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da Costa CP, Rodrigues JKF, de Morais VMS, de Andrade CADN, Neves PAF, Lima K. HIV-1 subtype frequency in Northeast Brazil: A systematic review and meta-analysis. J Med Virol 2020; 92:3219-3229. [PMID: 32266997 DOI: 10.1002/jmv.25842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/12/2020] [Indexed: 02/01/2023]
Abstract
Information on human immunodeficiency virus (HIV) molecular epidemiology is required to verify HIV/AIDS (acquired immune deficiency syndrome) epidemic dynamics in different regions, as well as provide support for response to antiretroviral therapy, transmission of resistance mutations, disease progression, and viral spread. The aim of this study was to conduct a systematic review and meta-analysis of the frequency of HIV-1 subtypes in Northeast Brazil. Seventy-six articles that refer to HIV-1 and its subtypes in the Northeast Brazil and published between 1 January 1999 and 31 August 2019 were identified. We included 27 articles for the qualitative synthesis, thus analyzing results from 4466 patients and 4298 genomic sequences. The results showed that subtypes B, F, and C and recombinant BF were responsible for 76% (IC95%: 71-80), 8% (IC95%: 5-11), 2% (IC95%: 2-3), and 7% (IC95%: 4-12) infections, respectively. The highest proportion of subtype B infections (82.2%) was observed in Piauí, while the subtype F had a high frequency in Pernambuco (23.4%). Bahia presented 11.6% of the proportion of recombinant BF. In addition, several recombinants such as AG, BC, BCF, and BD have been identified in the region. This is the first systematic review and meta-analysis on the HIV-1 subtype distribution in Northeast Brazil and has shown a high circulating viral diversity. Although subtype B is predominant in Brazil, a large frequency of non-B subtypes has also been found, which may have consequences for response to antiretroviral therapy, disease progression, and transmission. Thus, HIV molecular epidemiological data are essential for epidemic prevention and control strategies.
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Affiliation(s)
- Clevson P da Costa
- Unidade de Laboratório de Análises Clínicas, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Jessyca K F Rodrigues
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Viviane M S de Morais
- Departamento de Microbiologia, Universidade Federal Rural de Pernambuco da Unidade Acadêmica de Serra Talhada, Serra Talhada, Pernambuco, Brazil
- Setor de Virologia, Laboratório de Imunopatologia Keizo Asami, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Carlos A D N de Andrade
- Unidade de Laboratório de Análises Clínicas, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Patrícia A F Neves
- Unidade de Laboratório de Análises Clínicas, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Kledoaldo Lima
- Unidade de Laboratório de Análises Clínicas, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- European Virus Bioinformatics Center, Jena, Germany
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Transmitted drug resistance in patients with acute/recent HIV infection in Brazil. Braz J Infect Dis 2017; 21:396-401. [PMID: 28539254 PMCID: PMC9427834 DOI: 10.1016/j.bjid.2017.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
Introduction The widespread use of antiretroviral therapy increased the transmission of antiretroviral resistant HIV strains. Antiretroviral therapy initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance may jeopardize the early goals of early antiretroviral treatment among acute/recent HIV infected patients. Methods Patients with acute/recent HIV infection who underwent resistance test before antiretroviral treatment initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. Transmitted drug resistance was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without transmitted drug resistance was made using Kruskal–Wallis and Chi-square tests. Results Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall transmitted drug resistance prevalence was 16.3% (95% confidence interval [CI]: 8.1–30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1–24.5) was against non-nucleoside reverse transcriptase inhibitors, and K103N was the most frequently identified mutation. Conclusions The high prevalence of nonnucleoside reverse transcriptase inhibitors resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for antiretroviral naive individuals. Further studies on transmitted drug resistance among acutely/recently HIV-infected are needed to inform the predictors of transmitted resistance and the antiretroviral therapy outcomes among these population.
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Lima K, Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Increase in human immunodeficiency virus 1 diversity and detection of various subtypes and recombinants in north-eastern Brazil. J Med Microbiol 2017; 66:526-535. [PMID: 28425872 DOI: 10.1099/jmm.0.000447] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
PURPOSE Diverse human immunodeficiency virus 1 (HIV-1) subtypes and circulating recombinant forms are found in Brazil. The majority of HIV-1 molecular epidemiological studies in Brazil have been conducted in the southern and south-eastern regions of the country, although several recent studies in the north-eastern region have addressed this issue. The objective of this study was to molecularly characterize HIV-1 circulating in Pernambuco, north-eastern Brazil. METHODOLOGY A total of 64 samples were collected from 2002 to 2003, and another 103 were collected from 2007 to 2009. The protease and partial reverse transcriptase regions of the HIV-1 polymerase-encoding (pol) gene were sequenced, and subtyping, recombination and phylogenetic analyses were performed.Results/Key findings. Subtype B (60.9 %) was found to be predominant, followed by HIV-1 F (31.4 %). Several BF recombinants (4.2 %), and BC and AG recombinants were also identified. The intra-subtype genetic diversity was estimated to be 0.065 (sd±0.004) for HIV-1 B and 0.055 (sd±0.004) for HIV-1 F, reflecting a greater accumulation of mutations in subtype B (P<0.01). More codons were found to be under positive selective pressure in samples collected from 2007 to 2009, from individuals with a T-cell count≥200 cells mm-3 and from women. Coalescence data indicated that the subtype F population has been continuously expanding. CONCLUSIONS HIV-1 shows high genetic diversity in the state of Pernambuco. Thus, additional molecular evaluations of circulating strains will provide a better understanding of the epidemic and may lead to more effective preventive strategies.
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Affiliation(s)
- Kledoaldo Lima
- Tropical Medicine, Federal University of Pernambuco, Recife, PE, Brazil
| | - Élcio Leal
- Institute of Biotechnology, Federal University of Pará, Belém, PA, Brazil
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Machado LFA, Costa IB, Folha MN, da Luz ALB, Vallinoto ACR, Ishak R, Ishak MOG. Lower genetic variability of HIV-1 and antiretroviral drug resistance in pregnant women from the state of Pará, Brazil. BMC Infect Dis 2017; 17:270. [PMID: 28403828 PMCID: PMC5389155 DOI: 10.1186/s12879-017-2392-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 04/07/2017] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The present study aimed to describe the genetic diversity of HIV-1, as well as the resistance profile of the viruses identified in HIV-1 infected pregnant women under antiretroviral therapy in the state of Pará, Northern Brazil. METHODS Blood samples were collected from 45 HIV-1 infected pregnant to determine the virus subtypes according to the HIV-1 protease (PR) gene and part of the HIV-1 reverse transcriptase (RT) gene by sequencing the nucleotides of these regions. Drug resistance mutations and susceptibility to antiretroviral drugs were analyzed by the Stanford HIV Drug Resistance Database. RESULTS Out of 45 samples, only 34 could be amplified for PR and 30 for RT. Regarding the PR gene, subtypes B (97.1%) and C (2.9%) were identified; for the RT gene, subtypes B (90.0%), F (6.7%), and C (3.3%) were detected. Resistance to protease inhibitors (PI) was identified in 5.8% of the pregnant, and mutations conferring resistance to nucleoside reverse transcriptase inhibitors were found in 3.3%, while mutations conferring resistance to non-nucleoside reverse transcriptase inhibitors were found in 3.3%. CONCLUSIONS These results showed a low frequency of strains resistant to antiretroviral drugs, the prevalence of subtypes B and F, and the persistent low transmission of subtype C in pregnant of the state of Pará, Brazil.
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Affiliation(s)
- Luiz Fernando Almeida Machado
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil.
| | - Iran Barros Costa
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil
| | - Maria Nazaré Folha
- Reference Unit Specialized in Maternal-Child and Adolescent Care, Alcindo Cacela 1421, Sao Bras, CEP 66040-020, Belem, Pará, Brazil
| | - Anderson Levy Bessa da Luz
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil
| | - Antonio Carlos Rosário Vallinoto
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil
| | - Ricardo Ishak
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil
| | - Marluisa Oliveira Guimarães Ishak
- Virology Laboratory, Institute of Biological Sciences, Federal University of Pará, Augusto Correa 1, Guama, Belem, Para, CEP 66075-110, Brazil
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Avila-Rios S, Sued O, Rhee SY, Shafer RW, Reyes-Teran G, Ravasi G. Surveillance of HIV Transmitted Drug Resistance in Latin America and the Caribbean: A Systematic Review and Meta-Analysis. PLoS One 2016; 11:e0158560. [PMID: 27355626 PMCID: PMC4927069 DOI: 10.1371/journal.pone.0158560] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/19/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND HIV transmitted drug resistance (TDR) remains at moderate level in Latin America and the Caribbean (LAC). However, different epidemiologic scenarios could influence national and sub-regional TDR levels and trends. METHODS AND FINDINGS We performed a systematic review of currently available publications on TDR in antiretroviral treatment-naïve adults in LAC. Ninety-eight studies published between January 2000 and June 2015 were included according to critical appraisal criteria and classified by sub-region: Brazil (50), Mesoamerica (17), Southern Cone (16), Andean (8) and Caribbean (7). From these, 81 studies encompassing 11,441 individuals with data on DR mutation frequency were included in a meta-analysis. Overall TDR prevalence in LAC was 7.7% (95% CI: 7.2%-8.2%). An increasing trend was observed for overall TDR when comparing 2000-2005 (6.0%) and 2006-2015 (8.2%) (p<0.0001), which was associated with significant NNRTI TDR increase (p<0.0001). NRTI TDR decreased (4.5% vs. 2.3%, p<0.0001). NNRTI TDR increase was associated mainly with K101E, K103N and G190A. NRTI TDR decrease was associated mainly with M184V, K70R and T215Y. All sub-regions reached moderate overall TDR levels. The rapid increase in TDR to all antiretroviral classes in the Caribbean is notable, as well as the significant increase in NNRTI TDR reaching moderate levels in the Southern Cone. NRTI TDR was dominant in 2000-2005, mainly in the Caribbean, Mesoamerica and Brazil. This dominance was lost in 2006-2015 in all sub-regions, with the Southern Cone and the Caribbean switching to NNRTI dominance. PI TDR remained mostly constant with a significant increase only observed in the Caribbean. CONCLUSIONS Given the high conceptual and methodological heterogeneity of HIV TDR studies, implementation of surveys with standardized methodology and national representativeness is warranted to generate reliable to inform public health policies. The observed increasing trend in NNRTI TDR supports the need to strengthen TDR surveillance and programme monitoring and evaluation in LAC.
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Affiliation(s)
- Santiago Avila-Rios
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Omar Sued
- Clinical Research Section, Huésped Foundation, Buenos Aires, Argentina
| | - Soo-Yon Rhee
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Robert W. Shafer
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Gustavo Reyes-Teran
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Giovanni Ravasi
- Pan American Health Organization (PAHO), Washington DC, United States of America
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Lima K, de Souza Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Epidemiological, Clinical and Antiretroviral Susceptibility Characterization of Human Immunodeficiency Virus Subtypes B and Non-B in Pernambuco, Northeast Brazil. PLoS One 2016; 11:e0155854. [PMID: 27218259 PMCID: PMC4878750 DOI: 10.1371/journal.pone.0155854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background HIV-1 diversity causes important differences in the virus’ biological properties and their interactions with hosts, such as cell tropism, responses to antiretroviral therapy, drug-resistance, and disease progression. Objectives We evaluated the interrelationship of phylogenetic inference with epidemiological and laboratory data for HIV-1 isolates circulating in Pernambuco, Northeast Region—Brazil. Study design A total of 168 HIV-1 pol sequences were analysed, 64 were obtained from 2002–2003, and 104, from 2007–2009. Socio-demographic, clinical, and behavioural data were obtained from medical records. Laboratory testing enabled the determination of recent HIV-1 infections and co-infections with HBV, HCV, HTLV, or syphilis. Surveillance drug-resistance mutation analysis and antiretroviral susceptibility profiling were performed using HIV Drug-Resistance Database. Results HIV-1 non-B was associated with female, lower education, lower viral loads, and higher T cell counts mean. Frequencies of co-infection HIV-HBV, HIV-HCV, and HIV-syphilis were 27.8% (95% CI: 19.8–37.7), 1.04% (95% CI: 0.05–5.00) and 14.7% (95% CI: 8.6–23.0), respectively. Drug-resistant mutations rate was 2.98% (95% CI: 1.10–6.47). HIV-HBV subtype B co-infection was associated with men who have sex with men (MSM), higher education, higher viral loads and males. HIV-syphilis subtype non-B co-infection was associated with MSM status, lower T cell counts and males. Conclusions Data showed the importance of molecular characterisations of the HIV-1 epidemic and its relation with epidemiological and clinical characteristics of the population, as well as its association with other infectious diseases, so they can effort to improve preventive measures for health services and more information about the progress and effects of the epidemic in Northeastern–Brazil.
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Affiliation(s)
- Kledoaldo Lima
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
- * E-mail:
| | | | | | | | | | | | - Heloísa Ramos Lacerda
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Moura MES, da Guarda Reis MN, Lima YAR, Eulálio KD, Cardoso LPV, Stefani MMA. HIV-1 transmitted drug resistance and genetic diversity among patients from Piauí State, Northeast Brazil. J Med Virol 2015; 87:798-806. [PMID: 25649362 DOI: 10.1002/jmv.24087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2014] [Indexed: 11/10/2022]
Abstract
HIV-1 transmitted-drug-resistance and genetic diversity are dynamic and may differ in distinct locations/risk groups. In Brazil, increased AIDS incidence and related mortality have been detected in the Northeast region, differently from the epicenter in the Southeast. This cross-sectional study describes transmitted-dru- resistance and HIV-1 subtypes in protease/PR and reverse transcriptase/RT regions among antiretroviral naïve patients from Piauí State, Northeast Brazil. Among 96 patients recruited 89 (92.7%) had HIV-1 PR/RT regions sequenced: 44 females and 45 males, 22 self-declared as men who have sex with men. Transmitted-drug-resistance was investigated by CPR tool (Stanford HIV-1 Drug Resistance/SDRM). HIV-1 subtypes were assigned by REGA and phylogenetic inference. Overall, transmitted-drug-resistance rate was 11.2% (10/89; CI 95%: 5.8-19.1%); 22.7% among men who have sex with men (5/22; CI 95%: 8.8-43.4%), 10% in heterosexual men (2/20; CI 95%: 1.7-29.3%) and 6.8% in women (3/44; CI 95%: 1.8-17.4%). Singleton mutations to protease-inhibitor/PI, nucleoside-reverse-transcriptase-inhibitor/NRTI or non-nucleoside-reverse-transcriptase-inhibitor/NNRTI predominated (8/10): PI mutations (M46L, V82F, L90M); NRTI mutations (M41L, D67N) and NNRTI mutations (K103N/S). Dual class resistance mutations to NRTI and NNRTI were observed: T215L (NRTI), Y188L (NNRTI) and T215N (NRTI), F227L (NNRTI). Subtype B prevailed (86.6%; 77/89), followed by subtype F1 (1.1%, 1/89) and subtype C (1.1%, 1/89). B/F1 and B/C intersubtype recombinants represented 11.2% (10/89). In Piauí State extensive testing of incidence and transmitted-drug-resistance in all populations with risk behaviors may help control AIDS epidemic locally.
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Deep sequencing of HIV-1 near full-length proviral genomes identifies high rates of BF1 recombinants including two novel circulating recombinant forms (CRF) 70_BF1 and a disseminating 71_BF1 among blood donors in Pernambuco, Brazil. PLoS One 2014; 9:e112674. [PMID: 25401747 PMCID: PMC4234413 DOI: 10.1371/journal.pone.0112674] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/10/2014] [Indexed: 01/05/2023] Open
Abstract
Background The findings of frequent circulation of HIV-1 subclade F1 viruses and the scarcity of BF1 recombinant viruses based on pol subgenomic fragment sequencing among blood donors in Pernambuco (PE), Northeast of Brazil, were reported recently. Here, we aimed to determine whether the classification of these strains (n = 26) extends to the whole genome sequences. Methods Five overlapping amplicons spanning the HIV near full-length genomes (NFLGs) were PCR amplified from peripheral blood mononuclear cells (PBMCs) of 26 blood donors. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. The prevalence of viral variants containing drug resistant mutations (DRMs) was compared between plasma and PBMCs. Results Of the 26 samples studied, 20 NFLGs and 4 partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Two distinct BF1 recombinant profiles designated CRF70_BF1 and CRF71_BF1, with 4 samples in profile I and 11 in profile II were detected and thus constitute two novel recombinant forms circulating in PE. Evidence of dual infections was detected in four patients co-infected with distinct HIV-1 subtypes. According to our estimate, the new CRF71_BF1 accounts for 10% of the HIV-1 circulating strains among blood donors in PE. Discordant data between the plasma and PBMCs-virus were found in 15 of 24 donors. Six of these strains displayed major DRMs only in PBMCs and four of which had detectable DRMs changes at prevalence between 1-20% of the sequenced population. Conclusions The high percentage of the new RF71_BF1 and other BF1 recombinants found among blood donors in Pernambuco, coupled with high rates of transmitted DRMs and dual infections confirm the need for effective surveillance to monitor the prevalence and distribution of HIV variants in a variety of settings in Brazil.
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Prevalence of transmitted HIV-1 antiretroviral resistance among patients initiating antiretroviral therapy in Brazil: a surveillance study using dried blood spots. J Int AIDS Soc 2014; 17:19042. [PMID: 25249214 PMCID: PMC4172689 DOI: 10.7448/ias.17.1.19042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/28/2014] [Accepted: 08/20/2014] [Indexed: 11/09/2022] Open
Abstract
Introduction In Brazil, the use of antiretrovirals is widespread: more than 260,000 individuals are currently undergoing treatment. We conducted a survey targeting antiretroviral-naïve individuals who were initiating antiretroviral therapy (ART) according to local guidelines. This survey covered five Brazilian regions. Methods The HIV Threshold Survey methodology (HIV-THS) of the World Health Organization was utilized, and subjects were selected from seven highly populated cities representative of all Brazilian macro-regions. Dried blood spots (DBS) were collected on SS903 collection cards and were transported by regular mail at room temperature to a single central laboratory for genotyping. Results We analysed samples from 329 individuals initiating highly active antiretroviral therapy (HAART), 39 (11.8%) of whom were harbouring transmitted drug resistance (TDR). The mean CD4+ T cell count was 253 cells/µL, and the mean viral load was 142,044 copies/mL. The regional prevalence of resistance was 17.0% in the Northeast, 12.8% in the Southeast, 10.6% in the Central region, 8.5% in the North and 8.5% in the South. The inhibitor-specific TDR prevalence was 6.9% for nucleoside reverse transcriptase inhibitors, 4.9% for non-nucleoside reverse transcriptase inhibitors and 3.9% for protease inhibitors; 3.6% of individuals presented resistance to more than one class of inhibitors. Overall, there were trends towards higher prevalences of subtype C towards the South and subtype F towards the North. Of the DBS samples collected, 9.3% failed to provide reliable results. Discussion We identified variable TDR prevalence, ranging from intermediate to high levels, among individuals in whom HIV disease progressed, thus implying that resistance testing before initiating ART could be effective in Brazil. Our results also indicate that the use of DBS might be especially valuable for providing access to testing in resource-limited and remote settings.
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Coelho AV, Silva SP, de Alencar LC, Stocco G, Crovella S, Brandão LA, Guimarães RL. ABCB1andABCC1variants associated with virological failure of first-line protease inhibitors antiretroviral regimens in Northeast Brazil patients. J Clin Pharmacol 2013; 53:1286-93. [DOI: 10.1002/jcph.165] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/13/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Antonio V.C. Coelho
- Department of Genetics; Federal University of Pernambuco; Recife PE Brazil
- Laboratory of Immunopatology Keizo Asami (LIKA); Federal University of Pernambuco; Recife PE Brazil
| | - Suedja P.S. Silva
- Laboratory of Immunopatology Keizo Asami (LIKA); Federal University of Pernambuco; Recife PE Brazil
- Post-graduation Program of Therapeutic Innovation (PPGIT); Federal University of Pernambuco; Recife PE Brazil
| | | | - Gabriele Stocco
- Department of Life Sciences; University of Trieste; Trieste Italy
| | - Sergio Crovella
- Department of Genetics; Federal University of Pernambuco; Recife PE Brazil
- Laboratory of Immunopatology Keizo Asami (LIKA); Federal University of Pernambuco; Recife PE Brazil
| | - Lucas A.C. Brandão
- Department of Genetics; Federal University of Pernambuco; Recife PE Brazil
- Departament of Pathology; Federal University of Pernambuco; Recife PE Brazil
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Gaspareto KV, Mello FMMDA, Dias JRC, Meneguetti VAF, Storti MEG, Ferreira JLDP, Lança AM, Rodrigues R, Brígido LFDM, Teixeira JJV, Bertolini DA. Genetic diversity and primary resistance among HIV-1-positive patients from Maringá, Paraná, Brazil. Rev Inst Med Trop Sao Paulo 2012; 54:207-13. [PMID: 22850992 DOI: 10.1590/s0036-46652012000400005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 05/03/2012] [Indexed: 11/21/2022] Open
Abstract
The objective of this study is to identify subtypes of Human Immunodeficiency Virus type 1 (HIV-1) and to analyze the presence of mutations associated to antiretroviral resistance in the protease (PR) and reverse transcriptase (RT) regions from 48 HIV-1 positive treatment naïve patients from an outpatient clinic in Maringá, Paraná, Brazil. Sequencing was conducted using PR, partial RT and group-specific antigen gene (gag) nested PCR products from retrotranscribed RNA. Transmitted resistance was determined according to the Surveillance Drug Resistance Mutation List (SDRM) algorithm. Phylogenetic and SimPlot analysis of concatenated genetic segments classified sequences as subtype B 19/48 (39.6%), subtype C 12/48 (25%), subtype F 4/48 (8.3%), with 13/48 (27.1%) recombinant forms. Most recombinant forms were B mosaics (B/F 12.5%, B/C 10.4%), with one C/F (2.1%) and one complex B/C/F mosaic (2.1%). Low levels of transmitted resistance were found in this study, 2/48 (2.1% to NRTIs and 2.1% for PI). This preliminary data may subsidize the monitoring of the HIV evolution in the region.
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Affiliation(s)
- Karine Vieira Gaspareto
- Laboratório de Retrovírus, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, SP, Brazil
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Cavalcanti AMS, Brito AMD, Salustiano DM, Lima KOD, Silva SPD, Diaz RS, Lacerda HR. Primary resistance of HIV to antiretrovirals among individuals recently diagnosed at voluntary counselling and testing centres in the metropolitan region of Recife, Pernambuco. Mem Inst Oswaldo Cruz 2012; 107:450-7. [DOI: 10.1590/s0074-02762012000400002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 02/27/2012] [Indexed: 11/21/2022] Open
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Carvalho BC, Cardoso LPV, Damasceno S, Stefani MMDA. Moderate prevalence of transmitted drug resistance and interiorization of HIV type 1 subtype C in the inland North State of Tocantins, Brazil. AIDS Res Hum Retroviruses 2011; 27:1081-7. [PMID: 21417758 DOI: 10.1089/aid.2010.0334] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diverse Brazilian AIDS epidemic has reached small cities and scant molecular information is available about the epidemic in Northern Brazil, where the incidence is growing. This study describes transmitted drug resistance and subtypes in the protease (PR) and reverse transcriptase (RT) regions among naive patients recruited in Palmas, the capital of Tocantins State, a newly built city in Northern Brazil. PR/RT regions were retrotranscribed from plasma HIV-1 RNA and 52 were sequenced after direct nested PCR. HIV-1 subtypes were assigned by phylogenetic analysis. Transmitted drug resistance was analyzed by the Calibrated Population Resistance tool Stanford Surveillance Drug Resistance Mutation. Most patients included (59.6%) were males, the median age was 30 years and were mainly referred because of heterosexual or homosexual unprotected sex. One male patient was from the Karajás indigenous tribe. The prevalence of transmitted resistance was 11.5% (CI 95%, 4.4-23.4%): nonnucleoside RT inhibitor mutations (n=3), nucleoside RT inhibitor mutations (n=2), and protease inhibitor mutations (n=1). Dual or triple class resistance was not observed. HIV-1 subtype B(PR)/B(RT) represented 78.8%, 5.8% were subtype C(PR)/C(RT), and 1.9% were subtype F1(PR)/F1(RT). Recombinant viruses represented 13.5% (07/52): B(PR)/F1(RT) (n=1), B(PR)/BF1(RT) (n=4), and C(PR)/CF1(RT) (n=2). This study about the AIDS epidemic in the recently founded city of Palmas/Tocantins in inland Northern Brazil shows moderate levels of transmitted drug resistance and the circulation of diverse recombinant viruses. This pattern is similar to what has been described in major metropolitan cities, suggesting the influence of imported cases from the south/southeast. Moreover these results indicate that patients from this setting should be monitored regarding transmitted drug resistance mutations.
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Ferreira AS, Cardoso LPV, Stefani MMDA. Moderate prevalence of transmitted drug resistance and high HIV-1 genetic diversity in patients from Mato Grosso State, Central Western Brazil. J Med Virol 2011; 83:1301-7. [DOI: 10.1002/jmv.22128] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Gagliani LH, Alkmim Maia WT, Sá-Filho D, Janini LM, Sucupira MC, Caseiro MM, Diaz RS. The association between primary antiretroviral resistance and HAART virologic failure in a developing set. AIDS Res Hum Retroviruses 2011; 27:251-6. [PMID: 20977353 DOI: 10.1089/aid.2010.0150] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Santos is a Brazilian port city with high HIV incidence, high primary antiretroviral resistance levels, high HIV-1 BF recombinants prevalence, and high rates of antiretroviral virologic failure. We evaluated factors related to virologic failure after 48 weeks of HAART in this population. We compared demographic and HIV profiles among 43 individuals with virologic failure (group 1) and 37 with virologic success (group 2) after 48 weeks of HAART initiation. The overall primary antiretroviral resistance prevalence was 31.2%; 46.5% in group 1 and 13.5% in group 2 (p < 0.005). Nine patients from group 1 and seven from group 2 were infected by F or BF strains. Fifteen individuals presented with NRTI mutations, 13 with NNRTI mutations, three with PI mutations, and five with NRTI and NNRTI mutations. No significant differences were observed in baseline viral load, CD4, clade assignment, antiretrovirals used, or demographics among groups or patients harboring resistant versus wild-type viruses. In this region, there was a high prevalence of antiretroviral resistance among long standing infected patients whose disease had progressed. This finding supports the concept that resistance testing prior to ART initiation is cost effective. The association between primary antiretroviral resistance and virologic failure may suggest that primary resistance greatly impairs antiretroviral activity.
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Affiliation(s)
- Luiz Henrique Gagliani
- Federal University of São Paulo, São Paulo, Brazil
- Centro Universitário Lusíada, Santos, Brazil
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Ferreira F, Pinto J, Kakehasi F, Cleto S, Tupinambás U, Aleixo A, Cardoso C. Prevalence of primary drug resistance-associated mutations among HIV type 1 vertically Infected children in Belo Horizonte, Brazil. AIDS Res Hum Retroviruses 2010; 26:229-32. [PMID: 20156105 DOI: 10.1089/aid.2009.0146] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the past few years there has been increasing concern about the transmission of drug-resistant HIV. This study aimed to describe the frequency of primary mutations associated with HIV-1 drug resistance and the prevalence of genetic HIV subtypes in a population of vertically infected children before the initiation of HAART. At the time of genotypic testing, the median age was 6.0 years (IQR 25-75%: 3.8-9.2) and the median age at admission was 3.84 years (IQR 25-75%: 1.23-6.11). Antepartum maternal ARV exposure for PMTCT occurred for three (7.3%) mothers. According to the WHO criteria, primary ARV resistance mutations were detected in four out of 41 (9.8%) children. Subtype B was the most prevalent (63.4%). The relatively high prevalence of primary HIV-1 DRMs in this cohort of perinatally infected children in Brazil supports the local recommendation to perform resistance testing in all newly diagnosed children, regardless of age at diagnosis and antenatal ARV exposure.
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Affiliation(s)
- F.G.F. Ferreira
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - J.A. Pinto
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - F.M. Kakehasi
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - S. Cleto
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - U. Tupinambás
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - A.W. Aleixo
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - C.S. Cardoso
- School of Medicine, Federal University of Minas Gerais, Belo Horizonte, Brazil
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HIV-1 pol phylogenetic diversity and antiretroviral resistance mutations in treatment naïve patients from Central West Brazil. J Clin Virol 2009; 46:134-9. [DOI: 10.1016/j.jcv.2009.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 07/03/2009] [Accepted: 07/15/2009] [Indexed: 11/23/2022]
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Inocencio LA, Pereira AA, Sucupira MCA, Fernandez JCC, Jorge CP, Souza DF, Fink HT, Diaz RS, Becker IM, Suffert TA, Arruda MB, Macedo O, Simão MB, Tanuri A. Brazilian Network for HIV Drug Resistance Surveillance: a survey of individuals recently diagnosed with HIV. J Int AIDS Soc 2009; 12:20. [PMID: 19765271 PMCID: PMC2759910 DOI: 10.1186/1758-2652-12-20] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 09/18/2009] [Indexed: 12/27/2022] Open
Abstract
Use of antiretrovirals is widespread in Brazil, where more than 200,000 individuals are under treatment. Although general prevalence of primary antiretroviral resistance in Brazil is low, systematic sampling in large metropolitan areas has not being performed.The HIV Threshold Survey methodology (HIV-THS, WHO) was utilized, targeting Brazil's four major regions and selecting the six most populated state capitals: Sao Paulo, Rio de Janeiro, Salvador, Porto Alegre, Brasilia and Belem. We were able to sequence samples from 210 individuals with recent HIV diagnosis, 17 of them (8.1%) carrying HIV isolates with primary antiretroviral resistance mutations. Five, nine and four isolates showed mutations related to resistance to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs), respectively. Using HIV-THS, we could find an intermediate level of transmitted resistance (5% to 15%) in Belem/Brasilia, Sao Paulo and Rio de Janeiro. Lower level of transmitted resistance (<5%) were observed in the other areas. Despite the extensive antiretroviral exposure and high rates of virologic antiretroviral failure in Brazil, the general prevalence of primary resistance is still low. However, an intermediate level of primary resistance was found in the four major Brazilian cities, confirming the critical need to start larger sampling surveys to better define the risk factors associated with transmission of resistant HIV.
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Ferreira JLDP, Thomaz M, Rodrigues R, Harrad D, Oliveira CM, Oliveira CADF, Batista JPG, Ito TS, Brigido LFDM. Molecular characterisation of newly identified HIV-1 infections in Curitiba, Brazil: preponderance of clade C among males with recent infections. Mem Inst Oswaldo Cruz 2008; 103:800-8. [DOI: 10.1590/s0074-02762008000800010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 11/12/2008] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | - David Harrad
- Coordenação Municipal de DST/Aids de Curitiba, Brasil
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Abstract
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.
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Eyer-Silva WA, Couto-Fernandez JC, Silva-de-Jesus C, Morgado MG. Prevalence of HIV type 1 drug resistance mutations in treatment-naïve and experienced patients from resource-limited settings with universal access to antiretroviral therapy: a survey in two small Brazilian cities. Mem Inst Oswaldo Cruz 2008; 103:143-9. [DOI: 10.1590/s0074-02762008000200004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 03/20/2008] [Indexed: 11/22/2022] Open
Affiliation(s)
- Walter A Eyer-Silva
- Fiocruz, Brasil; Universidade Federal do Estado do Rio de Janeiro, Brasil; Programa Municipal de HIV-1/Aids de Saquarema, Brasil; Programa Municipal de HIV-1/Aids de Santo Antonio de Pádua, Brasil
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Cavalcanti AMS, Lacerda HR, Brito AMD, Pereira S, Medeiros D, Oliveira S. Antiretroviral resistance in individuals presenting therapeutic failure and subtypes of the human immunodeficiency virus type 1 in the Northeast Region of Brazil. Mem Inst Oswaldo Cruz 2007; 102:785-92. [PMID: 17992369 DOI: 10.1590/s0074-02762007005000109] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 09/17/2007] [Indexed: 11/21/2022] Open
Abstract
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.
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Gonsalez CR, Alcalde R, Nishiya A, Barreto CC, Silva FES, de Almeida A, Mendonça M, Ferreira F, Fernandes SS, Casseb J, Duarte AJS. Drug resistance among chronic HIV-1-infected patients naïve for use of anti-retroviral therapy in Sao Paulo city. Virus Res 2007; 129:87-90. [PMID: 17686543 DOI: 10.1016/j.virusres.2007.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/25/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
Primary infection with drug-resistant HIV appears to be increasing in the regions where HAART is widely available, which may reduce efficacy of first-line antiretroviral therapy. To determine prevalence of antiretroviral drug-resistant mutations in newly diagnosed subjects in a clinical setting where HAART has been widely used since 1997. One hundred and thirty-six HIV-1-infected adult patients were diagnosed with HIV infection between January 2000 and December 2006 in the HIV out-clinic at the HC/FMUSP, Sao Paulo city. These antiretroviral naïve patients were mainly referred from the blood bank, situated in the same building or elsewhere in the city. The samples were genotyped to provide HIV protease and reverse transcriptase sequence data. Major antiretroviral drug resistance mutations were classified according to Shafer et al. [Shafer, R.W., Rhee, S.Y., Pillay, D., et al., 2007. HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS 21, 215-223]. Thirteen cases had no DNA amplification, and 123 patients were successfully analyzed, with a mean age of 37 years and 89 (72%) were males. Antiretroviral drug resistance mutations were detected in 8/123 patients (6.5%), all eight were heterosexuals and HIV asymptomatic, the mean of the CD4 cells count was 323 cells/mm(3), and the RNA plasma viral load was 4.7 log(10)/mL. We found NRTI (n=2, 1.6%), NNRTI-resistant (n=2, 1.6%) mutations, and one cases with PI mutation (0.8%). Three cases (2.4%) showed mutations for NRTI, NNRTI or PI, simultaneously. Eighty-two percent were HIV-1 B subtype, and HIV-1 F (6.5%), HIV-1 C (5.7%) and recombinant viruses (5.8%) were observed. In an unselected cohort, primary drug resistance was seen in 6.5% of the naïve for drug ART use. These results indicate that HIV drug resistance testing should be a practical approach in monitoring first-line ART. In addition, HIV-1 C seems to be emerging in Sao Paulo city.
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Affiliation(s)
- Cláudio R Gonsalez
- Laboratory of Medical Investigation in Dermatology and Immunodeficiencies (LIM-56), University of Sao Paulo Medical School, Sao Paulo, Brazil
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