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Corado ADLG, Bello G, Leão RAC, Granja F, Naveca FG. HIV-1 genetic diversity and antiretroviral drug resistance among individuals from Roraima state, northern Brazil. PLoS One 2017; 12:e0173894. [PMID: 28301548 PMCID: PMC5354385 DOI: 10.1371/journal.pone.0173894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/28/2017] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Fabiana Granja
- Laboratório de Biologia Molecular, Universidade Federal de Roraima (UFRR), Boa Vista, Roraima, 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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Inzaule SC, Weidle PJ, Yang C, Ndiege K, Hamers RL, Rinke de Wit TF, Thomas T, Zeh C. Prevalence and dynamics of the K65R drug resistance mutation in HIV-1-infected infants exposed to maternal therapy with lamivudine, zidovudine and either nevirapine or nelfinavir in breast milk. J Antimicrob Chemother 2016; 71:1619-26. [PMID: 26953333 DOI: 10.1093/jac/dkw039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND K65R is a relatively rare drug resistance mutation (DRM) selected by the NRTIs tenofovir, didanosine, abacavir and stavudine and confers cross-resistance to all NRTIs except zidovudine. Selection by other NRTIs is uncommon. OBJECTIVES In this study we investigated the frequency of emergence of the K65R mutation and factors associated with it in HIV-1-infected infants exposed to low doses of maternal lamivudine, zidovudine and either nevirapine or nelfinavir ingested through breast milk, using specimens collected from the Kisumu Breastfeeding Study. METHODS Plasma specimens with viral load ≥1000 copies/mL collected from HIV-infected infants at 0-1, 2, 6, 14, 24 and 36 weeks of age and maternal samples at delivery were tested for HIV drug resistance using Sanger sequencing of the polymerase gene. Factors associated with K65R emergence were assessed using Fisher's exact test and the Wilcoxon rank-sum test. RESULTS K65R was detected in samples from 6 of the 24 infants (25%) who acquired HIV-1 infection by the age of 6 months. K65R emerged in half of the infants by 6 weeks and in the rest by 14 weeks of age. None of the mothers at delivery or the infants with a positive genotype at first time of positivity had the K65R mutation. Infants with K65R had low baseline CD4 cell counts (P = 0.014), were more likely to have DRMs earlier (≤6 weeks versus ≥14 weeks, P = 0.007) and were more likely to have multiclass drug resistance (P = 0.035). M184V was the most common mutation associated with K65R emergence. K65R had reverted by 3 months after cessation of breastfeeding. CONCLUSIONS A high rate of K65R emergence may suggest that ingesting low doses of lamivudine via breast milk could select for this mutation. The presence of this mutation may have a negative impact on future responses to NRTI-based ART. More in vitro studies are, however, needed to establish the molecular mechanism for this selection.
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Affiliation(s)
- Seth C Inzaule
- Kenya Medical Research Institute, Kisumu, Kenya Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Paul J Weidle
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chunfu Yang
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Raph L Hamers
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Tobias F Rinke de Wit
- Department of Global Health, Academic Medical Center of the University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Timothy Thomas
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clement Zeh
- Centers for Disease Control and Prevention, Kisumu, Kenya
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A single early introduction of HIV-1 subtype B into Central America accounts for most current cases. J Virol 2013; 87:7463-70. [PMID: 23616665 DOI: 10.1128/jvi.01602-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1 pol gene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n = 57) and the rest of the world (n = 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country.
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Ammaranond P, Sanguansittianan S. Mechanism of HIV antiretroviral drugs progress toward drug resistance. Fundam Clin Pharmacol 2011; 26:146-61. [PMID: 22118474 DOI: 10.1111/j.1472-8206.2011.01009.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapid replication rate of HIV-1 RNA and its inherent genetic variation have led to the production of many HIV-1 variants with decreased drug susceptibility. The capacity of HIV to develop drug resistance mutations is a major obstacle to long-term effective anti-HIV therapy. Incomplete suppression of viral replication with an initial drug regimen diminishes the clinical benefit to the patient and may promote the development of broader drug resistance that may cause subsequent treatment regimens to be ineffective. The increased clinical use of combination antiretroviral treatment for HIV-1 infection has led to the selection of viral strains resistant to multiple drugs, including strains resistant to all licensed nucleoside analog RT inhibitors and protease inhibitors. Therefore, it is important to understand the influence of such mutations on viral properties such as replicative fitness, fidelity, and mutation rates. Although research continues to improve our understanding of resistance, leading to refined treatment strategies and, in some cases, improved outcome, resistance to antiretroviral therapy remains a major cause of treatment failure among patients living with HIV-1.
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Affiliation(s)
- Palanee Ammaranond
- Department of Transfusion Medicine, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.
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DiazGranados CA, Mantilla M, Lenis W. Antiretroviral drug resistance in HIV-infected patients in Colombia. Int J Infect Dis 2010; 14:e298-303. [DOI: 10.1016/j.ijid.2009.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 04/17/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022] Open
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Castillo J, Comegna M, Quijada W, Jauvin V, Pinson P, Masquelier B, Fleury H, Castro E. Surveillance of HIV type 1 drug resistance among naive patients from Venezuela. AIDS Res Hum Retroviruses 2009; 25:1329-33. [PMID: 19954301 DOI: 10.1089/aid.2009.0118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have studied 65 HIV-1-infected untreated patients recruited in Caracas, Venezuela with TCD4 counts > or =350/microl. The reverse transcriptase and protease sequences of the virus were sequenced, aligned with reference HIV-1 group M strains, and analyzed for drug resistance mutations. Most of the viruses were subtype B genotype in both the protease and RT genomic regions. Five of the 62 virus isolates successfully amplified showed evidence of recombination between protease and RT, with their protease region being non-B while their RT region was derived from subtype B. Four strains were found bearing resistance mutations either to NRTIs, NNRTIs, or PIs. The prevalence of HIV-1 isolates bearing resistance mutations was therefore above the 5% threshold of WHO.
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Affiliation(s)
- Julio Castillo
- Department of Internal Medicine, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Mario Comegna
- Department of Infectious Diseases, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Wilmary Quijada
- Department of Internal Medicine, Vargas Hospital, Central University of Venezuela, Caracas, Venezuela
| | - Valérie Jauvin
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Patricia Pinson
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Bernard Masquelier
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Hervé Fleury
- Laboratoire de Virologie EA 2968, Université de Bordeaux, Bordeaux, France
| | - Erika Castro
- Laboratory of AIDS Immunopathogenesis, Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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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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Chan PA, Kantor R. Transmitted drug resistance in nonsubtype B HIV-1 infection. ACTA ACUST UNITED AC 2009; 3:447-465. [PMID: 20161523 DOI: 10.2217/hiv.09.30] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV-1 nonsubtype B variants account for the majority of HIV infections worldwide. Drug resistance in individuals who have never undergone antiretroviral therapy can lead to early failure and limited treatment options and, therefore, is an important concern. Evaluation of reported transmitted drug resistance (TDR) is challenging owing to varying definitions and study designs, and is further complicated by HIV-1 subtype diversity. In this article, we discuss the importance of various mutation lists for TDR definition, summarize TDR in nonsubtype B HIV-1 and highlight TDR reporting and interpreting challenges in the context of HIV-1 diversity. When examined carefully, TDR in HIV-1 non-B protease and reverse transcriptase is still relatively low in most regions. Whether it will increase with time and therapy access, as observed in subtype-B-predominant regions, remains to be determined.
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Rangel HR, Garzaro DJ, Torres JR, Castro J, Suarez JA, Naranjo L, Ossenkopp J, Martinez N, Gutierrez C, Pujol FH. Prevalence of antiretroviral drug resistance among treatment-naive and treated HIV-infected patients in Venezuela. Mem Inst Oswaldo Cruz 2009; 104:522-5. [PMID: 19547882 DOI: 10.1590/s0074-02762009000300020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 03/03/2009] [Indexed: 11/22/2022] Open
Abstract
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.
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Affiliation(s)
- Héctor Rafael Rangel
- Laboratorio de Virología Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
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Lloyd B, O'Connell RJ, Michael NL, Aviles R, Palou E, Hernandez R, Cooley J, Jagodzinski LL. Prevalence of resistance mutations in HIV-1-Infected Hondurans at the beginning of the National Antiretroviral Therapy Program. AIDS Res Hum Retroviruses 2008; 24:529-35. [PMID: 18366313 DOI: 10.1089/aid.2007.0172] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Honduran Ministry of Health (MOH) HIV antiretroviral treatment program began widespread treatment in 2003. We investigated the prevalence of antiretroviral genotypic resistance in specimens collected and archived from HIV-1-infected antiretroviral-naive patients presenting to initiate treatment between 1 July, 2002 and 30 June, 2003 in San Pedro Sula and Tegucigalpa, Honduras. Of 416 specimens collected, 336 (80.8%) were successfully genotyped. All genotypes were HIV-1, group M and 99.1% were subtype B. The prevalence of nucleoside reverse transcriptase inhibitor mutations was 7.7% with M184V and T215F/Y present in 6.0% and 3.0%, respectively. The prevalence of nonnucleoside reverse transcriptase inhibitor mutations was 7.1%. K103N mutations were present in 3.0% of study specimens. The prevalence of major protease inhibitor mutations was 2.7%. Overall, 9.2% of the specimens harbored clinically significant mutations that predict at least intermediate resistance to the Honduran first-line antiretroviral medications. These mutations were more common in San Pedro Sula (14.0%) than in Tegucigalpa (6.5%, p = 0.02). A significant number of patients presenting to initiate antiretroviral therapy in Honduran MOH clinics harbored HIV-1 isolates resistant to the MOH's first-line regimen and resistance varied by region. Further studies to assess the impact of the Honduran antiretroviral program on genotypic resistance are warranted.
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Affiliation(s)
- Bradley Lloyd
- Department of Infectious Disease, Wilford Hall Medical Center, Lackland AFB, Texas 78236
| | - Robert J. O'Connell
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | - Nelson L. Michael
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850
| | | | - Elsa Palou
- Instituto Nacional Del Tórax, Tegucigalpa, Honduras
| | | | - John Cooley
- Henry M. Jackson Foundation, Rockville, Maryland 20850
| | - Linda L. Jagodzinski
- Division of Retrovirology, Walter Reed Army Institute of Research, Rockville, Maryland 20850
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Sa-Filho D, Kallas EG, Sanabani S, Sabino E, Sucupira MC, Sanchez-Rosa AC, Tescarollo G, Tomiyama H, Bassichetto K, Janini LM, Diaz RS. Characterization of the full-length human immunodeficiency virus-1 genome from recently infected subjects in Brazil. AIDS Res Hum Retroviruses 2007; 23:1087-94. [PMID: 17919103 DOI: 10.1089/aid.2006.0173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Sabri Sanabani
- Fundação Pro Sangue/Hemocentro de São Paulo, São Paulo, Brazil
| | - Ester Sabino
- Fundação Pro Sangue/Hemocentro de São Paulo, São Paulo, Brazil
| | | | | | | | | | - Katia Bassichetto
- Coordenação Municipal de DST/AIDS, Secretaria Municipal de Saude de São Paulo, São Paulo, Brazil
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Bouchard M, Masquelier B, Moreno M, Deibis L, De Pérez GE, Fleury H, Castro E. HIV type 1 drug resistance among naive patients from Venezuela. AIDS Res Hum Retroviruses 2007; 23:482-5. [PMID: 17411383 DOI: 10.1089/aid.2006.0219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we characterize proviral DNA of 20 HIV-1 asymptomatic antiretroviral-naive patients from Venezuela in env, gag, and pol genes regions. Results from both env/gag HMA subtyping and phylogenetic analysis of pol partial sequences led to the description of clade B in all cases. Nevertheless, the high prevalence of polymorphisms was particularly evident among the protease sequences. A 10% prevalence of major resistance mutations to RTIs was found. Our data also suggested that the protease polymorphisms I62T and V77T could be considered as molecular markers of the subtype B local epidemic. In addition, we show how proviral DNA can be used as a reliable tool to follow trends of resistance mutation transmission.
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Affiliation(s)
- Morella Bouchard
- Immunology Institute, Central University of Venezuela, Caracas, Venezuela
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Ríos M, Delgado E, Pérez-Alvarez L, Fernández J, Gálvez P, de Parga EV, Yung V, Thomson MM, Nájera R. Antiretroviral drug resistance and phylogenetic diversity of HIV-1 in Chile. J Med Virol 2007; 79:647-56. [PMID: 17457921 DOI: 10.1002/jmv.20881] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study reports the analysis of human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) coding sequences from 136 HIV-1-infected subjects from Chile, 66 (49%) of them under antiretroviral (ARV) treatment. The prevalence of mutations conferring high or intermediate resistance levels to ARVs was 77% among treated patients and 2.5% among drug-naïve subjects. The distribution of resistance prevalence in treated patients by drug class was 61% to nucleoside RT inhibitors, 84% to nonnucleoside RT inhibitors, and 46% to PR inhibitors. Phylogenetic analysis revealed that 115 (85%) subjects were infected with subtype B viruses, 1 with a subtype F1 virus, and 20 (15%) carried BF intersubtype recombinants. Most BF recombinants grouped into two clusters, one related to CRF12_BF, while the other could represent a new circulating recombinant form (CRF). In conclusion, this is the first report analysing the prevalence of ARV resistance which includes patients under HAART from Chile. Additionally, phylogenetic analysis of the PR-RT coding sequences reveals the presence of BF intersubtype recombinants.
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Affiliation(s)
- Maritza Ríos
- Centro Nacional de Referencia de VIH/SIDA, Instituto de Salud Pública de Chile, Santiago, Chile
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Stankov S. [Development and role of comparative sequence analysis in medical virology]. ACTA ACUST UNITED AC 2006; 59:138-42. [PMID: 17066585 DOI: 10.2298/mpns0604138s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Development of the polymerase chain reaction and deoxyribonucleic acid sequencing techniques has enabled precise identification, classification and taxonomy of viruses. COMPARATIVE SEQUEENCE ANALYSIS: (Comparative sequence analysis methods can be used in medical virology for many practical purposes. They may be classified into three broad categories: I - reconstruction of genealogical relationships between individual viral isolatesfor detection and monitoring of sources, reservoirs and modes of viral transmission; II - virus genotyping, that is determination of relationships between genetic types of viruses and their phenotypic properties, which has important implications for immunoprophylaxis, therapy and prognosis of viral diseases, and III investigation of functional properties of defined viral sequences, of special importance for explanation of viral pathogenesis and design of antiviral drugs. FUTURE PROSPECTS The combination of DNA sequencing with polymerase chain reaction following reverse transcription with the use of random primers offers a universal means for diagnosis of viral infections.
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Collins ML, Sondel N, Cesar D, Hellerstein MK. Effect of nucleoside reverse transcriptase inhibitors on mitochondrial DNA synthesis in rats and humans. J Acquir Immune Defic Syndr 2005; 37:1132-9. [PMID: 15319672 DOI: 10.1097/01.qai.0000131585.77530.64] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) have been hypothesized to inhibit mitochondrial DNA polymerase gamma, resulting in decreased mtDNA synthesis and mitochondrial insufficiency in HIV-1-infected patients. mtDNA synthesis was measured directly using a stable isotope mass spectrometric method following NRTI treatment in rodents. 3'-Azido-3'-deoxythymidine (AZT) was added to water (1 mg/mL) and administered ad libitum to female Sprague-Dawley rats for 1-8 weeks (n = 4 or 5 animals/timepoint). Neither body weight nor food intake was affected by AZT intake. Untreated controls and AZT-treated rats were given 4% H2O as drinking water for 2 weeks. AZT (approximately 100 mg/kg/d) produced a significant (P < 0.05) decrease in cardiac and hindlimb muscle mtDNA fractional synthesis compared with control groups (from 13.8 +/- 4.2% to 7.0 +/- 4.8% and from 7.6 +/- 1.8% to 4.5 +/- 0.4%, respectively) after 4 weeks. Cytochrome c oxidase content in hindlimb muscle was also decreased by 50% compared with controls after 4 weeks of AZT treatment (P < 0.07) and a calculated index of absolute mitochondrial biogenesis rate was significantly reduced by week 2 of AZT (P < 0.05) in hindlimb muscle. In preliminary studies, platelet mtDNA enrichments were compared to monocyte nDNA enrichments (used as a marker of a fully turned over tissue) in healthy human subjects. Fractional synthesis of mtDNA in platelets reached 98 +/- 3% after 5 weeks of H2O labeling. It is concluded that NRTIs decrease mtDNA synthesis and oxidative enzyme content and thus mitochondrial biogenesis in rodents and that the effects of NRTIs on mitochondrial biogenesis in tissues of HIV-1- infected humans can in principle be measured using this approach.
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Affiliation(s)
- Michelle L Collins
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, CA 94720-3104, USA
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Sachdeva N, Sehgal S, Arora SK. Frequency of Drug-Resistant Variants of HIV-1 Coexistent With Wild-Type in Treatment-Naive Patients of India. J Int AIDS Soc 2005; 7:68. [PMID: 19825133 PMCID: PMC2804708 DOI: 10.1186/1758-2652-7-3-68] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Context Over the past few years, reports of emergence and transmission of drug-resistant strains of HIV have increased, especially in western countries. In the context of increased widespread use of zidovudine- and lamivudine-based combinations in India, coupled with the genetic diversity of HIV, it is essential to generate preliminary data on the frequency of zidovudine- and lamivudine-resistant variants of HIV-1 in North India. Objectives In the present study, the authors screened for mutations in the pol gene of HIV-1 associated with resistance to zidovudine and lamivudine in HIV-infected treatment-naive patients from North India. Design and Patients The mutations were screened at codons 70 and 215 (conferring resistance to zidovudine) and at codon 184 (conferring resistance to lamivudine) by using a nested amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) approach from the proviral DNA of 60 patients. Results Most of the patients showed a mixture of both wild-type and mutant virus. In all but 1 patient, wild-type virus was observed with respect to each codon. Mutant variants were also observed in many patients, especially at codon 70 (48 patients [80%]) and codon 184 (19 patients [31.67%]). In contrast, the frequency of mutation at codon 215 was found to be very low (1 patient [1.67%]). Conclusion In this sample of treatment-naive HIV-1-infected patients in North India, a high proportion of mutant variants harbored mutations in the pol gene at codons- 70 and 184 coexisting with wild-type HIV-1.
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Affiliation(s)
- Naresh Sachdeva
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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18
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Castro E, Moreno M, Deibis L, de Pérez G, Salmen S, Berrueta L. Trends of HIV-1 molecular epidemiology in Venezuela: introduction of subtype C and identification of a novel B/C mosaic genome. J Clin Virol 2005; 32:257-8. [PMID: 15722034 DOI: 10.1016/j.jcv.2004.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 11/03/2004] [Indexed: 11/20/2022]
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19
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Sa Filho DJD, Sanabani S, Diaz RS, Munerato P, Brunstein A, Fusuma E, Sabino EC, Janini LM. Analysis of full-length human immunodeficiency virus type 1 genome reveals a variable spectrum of subtypes B and f recombinants in São Paulo, Brazil. AIDS Res Hum Retroviruses 2005; 21:145-51. [PMID: 15725753 DOI: 10.1089/aid.2005.21.145] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombination is one of the major mechanisms contributing to human immunodeficiency virus type 1 (HIV-1) variability. Analysis of pol gene sequences of 215 HIV-1 samples from São Paulo, Brazil classified 189 sequences as subtype B (87.9%), 8 sequences as subtype F (3.7%), and 18 sequences (8.4%) as B/F recombinants. After the analysis of the pol gene, a subset of six recombinant samples composed of sequences with a related recombinant pol structure was selected for full-length genome analysis to identify a possible circulating recombinant form. According to full-length genome analysis, recombination was higher in gag, protease, reverse transcriptase, integrase, and vif. Identification of many distinct recombinant forms and the absence of an identifiable HIV-1 circulating recombinant form suggest that a high frequency of dual infections between HIV-1 subtypes B and F is occurring in São Paulo, Brazil.
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20
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Gale CV, Myers R, Tedder RS, Williams IG, Kellam P. Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. AIDS Res Hum Retroviruses 2004; 20:457-64. [PMID: 15186519 DOI: 10.1089/088922204323087697] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have developed a high throughput computational tool for assigning subtype to HIV-1, based solely on protease and reverse transcriptase (PR-RT) amino acid sequence, generated routinely for clinical assessment of genotypic drug resistance. Subtype-specific profiles were created by generation of position-specific scoring matrices (PSSMs) from multiple amino acids alignments of HIV-1 sequence data from GenBank, phylogenetically divided into subtypes A, AG, B, C, D, F/K, G, H, and J and the separate groups N and O. Query sequences of unknown subtype are aligned with these profiles and a score is derived by comparing each amino acid position in the unknown sequence to the normalized frequency distribution of amino acids at the corresponding positions in the subtype alignments. The highest score is used to assign subtype to the query sequence. Leave one out cross-validation analysis showed the Subtype Analyzer (STAR) was 99% accurate in subtype assignation. STAR can be updated with additional subtype-specific sequence data from sequence databases. STAR was used to classify HIV-1 PR-RT sequences from 843 HIV-1 clinical isolates submitted for drug resistance profiling in London. Within this dataset 26.9% of sequences were classified by STAR as non-B subtypes.
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Affiliation(s)
- Catherine V Gale
- Department of Infection, University College London, London W1T 4JF, UK
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21
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Abstract
BACKGROUND The use of highly-active anti-retroviral therapy (HAART) for treating HIV infections is increasing. Recent studies have demonstrated that HAART is improving both the length and quality of life in HIV-infected patients. Resistant strains of HIV arise when drug adherence is poor. This can lead to the transmission of drug-resistant strains of HIV to susceptible individuals. This can lead to suboptimal first-line therapy, if the resistance profile of the transmitted virus is unknown. OBJECTIVES To review the mechanisms of how drug resistance arises; the methods used to characterise drug resistance; the problems arising with compliance leading to the development of drug-resistant HIV strains; the evidence for the incidence, prevalence and trends in the transmission of resistant HIV strains in different risk groups; and the evidence of suboptimal response to first-line therapy where transmission of a resistant HIV strain has occurred. On the basis of this, a case is presented for the routine resistance testing of all newly diagnosed HIV-infected individuals. STUDY DESIGN Literature review. RESULTS AND CONCLUSIONS There is evidence, though limited at present, that transmission of drug-resistant HIV strains can lead to suboptimal response to first-line therapy in newly diagnosed HIV-infected individuals. As the use of HAART can only increase in the future, and compliance will always be a problem in such HAART-treated patients, baseline resistance testing should become a routine part of their management.
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Affiliation(s)
- Julian W Tang
- Department of Virology, Windeyer Institute of Medical Sciences, Royal Free and University College Medical Schools, 46 Cleveland Street, London W1T 4JF, UK
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22
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Brindeiro RM, Diaz RS, Sabino EC, Morgado MG, Pires IL, Brigido L, Dantas MC, Barreira D, Teixeira PR, Tanuri A. Brazilian Network for HIV Drug Resistance Surveillance (HIV-BResNet): a survey of chronically infected individuals. AIDS 2003; 17:1063-9. [PMID: 12700457 DOI: 10.1097/00002030-200305020-00016] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To study the prevalence of HIV drug resistance mutations and subtype distribution in a Brazilian drug-naive population. Asymptomatic, drug-naive HIV-1-infected individuals were targeted in 13 voluntary counseling and testing centers spread around the country. METHODS Plasma viral RNA was extracted from 535 HIV-1-positive subjects. Protease (PR) and reverse transcriptase (RT) genomic regions were sequenced for subtype determination and analysis of drug resistance mutations. RESULTS Eight samples (2.24 %) showed primary mutations related to protease inhibitor (PI) resistance, eight (2.36%) to nucleoside reverse transcriptase inhibitors (NRTI) and seven (2.06%) to non-nucleoside reverse transcriptase inhibitors (NNRTI). Accessory mutations were found in the PR gene at the following positions: L63P/V/T/A/I [153/345 (44.3%)], M36I/L [149/345 (43.2%)], L10I/F/V [82/345 (23.8%)], V77I [60/345 (17.4%)], A71V/T [11/345 (3.2%)], K20M/R [10/345 (2.9%)], and V82I [4/345 (1.2%)]. Mutations known to be associated with reduced sensitivity to NRTI or NNRTI (V118I, E44D, K219R, T69A, and V75L) were found in a low prevalence (0.6-2.4%). A high proportion of the isolates from subtype C was found in the southern states. Subtype F-related viruses were the main non-B variant in the rest of the country. CONCLUSIONS Brazil has a low prevalence of drug-resistant strains circulating among recently diagnosed individuals. However, there was an increase in these rates compared with similar studies performed with samples collected in Brazil from 1996 to 1998. Continued surveys are required to detect trends in these rates, but routine genotypic testing in the drug-naive population prior to antiretroviral initiation is not required in Brazil.
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Affiliation(s)
- Rodrigo M Brindeiro
- Laboratory of Molecular Virology, Department of Genetics, Federal University of Rio de Janeiro, Brazil
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23
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Castro E, Echeverría G, Deibis L, González de Salmen B, Dos Santos Moreira A, Guimarães ML, Bastos FI, Morgado MG. Molecular epidemiology of HIV-1 in Venezuela: high prevalence of HIV-1 subtype B and identification of a B/F recombinant infection. J Acquir Immune Defic Syndr 2003; 32:338-44. [PMID: 12626896 DOI: 10.1097/00126334-200303010-00015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The authors assessed HIV-1 variability in two distinct areas of Venezuela (the capital Caracas and Margarita Island) through the analysis of blood specimens and clinical and epidemiologic data of 72 persons. Proviral DNA was evaluated through heteroduplex mobility assay (HMA) based on the envelope region. Additionally, FOK I restriction enzyme digestion assay was performed in all subtype B ED31/33 amplified products to check the presence of the typical Brazilian subtype B GWGR variant. Sequencing and phylogenetic analysis for C2-V3 region of gp120 was performed in selected cases. The vast majority of samples were found to belong to subtype B, with a North American/European RFLP profile. An F subtype HIV-1 based on the region was identified for the first time in Venezuela. Genetic analyses of the protease and reverse transcriptase fragments of this sample depicted a recombinant B/F genetic profile. The discrimination capacity of HIV-1 subtypes using the primer set ED3/14-ED31/33 among the Caracas samples was found to be higher than for those from Margarita Island. The authors' results point to relevant differences between the samples of continental and Caribbean regions of Venezuela, requiring further evaluation of larger samples.
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Affiliation(s)
- Erika Castro
- Department of Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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24
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Ammaranond P, Cunningham P, Oelrichs R, Suzuki K, Harris C, Leas L, Grulich A, Cooper DA, Kelleher AD. Rates of transmission of antiretroviral drug resistant strains of HIV-1. J Clin Virol 2003; 26:153-61. [PMID: 12600647 DOI: 10.1016/s1386-6532(02)00114-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND It is clear that transmission of drug resistant HIV-1 is possible and occurs regularly. However, there is a lack of clarity concerning the true rate of this transmission in a given population, the impact of combination therapies on this rate, and the contribution of transmitted resistant virus to treatment failure either in an individual or on a population basis. OBJECTIVES To provide a review of our current understanding of rates of transmission of drug resistant HIV-1 in various populations and to report the results of a study conducted to determine this rate in Sydney, Australia in the years 1992-2000. STUDY DESIGN A review of the literature combined with a prospective study of antiretroviral drug resistance in 130 individuals who were diagnosed with symptomatic primary infection at St. Vincent's Hospital, Sydney, Australia between 1992 and 2000. Sequencing of reverse transcriptase (RT) and protease (PR) was performed by the TruGene HIV-1 genotyping kit (Visible Genetics Inc.). RESULTS The results found in the Sydney population contrast with much of the literature. The prevalence of mutations that conferred primary resistance to protease inhibitors (PIs) was only 0.8% at position V82I. Secondary mutations/polymorphisms were seen in the PR at position L10I/V, K20R, M36I, L63P, A71T/V, or V77I in 60%. L63P was the most frequently found mutation (46.3%). The incidence of protease-resistant strains of HIV in primary HIV-1 infection did not change after the introduction of PIs in 1996. The distribution of the most common resistance mutations in the RT was as follows; M41L (8.5%) and T215Y (8.5%) and K70R (4.8%). The frequency of mutations associated with NRTI resistance was significantly lower in the post 1995 samples (43.9 vs. 19.1%, P < 0.05). Moreover, both M41L and K70R, but not T215Y, occurred with significantly decreased frequency in the post 1995 samples. CONCLUSIONS In contrast to other studies we found no increase in the rate of PR resistance and a decrease in the rate of RT resistance in recently transmitted virus over the period 1992-2000. The reasons for the differences between these results and those reported from elsewhere may relate to treatment regimens used in the transmitting population and may have implications for treatment policies in this country.
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Affiliation(s)
- Palanee Ammaranond
- National Centre in HIV Epidemiology and Clinical Research, University of New South Wales, 376 Victoria Street, Darlinghurst, Sydney 2010, NSW, Australia
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25
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Dumans AT, Soares MA, Pieniazek D, Kalish ML, De Vroey V, Hertogs K, Tanuri A. Prevalence of protease and reverse transcriptase drug resistance mutations over time in drug-naïve human immunodeficiency virus type 1-positive individuals in Rio de Janeiro, Brazil. Antimicrob Agents Chemother 2002; 46:3075-9. [PMID: 12183276 PMCID: PMC127402 DOI: 10.1128/aac.46.9.3075-3079.2002] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The prevalence of mutations that confer resistance to protease inhibitors and to nucleoside and nonnucleoside reverse transcriptase inhibitors in 49 blood samples from drug-naïve human immunodeficiency virus type 1-infected blood donors living in Rio de Janeiro state, Brazil, in 1998 was evaluated genotypically and phenotypically.
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Affiliation(s)
- Ana T Dumans
- Unidade de Genetica, Departamento de Ciencias Morfologicas, Instituto Biomedico, Universidade do Rio de Janeiro, Brazil
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26
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Morgado MG, Guimarães ML, Galvão-Castro B. HIV-1 polymorphism: a challenge for vaccine development - a review. Mem Inst Oswaldo Cruz 2002; 97:143-50. [PMID: 12016434 DOI: 10.1590/s0074-02762002000200001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The perspective for the development of anti-HIV/AIDS vaccines became a target sought by several research groups and pharmaceutical companies. However, the complex virus biology in addition to a striking genetic variability and the limited understanding of the immunological correlates of protection have made this an enormous scientific challenge not overcome so far. In this review we presented an updating of HIV-1 subtypes and recombinant viruses circulating in South American countries, focusing mainly on Brazil, as one of the challenges for HIV vaccine development. Moreover, we discussed the importance of stimulating developing countries to participate in the process of vaccine evaluation, not only testing vaccines according to already defined protocols, but also working together with them, in order to take into consideration their local information on virus diversity and host genetic background relevant for the vaccine development and testing, as well as including local virus based reagents to evaluate the immunogenicity of the candidate vaccines.
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Affiliation(s)
- M G Morgado
- Laboratório de AIDS e Imunologia Molecular, Departamento de Imunologia, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, 21045-900, Brasil.
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27
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Thomson MM, Delgado E, Herrero I, Villahermosa ML, Vázquez-de Parga E, Cuevas MT, Carmona R, Medrano L, Pérez-Álvarez L, Cuevas L, Nájera R. Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences. J Gen Virol 2002; 83:107-119. [PMID: 11752707 DOI: 10.1099/0022-1317-83-1-107] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.
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MESH Headings
- Argentina
- Base Sequence
- DNA, Viral
- Female
- Gene Products, gag/genetics
- Gene Products, gag/physiology
- Gene Products, rev/genetics
- Gene Products, rev/physiology
- Genetic Variation
- Genome, Viral
- HIV Antigens/genetics
- HIV Antigens/physiology
- HIV Envelope Protein gp41/genetics
- HIV Envelope Protein gp41/physiology
- HIV Infections/virology
- HIV Reverse Transcriptase/genetics
- HIV Reverse Transcriptase/physiology
- HIV-1/classification
- HIV-1/genetics
- Human Immunodeficiency Virus Proteins
- Humans
- Male
- Molecular Sequence Data
- Mosaicism
- Phylogeny
- Protein Structure, Tertiary
- Recombination, Genetic
- Sequence Analysis, Protein
- Sequence Analysis, RNA
- Viral Proteins
- Viral Regulatory and Accessory Proteins/genetics
- Viral Regulatory and Accessory Proteins/physiology
- gag Gene Products, Human Immunodeficiency Virus
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Michael M Thomson
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Delgado
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Isabel Herrero
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Luisa Villahermosa
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Elena Vázquez-de Parga
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - María Teresa Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rocío Carmona
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Leandro Medrano
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Lucía Pérez-Álvarez
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Laureano Cuevas
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
| | - Rafael Nájera
- Department of Viral Pathogenesis, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo, Km. 2, 28220 Majadahonda, Madrid, Spain1
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