 3.4% (2/58) of ARTn HIV-1-infected patients (1.7% NRTI, 1.7% NNRTI), but not among those with HIV-2. Among ARTexp patients, DRM was observed in 47.8% (33/69) of HIV-1 (37.7% NRTI, 37.7% NNRTI, 7.4% PI, 33.3% for two classes) and 17.6% (3/17) of HIV-2-infections (17.6% NRTI, 11.8% PI, 11.8% both). This study indicates that Cape Verde has a complex and unique HIV-1 molecular epidemiological scenario dominated by HIV-1 subtypes G, CRF02_AG and F1 and HIV-2 subtype A. The occurrence of TDRM and the relatively high level of DRM among treated patients are of concern. Continuous monitoring of patients on ART, including genotyping, are public policies to be implemented.

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.

The HIV-1 epidemic in Bolivia is dominated by subtype B and CRF12_BF "family" strains

BACKGROUND

Molecular epidemiological studies of HIV-1 in South America have revealed the occurrence of subtypes B, F1 and BF1 recombinants. Even so, little information concerning the HIV-1 molecular epidemiology in Bolivia is available. In this study we performed phylogenetic analyses from samples collected in Bolivia at two different points in time over a 10 year span. We analyzed these samples to estimate the trends in the HIV subtype and recombinant forms over time.

MATERIALS AND METHODS

Fifty one HIV-1 positive samples were collected in Bolivia over two distinct periods (1996 and 2005). These samples were genetically characterized based on partial pol protease/reverse transcriptase (pr/rt) and env regions. Alignment and neighbor-joining (NJ) phylogenetic analyses were established from partial env (n = 37) and all pol sequences using Mega 4. The remaining 14 env sequences from 1996 were previously characterized based on HMA-env (Heteroduplex mobility assay). The Simplot v.3.5.1 program was used to verify intragenic recombination, and SplitsTree 4.0 was employed to confirm the phylogenetic relationship of the BF1 recombinant samples.

RESULTS

Phylogenetic analysis of both env and pol regions confirmed the predominance of "pure" subtype B (72.5%) samples circulating in Bolivia and revealed a high prevalence of BF1 genotypes (27.5%). Eleven out of 14 BF1 recombinants displayed a mosaic structure identical or similar to that described for the CRF12_BF variant, one sample was classified as CRF17_BF, and two others were F1pol/Benv. No "pure" HIV-1 subtype F1 or B" variant of subtype B was detected in the present study. Of note, samples characterized as CRF12_BF-related were depicted only in 2005.

CONCLUSION

HIV-1 genetic diversity in Bolivia is mostly driven by subtype B followed by BF1 recombinant strains from the CRF12_BF "family". No significant temporal changes were detected between the mid-1990s and the mid-2000s for subtype B (76.2% vs 70.0%) or BF1 recombinant (23.8% vs 30.0%) samples from Bolivia.

Lower prevalence of human immunodeficiency virus type 1 Brazilian subtype B found in northeastern Brazil with slower progression to AIDS

Besides being extremely useful in measuring the level of HIV-1 diversity and prevalence in populations, the molecular analysis of genomic sequences provides crucial surveillance support and aids in the development of new therapies and effective vaccines. The present study focused on gag and env DNA and amino acid sequences that were generated from samples taken from 61 infected patients in the City of Salvador, Bahia, located in northeastern Brazil. In order to determine selective pressure and predict coreceptor usage, Bioinformatics tools were employed in phylogeny reconstruction. Fifty-six (91.8%) viruses were classified as belonging to subtype B, three (4.9%) from F1, and two (3.3%) from BF1 recombinants. Based on the characterization of the V3 region, the subtype B strains were represented by eight (18.2%) Brazilian variants (B'-GWGR), 20 (46.5%) European/EUA B variants (GPGR), and 15 (34.9%) GXGX variants. The mean time elapsed since diagnosis was 13 years among subtype B' and 9 years in subtype B. The mean dN/dS ratios from the GWGR, GPGR, and GXGX groups, when compared to an HXB2 reference, were 0.72, 0.77, and 0.67, respectively. Seventy-six percent of the viruses studied were predicted to use the CCR5 coreceptor for cell entry (R5 viruses), while 24% were predicted to use the CXCR4 or were classified as dual tropic viruses. The prevalence of subtypes B' and recombinant B/F1 was shown to be lower than findings from previous studies performed both in Brazil (B') and in Bahia (B/F1). The association between subtype B' and a lengthy period of time since diagnosis can be correlated with a slower disease progression in infected patients, when compared with those infected with subtype B.

The detection of in vivo and in vitro HIV type 1 B/F profiles in Brazil using a real-time PCR assay for five HIV type 1 genomic regions

We sought to determine the frequency and profile of HIV-1 BF recombinants in vitro and in vivo. Laboratory HIV-1 strains from subtypes B and F were cocultured and evaluated. Clinical samples from the city of Santos, Brazil, where the first HIV-1 B/F circulating recombinant forms (CRF) were described, were also assessed. Five real-time PCR assays were developed to equally amplify subtypes B and F, and subtype-specific probes were developed and optimized. To validate the PCR systems, clinical samples from Santos were sequenced and phylogenetically analyzed. The real-time PCR assays were performed on these samples and on the supernatant of an in vitro competition assay to assess emergent recombinant strains. Out of 157 clinical samples, 62.1% were defined as subtype B, 3.0% were subtype F, 16.7% presented the CRF28_BF profile, and 13.6% of the samples presented the CRF29_BF profile. The specificity and sensitivity in the discrimination assay for this sample panel were 93% and 92%, respectively. The HIV that emerged from the coinfected cell culture closely resembled the CRF28_BF profile. The first-described CRFs are still fixed in this geographic region of Brazil, and the in vitro emerging strains detected by real-time PCR suggest that in addition to the shaping of recombinant strains by immune selection, viral structures may also play an important role in emerging CRFs.

Prevalence, estimated HIV-1 incidence and viral diversity among people seeking voluntary counseling and testing services in Rio de Janeiro, Brazil

BACKGROUND

BED-EIA HIV-1 Incidence Test (BED-CEIA) has been described as a tool to discriminate recent (RS) from long-term (LTS) seroconversion of HIV-1 infection, contributing to a better understanding of the dynamics of the HIV/AIDS epidemic over time. This study determined the prevalence, estimated incidence and HIV-1 subtype infection among individuals seeking testing in Voluntary Counseling and Testing centers (VCTs) from Rio de Janeiro, Brazil.

METHODS

Demographics and behavioral data were obtained from 434 individuals, diagnosed as HIV-positive among 9,008 volunteers screened from November 2004 to October 2005 in three VCTs located in the Rio de Janeiro Metropolitan area, Brazil. BED-CEIA protocol was performed to identify RS. DNA samples from RS and a subset of LTS (under a proportion of 1:2) were selected for gp120 C2-V3 and pol (protease and reverse transcriptase) regions genomic sequencing.

RESULTS

Overall HIV-1 prevalence was 4.8%. Sixty-one of 434 seropositive individuals were classified as RS, corresponding to an incidence rate of 1.68%/year (95%CI 1.26% -2.10%). Estimated incidence between Men Who Have Sex with Men (MSM) was 11 times higher than among heterosexual men and 55% of the new cases were identified in volunteers aged 25-40 years. A similar distribution of different HIV-1 subtypes was found among RS and LTS.

CONCLUSIONS

Our data suggest that prevention for MSM remains a challenge and efforts focusing on prevention targeting this population should be prioritized. No significant changes in HIV-1 subtypes were observed among the RS and LTS subgroups. One case of HIV-1 AUK (pol)/A (env) recombinant genome was detected for the first time in Brazil.

Near full-length genome characterization of HIV type 1 unique BC recombinant forms from Southern Brazil

Abstract In southern Brazil, CRF31_BC is the major HIV-1 recombinant form and URFs_BC occurs very infrequently. The near full-length genomes of four samples displaying a similar recombination profile in the integrase region and different profiles in the protease/reverse transcriptase regions were analyzed to elucidate their mosaic structure and to describe for the first time the near full-length genomes of URFs_BC circulating in Brazil. For this purpose, overlapping PCR amplifications followed by direct sequencing were carried out. Despite the observation that these samples share a similar recombination profile in the integrase region, phylogenetic, bootscan, and informative site analyses revealed that the four samples displayed distinct mosaic structures. Additional recombination events occurred mainly in the gag, reverse transcriptase, and env regions. Our data provide the first description of the near full-length genomes of URFs_BC in Brazil and offer important insights about the complexity of HIV-1 recombinant strains currently in circulation in the south of Brazil.

Primary antiretroviral drug resistance among HIV type 1-infected individuals in Brazil

Infection with drug-resistant human immunodeficiency virus type 1 (HIV-1) has been documented in all countries that have surveyed for it and may result in an unfavorable response to therapy. The prevalence and characteristics of individuals with transmitted resistance to antiretroviral drugs have been scarcely described in Brazil. We performed antiretroviral resistance testing prior to initiation of therapy in 400 subjects enrolled from 20 centers in 13 Brazilian cities between March and September 2007. Genotyping was conducted using PCR-amplified HIV pol products by automated sequencing, and genotype interpretation was done according to the IAS-USA consensus. Of 400 eligible participants, 387 (95.8%) were successfully tested. Seven percent of antiretroviral-naive patients carried viruses with one or more major mutation associated with drug resistance. The prevalence of these mutations was 1.0% for protease inhibitors, 4.4% for nonnucleoside reverse transcriptase inhibitors, and 1.3% for nucleoside reverse transcriptase inhibitors. The frequency of multidrug resistance among the resistant strains was 13.6%. Among subjects infected with drug-resistant virus, the majority were infected with subtype B viruses (91%). Subjects from the city of São Paulo had higher transmitted resistance mutations compared to the rest of the country. Reporting a partner taking antiretroviral medications was associated with a higher chance of harboring HIV variants with major drug resistance mutations [odds ratio = 2.57 (95% confidence interval, 1.07-6.16); p = 0.014]. Resistance testing in drug-naive individuals identified 7% of subjects with mutations associated with reduced susceptibility to antiretroviral drugs. Continued surveillance of drug-resistant HIV-1 in Brazil is warranted when guidelines for HIV prophylaxis and treatment are updated. Resistance testing among drug-naive patients prior to treatment initiation should be considered, mainly directed at subjects whose partners are already on antiretroviral therapy.

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.

Prevalence of HIV-1 Subtypes in Brazilian Children With Perinatally Acquired Infection

HIV-1 infection has increased among women in recent years. The HIV-1 env gene (structural gene) has the greatest variation in all the HIV gene regions. In this study, 58 samples from infants infected with HIV-1 via perinatal transmission were analyzed. All the 58 samples were submitted to Nested-polymerase chain reaction of the env gene region for posterior viral genotyping using EN 70 and EN 85 (first polymerase chain reaction) and EN 80 and EN 95 (second polymerase chain reaction) primers, with the product of the 682 base pair amplification. After Nested-polymerase chain reaction for genotyping, purification of the product, and direct sequencing in a MegaBace 1000 automatic sequencer, 56 genotypes were found in the 58 HIV-1-positive children of the study, where 47 (83.93%) were HIV-1 subtype B infected and 9 (16.07%) were HIV-1 subtype F1 infected. The results demonstrate the predominance of subtype B followed by subtype F in Southeast Brazil.

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.

Molecular epidemiology of HIV-1 in Santa Catarina State confirms increases of subtype C in Southern Brazil

Recent studies have demonstrated an increased prevalence of human immunodeficiency virus type 1 (HIV-1) subtype C in southern Brazil. Although Santa Catarina State (SC) is located in this area and presents one of the country's highest incidences of HIV/AIDS, knowledge on the molecular epidemiology of HIV-1 in such State is lacking. The aim of this study was to investigate the HIV-1 molecular diversity and epidemiological profile of HIV-1-infected patients from SC. DNA samples were PCR amplified and HIV-1 subtypes were determined using both env and gag genes by direct sequencing. Phylogenetic analyses revealed that 48% were subtype C and 23% were subtype B. Possible recombinant forms were observed for both B/C (23%) and B/F (6%) subtypes. Our results, for the first time, identifies HIV-1 subtype C as a major clade circulating in SC and contributes to the understanding of HIV epidemics in the country by confirming the epidemic spread of the HIV-1 subtype C in southern Brazil.

HIV-1 seroprevalence in the general population of Salvador, Bahia State, Northeast Brazil

To estimate HIV-1 seroprevalence in the general population of Salvador, Bahia, Brazil, we conducted a cross-sectional survey of 3,437 residents from 1998 to 2000. Subjects were drawn from 30 sentinel areas representing a wide range of living conditions. Plasma samples were screened for HIV-1 antibodies by ELISA and confirmed by immunofluorescent assay. Subtype determination by HMA was performed after proviral DNA amplification. Phylogenetic analysis using parsimony was performed with the neighbor-joining method. Overall HIV-1 seroprevalence was 0.55% (19/3,446): 0.8% for men and 0.36% for women. Seroprevalence was higher in the 31-45-year age group (1%) and among persons with family income less than twice the minimum wage (0.78%) as compared to 0.33% for the higher income group. Syphilis was detected in 37% of HIV seropositive individuals. Phylogenetic inferences identified 10 samples as subtype B in the env region and 2 samples with Benv/Fgag/Fpol and Fenv/Bgag. Age > or = 30 years, male gender, and income < or = 2 times the minimum wage were identified as risk factors for HIV-1 infection. Extrapolating the proportion of seropositive individuals to Salvador, the number of HIV-1 infected individuals was estimated at 13,750.

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.

Increasing genetic distance to HIV-1 subtype B and F1 consensus sequences in the Brazilian epidemic: a challenge for vaccine strategies based on central immunogens?

It has been postulated that the non-synonymous divergence (distance to the subtype consensus sequence) observed in several HIV-1 subtype populations during 1990s attained the maximum limit that is compatible with viral fitness or survival, at least in the V3 env gene domain. To test this hypothesis, 145 subtype B and 64 subtype F env V3 sequences isolated from Brazilian HIV-1 positive patients between 1989 and 2004 were analyzed. HIV-1 env V3 sequences were grouped by year of collection and the mean intra-subtype diversity and divergence were examined at synonymous, non-synonymous, and amino acid level. The analyses clearly show that the mean intra-subtype divergence constantly increases in both subtype populations in the last 15 years, and more importantly, this trend was not only driven by a significant increase of the synonymous distance but also by a significant increase of the non-synonymous and amino acid distances between Brazilian circulating viruses and subtype consensus sequences. These results clearly disagree with the notion that the non-synonymous distance to the HIV-1 subtype consensus observed at population level had already attained the maximum limit, and suggest that the likelihood for success of vaccines based on "central" immunogens, as those based on any other empirically selected viral sequence, could be continuously diminishing over time.

Genetic and biologic characterization of HIV type 1 subtype C isolates from south Brazil

The molecular and biological properties of HIV-1 subtype C strains from South Brazil were investigated. We sequenced gag and env fragments of viruses from 22 HIV-1-infected individuals from Porto Alegre City, which has the highest frequency of subtype C in the country. The sequences were then compared with other subtype B, C, and F strains isolated in Brazil and other countries using phylogenetic methods. Amino acid signatures were identified and correlated with phenotypic characteristics. We identified six strains with subtype C (27.3%), eight subtype B (36.4%), one subtype F (4.5%), six C/B recombinants (27.3%), and one B/F recombinant (4.5%). The Brazilian subtype C sequences formed a unique phylogenetic group and presented 6 and 18 specific amino acid signatures in gag and env, respectively. Three distinct patterns of C/B recombinants presented characteristic Brazilian amino acid substitutions. Subtype C viruses were predominantly R5 and non-syncytium-inducing, while C/B recombinants were R5/X4 and syncytium-inducing viruses. These findings suggest that subtype C viruses circulating in Brazil are the result of a unique introduction into the country. Recombination events between subtypes B and C have been occurring frequently for more than 10 years in South Brazil. Biological characterization confirms the hypothesis that subtype C is distinct from the others in the evolution of coreceptor utilization.

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.

Trends in drug resistance mutations in antiretroviral-naïve intravenous drug users of Rio de Janeiro

DNA sequencing of a pol gene fragment from drug-naive injecting drug users samples obtained at two time points of the Brazilian AIDS epidemic (Pre-HAART era: 1994 to early 1997, n = 27; post-HAART era: 1999-2001, n = 38) was undertaken to assess HIV-1 antiretroviral drug resistance mutations and subtyping profiles. Genotypic analysis revealed the presence of PR primary L90M, D30N, M46I, and V82A mutations in 7.9% of the post-HAART group, and a high frequency of secondary mutations (84.2%). Nucleoside RT-associated mutations were observed in 13.2%. In the pre-HAART group, a higher frequency of RT mutations was observed (22.2%) and no PR primary mutations were found, in agreement with the introduction of protease inhibitors (PIs) in therapy during the same period. The identification of 7.9% of drug-naive injecting drug users already bearing RT/PR primary resistance mutations in the post-HAART era group constitutes a major concern in terms of dissemination of drug resistant viruses. The resistance mutations profile of the individuals may reflect the context of antiretroviral treatment in Brazil at the sample collection periods (1994-1997 and 1999-2001). In spite of the differences observed in the drug resistance profiles, similar frequencies of subtype B (63.0 vs. 73.7%), F (22.2 vs. 10.5%), and recombinant B/F (14.8 vs. 15.8%) viruses were found, respectively, in the pre- and post-HAART groups.

Evolutionary history of HIV-1 subtype B and F infections in Brazil

OBJECTIVE

To reconstruct the onset date of the HIV-1 B and F epidemics in Brazil based on virus diversification over time.

DESIGN

We studied HIV-1 env V3 sequences (210 nt) with a known sampling year isolated from HIV-1 positive patients from Brazil between 1989 and 1997: 101 subtype B sequences and 41 subtype F sequences.

METHODS

HIV-1 V3 env sequences were grouped by year of collection and the relationship between the sampling years of HIV-1 sequences and their genetic distance to the reconstructed common ancestor (intra-population divergence) or to other sequences from the same year (intra-population diversity) was examined by using linear regression analysis.

RESULTS

Regression analysis of nucleotide distances, revealed a highly significant positive correlation between sampling years of subtype B and F V3 sequences and their intra-population divergence (P < 0.001) or diversity (P < 0.0001). In both subtype populations, the divergence and diversity increased at a rate of 0.5 and 0.9% per year, respectively. Considering these evolutionary rates, we estimate the onset of the subtype B and F HIV-1 epidemics in Brazil during early 1970s and early 1980s, respectively.

CONCLUSIONS

The consistent correlation between divergence and diversity of the V3 sequences with their sampling years indicates that the molecular clock is operational in the evolution of the HIV-1 in Brazil's epidemic, and show that subtypes B and F are evolving at a similar rate over time. The dating results suggest a discontinuous introduction of these subtypes in the Brazilian population.

BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools

Most Internet online resources for investigating HIV biology contain either bioinformatics tools, protein information or sequence data. The objective of this study was to develop a comprehensive online proteomics resource that integrates bioinformatics with the latest information on HIV-1 protein structure, gene expression, post-transcriptional/post-translational modification, functional activity, and protein-macromolecule interactions. The BioAfrica HIV-1 Proteomics Resource http://bioafrica.mrc.ac.za/proteomics/index.html is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. The HIV-1 Protein Data-mining Tool includes a set of 27 group M (subtypes A through K) reference sequences that can be used to assess the influence of genetic variation on immunological and functional domains of the protein. The BLAST Structure Tool identifies proteins with similar, experimentally determined topologies, and the Tools Directory provides a categorized list of websites and relevant software programs. This combined database and software repository is designed to facilitate the capture, retrieval and analysis of HIV-1 protein data, and to convert it into clinically useful information relating to the pathogenesis, transmission and therapeutic response of different HIV-1 variants. The HIV-1 Proteomics Resource is readily accessible through the BioAfrica website at: http://bioafrica.mrc.ac.za/proteomics/index.html.

Antiretroviral resistance and genetic diversity of human immunodeficiency virus type 1 isolates from the Federal District, Central Brazil

In the context of universal access to antiretroviral therapy, the surveillance of human immunodeficiency virus type 1 (HIV-1) genetic diversity and resistance becomes pivotal. In this work our purpose was to describe the genetic variability; prevalence of drug-resistance mutations; and genotypic resistance profiles in HIV-1 infected individuals under antiretroviral treatment, from the Federal District, Brasilia, Central Brazil. The entire viral protease and codons 19 to 234 of the reverse transcriptase gene from 45 HIV-1 isolates were amplified and sequenced for subtyping and genotyping. By phylogenetic analysis, 96% of the samples clustered with subtype B and the remaining 4% with HIV-1 subtype F sequences. One major protease inhibitor resistance-associated mutation, I50V, was detected in 38% of the samples. Minor mutations were also found at the protease gene: L10I/V (7%), K20M (2%), M36I (11%), L63P (20%), A71T (2%), and V77I (7%). Many mutations associated with reduced susceptibility to nucleoside or non-nucleoside reverse transcriptase inhibitors were detected: M41L (11%), E44D (4%), D67N (11%), T69D (2%), K70R (11%), L74V (2%), L100I (4%), K103N (18%), V118I (9%), Y181C (11%), M184V (18%), G190A (4%), T215Y (4%), and K219E (4%). This study has shown that 84% of the studied population from the Federal District, showing evidences of therapy failure, presented viral genomic mutations associated with drug resistance. The main antiretrovirals to which this population showed resistance were the PI amprenavir (38%), the NNRTIs delavirdine, nevirapine (31%), and efavirenz (24%), and the NRTIs lamivudine (18%), abacavir, and zidovudine (13%).

Human immunodeficiency virus type 1 neutralization by plasma from B or F genotype infected individuals

Anti-human immunodeficiency virus type 1 (HIV-1) "binding antibodies" (antibodies capable of binding to synthetic peptides or proteins) occur throughout HIV-1 infection, are high-titered and highly cross-reactive, as confirmed in this study by analyzing plasma from B and F genotype HIV-1 infected individuals. Plasma from individuals infected with clade F HIV-1 displayed the most frequent cross-reactivity, in high titers, while Bbr plasma showed much higher specificity. Similarly, neutralization of a reference HIV-1 isolate (HIV-1 MN) was more frequently observed by plasma from F than B genotype infected individuals. No significant difference was seen in neutralization susceptibility of primary B, Bbr or F clade HIV-1 by plasma from individuals infected with the classical B (GPGR) or F HIV-1, but Bbr (GWGR) plasma were less likely to neutralize the F genotype primary HIV-1 isolates. The data indicate that both B and F genotype derived vaccines would be equally effective against B and F HIV-1 infection, with a slightly more probable effectiveness for F than B genotype. Although the Bbr variant appears to induce a much more specific humoral immune response, the susceptibility in neutralizing the Brazilian HIV-1 B genotype Bbr variant is similar to that observed with the classical B genotype HIV-1.

HIV-1 infection among injection and ex-injection drug users from Rio de Janeiro, Brazil: prevalence, estimated incidence and genetic diversity

BACKGROUND AND OBJECTIVES

Due to their behavioral conditions and vulnerability, injection drug users (IDUs) are prone to multiple simultaneous or sequential infections with distinct HIV-1 subtypes and variants, making them a key population for molecular epidemiology surveillance. In the present study, we evaluated HIV-1 infection seroprevalence, genetic diversity and estimated incidence among IDUs and ex-injection drug users (ex-IDUs) from Rio de Janeiro, Brazil.

STUDY DESIGN

Six hundred and eight IDUs and ex-IDUs, recruited between 1999 and 2001, were interviewed and agreed to donate 30 ml of blood. The serologic status for HIV infection was determined by two ELISAs and confirmed by IFA. CD4+ T-cell percentages were assessed by flow cytometry. HIV-1 positive samples were submitted to viral load quantification. DNA samples were PCR amplified and HIV-1 subtypes were determined using env and gag HMA.

RESULTS AND CONCLUSIONS

Forty-eight (7.89%) individuals were seropositive for HIV-1 infection. The seroincidence of HIV-1 infection was estimated as 0.76%. HIV-1 env and gag subtyping identified 29 (69%) samples as belonging to subtype B, 7 (16.7%) to subtype F, and 6 (14.3%) discordant env/gag genomes infections, indicating the circulation of recombinant viruses in this population.

Molecular epidemiology of human immunodeficiency virus-1 in the state of Ceará, Northeast, Brazil

We analyzed, by env and gag heteroduplex mobility assay, 149 human immunodeficiency virus (HIV-1) positive samples collected in Ceará during the year 2000. The prevalence of subtype B was 81.2% and the prevalence of subtype F and B/F recombinants were both 2.7%. Eight (5.4%) and 12 (8%) out of 149 samples showed indeterminate results in the env and gag analysis respectively. By FokI restriction fragment length polymorphism, 34% of the subtype B samples were identified as the typical Brazilian subtype B. In the present study, we identified HIV-1 subtype F and B/F in Ceará for the first time. Our results contribute to the understanding of HIV in Brazil, and may prove useful for the development of vaccine candidates.

Anti-human immunodeficiency virus-1 antibody titers in injection drug users compared to sexually infected individuals

Sera from infected injection drug users (IDU) have shown to have antibodies against synthetic human immunodeficiency virus-1 (HIV-1) envelope peptides more frequently. In this study, reactivity of 48 IDU plasma were compared to 60 plasmas obtained from sexually infected individuals (S). The overall reactivity of plasma from IDU compared to S was higher, and the reactivity titers were much higher for IDU plasma than S. IDU plasma also showed a broader antibody response. The higher reactivity titers were observed mainly for the gp41 immunodominant epitope and V3 peptides corresponding to the consensus sequences of HIV-1 subtypes/variants prevalent in Brazil (B, F, C) indicating the specificity in the higher immune response of IDU.