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de Almeida Rego FF, de Moraes L, Giovanetti M, Silva JAG, Torres FG, de Oliveira Silva M, da Purificação Pereira da Silva M, Van Weyenbergh J, Santos LA, Khouri R. Genomic Detection of the Emerging, Highly Pathogenic HIV-1 Subtype D in Bahia, Northeast Brazil. Viruses 2023; 15:1650. [PMID: 37631993 PMCID: PMC10458544 DOI: 10.3390/v15081650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: To achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African, and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains.
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Affiliation(s)
- Filipe Ferreira de Almeida Rego
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
| | - Laise de Moraes
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima, 1715, Barro Preto, Belo Horizonte 30190-002, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico, 21-00128 Rome, Italy
| | - José Adriano Góes Silva
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Felipe Guimarães Torres
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
| | - Marcio de Oliveira Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Maria da Purificação Pereira da Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador 40110-050, Bahia, Brazil; (M.d.O.S.); (M.d.P.P.d.S.)
| | - Johan Van Weyenbergh
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
| | - Luciane Amorim Santos
- Escola Bahiana de Medicina e Saúde Pública, Avenida Dom João VI, 275, Brotas, Salvador 40290-000, Bahia, Brazil; (F.F.d.A.R.); (L.A.S.)
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Candeal, Salvador 40296-710, Bahia, Brazil; (L.d.M.); (J.A.G.S.); (F.G.T.)
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Praça Ramos de Queirós, s/n, Largo do Terreiro de Jesus, Salvador 40026-010, Bahia, Brazil
- Rega Institute for Medical Research, Department of Immunology, Microbiology and Transplantation, KU Leuven, Herestraat 49-Box 1030, 3000 Leuven, Belgium;
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de Moraes L, Santos LA, Arruda LB, da Silva MDPP, Silva MDO, Silva JAG, Ramos A, dos Santos MB, Torres FG, Orge C, Teixeira AMDS, Vieira TS, Ramírez L, Soto M, Grassi MFR, de Siqueira IC, Costa DL, Costa CHN, Andrade BDB, Akrami K, de Oliveira CI, Boaventura VS, Barral-Netto M, Barral A, Vandamme AM, Van Weyenbergh J, Khouri R. High seroprevalence of Leishmania infantum is linked to immune activation in people with HIV: a two-stage cross-sectional study in Bahia, Brazil. Front Microbiol 2023; 14:1221682. [PMID: 37601355 PMCID: PMC10436095 DOI: 10.3389/fmicb.2023.1221682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 08/22/2023] Open
Abstract
Visceral leishmaniasis is an opportunistic disease in HIV-1 infected individuals, unrecognized as a determining factor for AIDS diagnosis. The growing geographical overlap of HIV-1 and Leishmania infections is an emerging challenge worldwide, as co-infection increases morbidity and mortality for both infections. Here, we determined the prevalence of people living with HIV (PWH) with a previous or ongoing infection by Leishmania infantum and investigated the virological and immunological factors associated with co-infection. We adopted a two-stage cross-sectional cohort (CSC) design (CSC-I, n = 5,346 and CSC-II, n = 317) of treatment-naïve HIV-1-infected individuals in Bahia, Brazil. In CSC-I, samples collected between 1998 and 2013 were used for serological screening for leishmaniasis by an in-house Enzyme-Linked Immunosorbent Assay (ELISA) with SLA (Soluble Leishmania infantum Antigen), resulting in a prevalence of previous or ongoing infection of 16.27%. Next, 317 PWH were prospectively recruited from July 2014 to December 2015 with the collection of sociodemographic and clinical data. Serological validation by two different immunoassays confirmed a prevalence of 15.46 and 8.20% by anti-SLA, and anti-HSP70 serology, respectively, whereas 4.73% were double-positive (DP). Stratification of these 317 individuals in DP and double-negative (DN) revealed a significant reduction of CD4+ counts and CD4+/CD8+ ratios and a tendency of increased viral load in the DP group, as compared to DN. No statistical differences in HIV-1 subtype distribution were observed between the two groups. However, we found a significant increase of CXCL10 (p = 0.0076) and a tendency of increased CXCL9 (p = 0.061) in individuals with DP serology, demonstrating intensified immune activation in this group. These findings were corroborated at the transcriptome level in independent Leishmania- and HIV-1-infected cohorts (Swiss HIV Cohort and Piaui Northeast Brazil Cohort), indicating that CXCL10 transcripts are shared by the IFN-dominated immune activation gene signatures of both pathogens and positively correlated to viral load in untreated PWH. This study demonstrated a high prevalence of PWH with L. infantum seropositivity in Bahia, Brazil, linked to IFN-mediated immune activation and a significant decrease in CD4+ levels. Our results highlight the urgent need to increase awareness and define public health strategies for the management and prevention of HIV-1 and L. infantum co-infection.
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Affiliation(s)
- Laise de Moraes
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Luciane Amorim Santos
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brazil
| | - Liã Bárbara Arruda
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, United Kingdom
| | | | - Márcio de Oliveira Silva
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador, Brazil
| | - José Adriano Góes Silva
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador, Brazil
| | - André Ramos
- Centro Estadual Especializado em Diagnóstico, Assistência e Pesquisa, Secretaria de Saúde do Estado da Bahia, Salvador, Brazil
| | | | | | - Cibele Orge
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | | | | | - Laura Ramírez
- Departamento de Biología Molecular, Facultad de Ciencias, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Manuel Soto
- Departamento de Biología Molecular, Facultad de Ciencias, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria Fernanda Rios Grassi
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brazil
| | | | - Dorcas Lamounier Costa
- Laboratório de Leishmanioses, Instituto de Doenças Tropicais Natan Portella, Universidade Federal do Piauí, Teresina, Brazil
| | - Carlos Henrique Nery Costa
- Laboratório de Leishmanioses, Instituto de Doenças Tropicais Natan Portella, Universidade Federal do Piauí, Teresina, Brazil
| | - Bruno de Bezerril Andrade
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brazil
| | - Kevan Akrami
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Camila Indiani de Oliveira
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador, Brazil
| | - Viviane Sampaio Boaventura
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Hospital Santa Izabel, Salvador, Brazil
| | - Manoel Barral-Netto
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Aldina Barral
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Johan Van Weyenbergh
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Ricardo Khouri
- Programa de Pós-graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Brazil
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
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Oliveira RC, Gräf T, Rego FFDA, Silva GPSA, Giovanetti M, Monteiro Cunha JP. Dynamic Dispersion of HIV-1 Subtype C Toward Brazilian Northeastern Region. AIDS Res Hum Retroviruses 2021; 37:913-921. [PMID: 34036794 DOI: 10.1089/aid.2020.0308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The subtype C accounts for >50% of HIV type 1 (HIV-1) infections worldwide and it is currently the predominant viral form in South Brazil. Subtype C has been reported in all Brazilian regions; however, the phylogenetic relationship among strains circulating in those regions still remains unclear. This study aimed to investigate the origin and dynamic dispersion of HIV-1 subtype C toward Northeast Brazil. Our phylogenetic analysis suggests that most subtype C strains circulating in Brazil (99%) are descendant from the main lineage whose entrance in the country was previously described in the 1970s. According to the literature, additional introductions of subtype C were reported in the country through the Southeast region and in this study we identified another entry event that occurred most likely through the North region. Furthermore, our analysis suggests that the spread of subtype C to Brazilian Northeastern states occurred through multiple independent introductions of the main lineage that originated in South Brazil between mid-1980s and late 1990s. Despite the observation of eventual new HIV-1 subtype C introductions, our results highlight the predominance of a single lineage of this subtype in Brazil and the importance of South region in its dissemination throughout the country.
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Affiliation(s)
- Rodrigo Cunha Oliveira
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz—FIOCRUZ, Salvador, Brazil
| | | | | | - Marta Giovanetti
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz—FIOCRUZ, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Joana Paixão Monteiro Cunha
- Núcleo de Bioinformática, Departamento de Bioquímica e Biofísica, Universidade Federal da Bahia, Salvador, Brazil
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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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Molecular and geographic characterization of hiv-1 bf recombinant viruses. Virus Res 2019; 270:197650. [PMID: 31279829 DOI: 10.1016/j.virusres.2019.197650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 01/21/2023]
Abstract
The Human Immunodeficiency Virus Type 1 (HIV-1) presents a wide genetic variability, which is represented by four groups, nine subtypes of group M and several recombinant forms. Among these, the BF recombinants have been distinguished by a high global dispersion and an increase in number and diversity. To date, 15 BF Circulating Recombinant Forms (CRFs) and diverse BF Unique Recombinant Forms (URFs) have been described. In Brazil, nine CRF_BF have been identified. The aim of this work was to perform molecular and geographic characterization of HIV-1 BF recombinant strains. Near full-length genomes of 265 BF recombinant viruses were collected from public databases and molecular analyses were performed. These sequences were originally retrieved between 1993-2006 and isolated from 16 countries (51.3% from Brazil). Diagnostic's year analysis showed that BF recombinants circulate in Brazil since at least 1985. Most sequences displayed recombination in the pol (84.9%), gag (69.3%) and env (51.4%) regions. The subtype B predominated in all accessory and regulatory genes, except in vif, in which the F subtype was predominant (40.4%). Twelve regions with a recombination rate higher than 10% were identified, especially one region inside p24 gene (1359-1397) whose recombination was present in more than 30% of the sequences. Coreceptor usage prediction during viral entry showed that BF recombinants preferentially use CCR5 (67.2%) and the most frequent tetrapeptides found in the V3 loop were GPGR (47.9%) and GPGQ (21.1%). The frequency of X4/dual viruses was lower amongst F subtype (25.8%) V3 sequences, compared with B subtype (43%). In addition, mutations associated with intermediate or high resistance levels to PI (10.6%), NRTI (15.0%), NNRTI (14.0%) and INSTI (2.6%) were identified. The great diversity of the recombination patterns evidences that the recombination between the subtypes B and F is frequent, reflecting a probable high rate of dual infection and the acquisition of advantageous characteristics for viral fitness.
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Amaral AG, Oliveira IB, Carneiro DC, Alcantara LC, Monteiro-Cunha JP. An overview of the molecular and epidemiological features of HIV-1 infection in two major cities of Bahia state, Brazil. Mem Inst Oswaldo Cruz 2017; 112:411-418. [PMID: 28591401 PMCID: PMC5446230 DOI: 10.1590/0074-02760160458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/10/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The high mutation rate of the human immunodeficiency virus (HIV) has created a public health challenge because the use of antiretroviral drugs can generate selective pressure that drives resistance in these viruses. OBJECTIVE The aim of this work was to characterise the molecular and epidemiological profile of HIV in Bahia, Brazil. METHODS DNA sequences from regions of HIV gag, pol, and env genes were obtained from previous studies performed in this area between 2002 and 2012. Their genotype and drug-resistance mutations were identified using bioinformatics tools. Clinical and epidemiological data were analysed. FINDINGS Among 263 individuals (46.4% male), 97.5% were asymptomatic and 49.1% were receiving treatment. Most of the individuals were 31 to 40 years old (36.9%) and infected through heterosexual contact (40.7%). The predominant genotype was B (68.1%) followed by BF recombinants (18.6%). Among the individuals infected with either F or BF genotypes, 68.4% were women and 76.8% were infected through heterosexual transmission. The prevalence of associated mutations conferring antiretroviral resistance was 14.2%, with 3.8% of all mutations conferring resistance to protease inhibitors, 9.43% to nucleoside reverse transcriptase inhibitors, and 8.5% to non-nucleoside reverse transcriptase inhibitors. Drug resistance was higher in individuals receiving treatment (26.1%) than in the drug-naïve (4.3%) individuals. MAIN CONCLUSIONS This study will contribute to the understanding and monitoring of HIV epidemic in this Brazilian region.
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Affiliation(s)
- Amanda Gm Amaral
- Universidade Federal da Bahia, Departamento de Biofunção, Núcleo de Bioinformática, Salvador, BA, Brasil
| | - Isabele B Oliveira
- Universidade Federal da Bahia, Departamento de Biofunção, Núcleo de Bioinformática, Salvador, BA, Brasil
| | - Diego C Carneiro
- Universidade Federal da Bahia, Departamento de Biofunção, Núcleo de Bioinformática, Salvador, BA, Brasil
| | - Luiz Cj Alcantara
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil
| | - Joana P Monteiro-Cunha
- Universidade Federal da Bahia, Departamento de Biofunção, Núcleo de Bioinformática, Salvador, BA, Brasil.,Fundação Bahiana para o Desenvolvimento das Ciências, Escola Bahiana de Medicina e Saúde Pública, Salvador, BA, Brasil
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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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9
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Filho AWDO, Brites C. Geolocalization of HIV-1 subtypes and resistance mutations of patients failing antiretroviral therapy in Salvador - Brazil. Braz J Infect Dis 2017; 21:234-239. [PMID: 28363087 PMCID: PMC9428007 DOI: 10.1016/j.bjid.2017.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/05/2022] Open
Abstract
Background Geographical distribution of HIV variants is an important way to understand the circulation and spread of such viral strains. Objectives To evaluate the spatial distribution of HIV-1 variants in patients failing antiretroviral therapy, in Salvador, Brazil. Methods We performed a cross-sectional evaluation of HIV resistance test reports of patients who underwent genotyping tests in a referral center in Salvador, Brazil, for the years 2008–2014. The laboratory database contains around 2500 resistance reports of patients failing antiretroviral therapy. Genotypic tests were performed by sequencing of HIV-1 POL region (TrueGene, Siemens). We assessed HIV-1 resistance mutations and subtype, as well as residential address, age, and gender of patients. Results We evaluated 1300 reports, 772 (59.4%) of them from male patients. As expected, subtype B predominated (79%) followed by subtypes F1 (6.7%) and BF (6.5%). The most frequent mutations in HIV-1 reverse transcriptase were 184V (79.1%), 41L (33.5%), 67N (30.4%), 103N (42.4%), and 108I (11.1%). Most frequent mutations in HIV-1 protease were 63P (52.4%), 36I (47.9%), 15 V (33.0%), 62 V (28.1%) and 13 V (25.8%). Some mutations (41L, 215Y, 210W) were significantly more frequent among men. We detected a significantly higher accumulation of 103N mutation in specific areas of Salvador. We identified a more restricted circulation pattern for subtype FB (more frequent in some regions), and F1 (almost absent in a specific region). Conclusion Our results suggest that specific subtypes/resistance mutations present a distinct frequency rate in specific areas of Salvador, probably due to a restricted circulation pattern. This trend to clustering was observed in regions covered by AIDS referral centers, suggesting that pattern of care for such patients can interfere in virological outcomes.
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Affiliation(s)
| | - Carlos Brites
- LAPI - Laboratório de Pesquisa em Infectologia, Faculdade de Medicina, Universidade Federal da Bahia, Salvador, BA, Brazil.
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10
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da Costa CM, Costa de Oliveira CM, Chehuan de Melo YF, Delatorre E, Bello G, Couto-Fernandez JC. High HIV-1 Genetic Diversity in Patients from Northern Brazil. AIDS Res Hum Retroviruses 2016; 32:918-22. [PMID: 27091699 DOI: 10.1089/aid.2016.0044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The HIV-1 epidemic in Brazil is driven by subtypes B, F1, and C and recombinants forms among those subtypes. The distribution of HIV-1 subtypes, however, may vary across different Brazilian regions and the molecular epidemiologic profile in Northern Brazil remains poorly explored. HIV-1 pol sequences were obtained from 305 patients failing antiretroviral therapy followed at outpatient clinics from five Northern Brazilian states. The most prevalent HIV-1 clade observed in the Northern Brazilian region was subtype B (81%), followed by BF1 recombinants (10%), subtype F1 (4%), subtype C (3%), BC recombinants (2%), and BU recombinants (1%). Although HIV-1 subtype B was the predominant HIV-1 clade in Northern Brazil, its prevalence greatly varies among different states, ranging from 63% in Rondônia to 92% in Acre. Among the 37 HIV-1 recombinant sequences detected in the Northern Brazilian region, nine (24%) displayed a unique recombinant form structure, five (14%) a CRF28/29_BF-like structure, and four (11%) a CRF31_BC-like structure. Two other BF1 recombinant patterns were identified in 16 (43%) and three (8%) samples that may correspond to two potentially new CRFs_BF characteristic of the Northern region. This study reveals that despite the low spatial connectivity with other Brazilian regions, the genetic complexity of the HIV-1 epidemic in Northern Brazil is very high and that the molecular epidemiologic pattern may vary across different northern states, reflecting a complex epidemic with multiple independent viral introductions into this Brazilian region.
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Affiliation(s)
- Carolina Marinho da Costa
- Laboratório de Genotipagem de HIV, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Secretaria de Estado da Saúde. Governo do Estado do Amazonas, Manaus, Brazil
- Universidade do Estado do Amazonas, Manaus, Brazil
| | - Cintia Mara Costa de Oliveira
- Laboratório de Genotipagem de HIV, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Secretaria de Estado da Saúde. Governo do Estado do Amazonas, Manaus, Brazil
| | - Yonne Francis Chehuan de Melo
- Laboratório de Genotipagem de HIV, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Secretaria de Estado da Saúde. Governo do Estado do Amazonas, Manaus, Brazil
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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11
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Pernas B, Mena A, Cañizares A, Grandal M, Castro-Iglesias A, Pértega S, Pedreira JD, Poveda E. Trends on epidemiological, virological, and clinical features among newly diagnosed HIV-1 persons in Northwest Spain over the last 10 years. J Med Virol 2015; 87:1319-26. [PMID: 25777786 DOI: 10.1002/jmv.24185] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2015] [Indexed: 12/21/2022]
Abstract
To describe temporal trend and characteristics of newly HIV-diagnosed patients in a medical care area in Northwest Spain over the last 10 years. All newly diagnosed patients for HIV-infection from 2004 to 2013 at a reference medical care area in Northwest of Spain were identified. Epidemiological, virological, immunological, and clinical data, as well as HIV genotype and drug resistance information were recorded. A total of 565 newly HIV-diagnosed patients were identified. The number of new cases increased in the last 5 years (66 cases/year). Overall, 53.1% had a median CD4 counts < 350 cells/µl and 33.6% had an AIDS defining criteria. Non-B variants were found in 34.4% of patients being subtype F (25.8%) the most common non-B subtype. The rate of transmitted drug resistance (TDR) over the study period was 3.7%, but a decreased to 2.6% was observed in the last 5 years. The most prevalent TDR mutations were: T215 revertants (1.5%), K219QENR (1.2%), for NRTIs; K103N (1.9%), for NNRTIs; L90M (0.3%), for PIs. Overall, 73.2% of patients started antiretroviral treatment and 9.9% of patients died during follow-up. The number of newly HIV diagnosed patients increased since year 2009. There is a high prevalence of late diagnosis (53%) and 33% had an AIDS defining criteria. Interestingly, the most prevalent non-B subtype in our population was F (25.8%). These findings support the need to facilitate the access for HIV testing to reduce the rate of late HIV diagnosis, improve the clinical outcome and prevent HIV transmission.
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Affiliation(s)
- B Pernas
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Mena
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Cañizares
- Service of Microbiology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - M Grandal
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - A Castro-Iglesias
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - S Pértega
- Clinical Epidemiology and Biostatistics Unit, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - J D Pedreira
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
| | - E Poveda
- Division of Clinical Virology, INIBIC-Complejo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, Universidade da Coruña, A Coruña, Spain
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12
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Shankarappa R, Mullins JI. Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. J Virol Methods 2013; 194:169-77. [PMID: 23994080 DOI: 10.1016/j.jviromet.2013.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
Heteroduplex mobility (HMA) and tracking assays (HTA) are used to assess genetic relationships between DNA molecules. While distinguishing relationships between clonal or nearly clonal molecules is relatively straightforward, inferring population structures is more complex. To address this issue, HIV-1 quasispecies with varying levels of diversity were studied using both HTA and DNA sequencing. Viral diversity estimates and the temporal features of virus evolution were found to be generally concordant between HTA and DNA sequencing. In addition, the distribution of pairwise differences and the rates of virus divergence were similar between the two methods. These findings support the use of HTA to characterize variant populations of DNA and strengthen previous inferences concerning the evolution of HIV-1 over the course of infection.
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Affiliation(s)
- Raj Shankarappa
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195-8070, United States
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13
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Santos LA, Monteiro-Cunha JP, Araujo AF, Brites C, Galvao-Castro B, Alcantara LCJ. Detection of distinct human immunodeficiency virus type 1 circulating recombinant forms in northeast Brazil. J Med Virol 2012; 83:2066-72. [PMID: 22012712 DOI: 10.1002/jmv.22170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The extraordinary genetic diversity and immune evasion of human immunodeficiency virus (HIV) pose significant challenges for vaccine development and antiretroviral therapy efficacy. The objective of this study was to characterize the molecular profile of HIV-1 epidemic in Salvador, Bahia, Brazil, determining the genetic subtypes and the presence of antiretroviral resistance mutations. HIV-1 pol DNA sequences from 57 individuals infected with HIV were obtained by PCR, followed by sequencing. The subtypes were determined by phylogenetic analyses and the intersubtype recombination was investigated by bootscanning. The pol subtypes were compared with gag and env subtypes. Antiretroviral susceptibility was evaluated through the Stanford HIV resistance Database. The subtypes frequencies were: 77.2% of subtype B, 1.8% of subtype F1, and 21.0% of BF recombinant forms. Two intergenic and three intragenic BF recombinant patterns were observed. Six (10.5%) viruses were related to CRF28/CRF29, two were related to CRF12 (3.5%), and one (1.8%) was CRF39. Fourteen (24.6%) strains carried one or more mutations associated with at least intermediate resistance: 24.6% had resistance to nucleoside reverse transcriptase inhibitors, 21.0% to non-nucleoside reverse transcriptase inhibitors, and 7% to protease inhibitors. The substitutions I54V (7.0%), M184V (14.0%), and K103N (10.5%) were the most frequent within each class of drugs. The results show a high diversity of BF genotypes and a lower prevalence of major reverse transcriptase and protease drug resistance mutations in Salvador, compared with other regions of Brazil. These findings may contribute to improve treatment strategies of patients infected with HIV-1 from this Brazilian region.
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Affiliation(s)
- Luciane Amorim Santos
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
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14
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Monteiro-Cunha JP, Araujo AF, Santos E, Galvao-Castro B, Alcantara LCJ. Lack of high-level resistance mutations in HIV type 1 BF recombinant strains circulating in northeast Brazil. AIDS Res Hum Retroviruses 2011; 27:623-31. [PMID: 21087197 DOI: 10.1089/aid.2010.0126] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract The genetic variability and the prevalence of drug resistance-associated mutations (DRAM) of HIV-1 isolates from 50 women and 8 children from Feira de Santana, Bahia, Brazil were investigated. DNA samples were obtained and pol sequences were generated by PCR and direct sequencing. Phylogenetic analysis showed that 39 (67.2%) samples were subtype B, four (6.9%) F, one (1.7%) C, and 14 (24.1%) BF recombinants. Four different BF recombination patterns were detected. Twelve (20.7%) samples shared the same breakpoint within the reverse transcriptase (RT) sequence. Fifty-five (94.8%) isolates showed several resistance-associated mutations in the RT and the protease (PR) genes. Ten (17.2%) isolates presented mutations associated with a high level of resistance: nine (15.5%) to nucleoside RT inhibitors (NRTI), four (6.9%) to nonnucleoside RT inhibitors (NNRTI), and three (5.2%) to PR inhibitors (PIs). Subtype B-infected patients had, on average, 0.5 high-level DRAM per sequence while no mutations were observed in BF recombinants, although the two groups were under ARV for a similar period of time. Our data indicate the predominance of the subtype B, followed by BF recombinants in this population, and the dissemination of a recombinant strain in Bahia, which could be related to adaptive advantages of these variants over the predominant subtype B.
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Affiliation(s)
- Joana Paixao Monteiro-Cunha
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Adriano Fernando Araujo
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
| | - Edson Santos
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
| | - Bernardo Galvao-Castro
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório Avançado de Saúde Pública (LASP), Centro de Pesquisa Gonçalo Moniz (CPqGM), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Bahia, Brazil
- Fundação Bahiana para o Desenvolvimento das Ciências (FBDC), Escola Bahiana de Medicina e Saúde Pública (EBMSP), Salvador, Bahia, Brazil
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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15
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Dilernia DA, Jones LR, Pando MA, Rabinovich RD, Damilano GD, Turk G, Rubio AE, Pampuro S, Gomez-Carrillo M, Salomón H. Analysis of HIV type 1 BF recombinant sequences from South America dates the origin of CRF12_BF to a recombination event in the 1970s. AIDS Res Hum Retroviruses 2011; 27:569-78. [PMID: 20919926 PMCID: PMC3131829 DOI: 10.1089/aid.2010.0118] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 epidemics in South America are believed to have originated in part from the subtype B epidemic initiated in the Caribbean/North America region. However, circulation of BF recombinants in similar proportions was extensively reported. Information currently shows that many BF recombinants share a recombination structure similar to that found in the CRF12_BF. In the present study, analyzing a set of 405 HIV sequences, we identified the most likely origin of the BF epidemic in an early event of recombination. We found that the subtype B epidemics in South America analyzed in the present study were initiated by a founder event that occurred in the early 1970s, a few years after the introduction of these strains in the Americas. Regarding the F/BF recombinant epidemics, by analyzing a subtype F genomic segment within the viral gene gag present in the majority of the BF recombinants, we found evidence of a geographic divergence very soon after the introduction of subtype F strains in South America. Moreover, through analysis of a subtype B segment present in all the CRF12_BF-like recombination structure, we estimated the circulation of the subtype B strain that gave rise to that recombinant structure around the same time period estimated for the introduction of subtype F strains. The HIV epidemics in South America were initiated in part through a founder event driven by subtype B strains coming from the previously established epidemic in the north of the continent. A second introduction driven by subtype F strains is likely to have encountered the incipient subtype B epidemic that soon after their arrival recombined with them, originating the BF epidemic in the region. These results may explain why in South America the majority of F sequences are found as BF recombinants.
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Affiliation(s)
- Dario A. Dilernia
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Leandro R. Jones
- División de Biología Molecular, Estación de Fotobiología “Playa Unión,” Rawson, Chubut, Argentina
| | - Maria A. Pando
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Roberto D. Rabinovich
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Gabriel D. Damilano
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Gabriela Turk
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Andrea E. Rubio
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Sandra Pampuro
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Manuel Gomez-Carrillo
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
| | - Horacio Salomón
- Centro Nacional de Referencia para el SIDA, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Capital Federal, Buenos Aires, Argentina
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Rapid identification of human immunodeficiency virus type 1 CRF01_AE and BC recombinants by subtype-specific PCR. J Virol Methods 2010; 171:339-44. [PMID: 21126539 DOI: 10.1016/j.jviromet.2010.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Revised: 11/17/2010] [Accepted: 11/22/2010] [Indexed: 11/22/2022]
Abstract
A subtype-specific PCR approach is described for the identification of HIV-1 intersubtype CRF01_AE and BC recombinants, the two predominant subtypes in Southern China. Primers were designed based on the env and gag regions of the HIV-1 genome. Nested PCRs with primers targeting the env region were performed to amplify subtype C, CRF01_AE, or BC recombinants. To differentiate BC recombinants from subtype C virus, a BC recombinant specific gag PCR was then performed. In order to identify the CRF07_BC and CRF08_BC recombinant forms, an additional PCR step was included. Four HIV-1 samples of known subtype, 77 samples with unknown-subtype, and 30 HIV-negative control samples were tested by the new assay. The results of this PCR-based subtyping approach were compared with that of a sequence-based phylogenetic analysis. In total, 73 (94.8%) samples were amplified by the subtype-specific PCR reactions, of which 39 were identified as CRF01_AE, 14 as CRF07_BC, and 20 as CRF08_BC. The sensitivity of this assay was 90.7% for the CRF01_AE recombinant and 100% for BC recombinants. The specificity was 100% when used to identify 30 HIV-negative samples. The reproducibility was 93.8% for CRF01_AE, and 100% for BC recombinants. This subtype-specific PCR technique represents a simple, rapid, and low-cost assay for the identification of HIV-1 CRF01_AE and BC recombinants in Southern China.
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17
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Araujo AF, Brites C, Monteiro-Cunha J, Santos LA, Galvao–Castro B, Alcantara LCJ. Lower prevalence of human immunodeficiency virus type 1 Brazilian subtype B found in northeastern Brazil with slower progression to AIDS. AIDS Res Hum Retroviruses 2010; 26:1249-54. [PMID: 20854208 DOI: 10.1089/aid.2010.0068] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Besides being extremely useful in measuring the level of HIV-1 diversity and prevalence in populations, the molecular analysis of genomic sequences provides crucial surveillance support and aids in the development of new therapies and effective vaccines. The present study focused on gag and env DNA and amino acid sequences that were generated from samples taken from 61 infected patients in the City of Salvador, Bahia, located in northeastern Brazil. In order to determine selective pressure and predict coreceptor usage, Bioinformatics tools were employed in phylogeny reconstruction. Fifty-six (91.8%) viruses were classified as belonging to subtype B, three (4.9%) from F1, and two (3.3%) from BF1 recombinants. Based on the characterization of the V3 region, the subtype B strains were represented by eight (18.2%) Brazilian variants (B'-GWGR), 20 (46.5%) European/EUA B variants (GPGR), and 15 (34.9%) GXGX variants. The mean time elapsed since diagnosis was 13 years among subtype B' and 9 years in subtype B. The mean dN/dS ratios from the GWGR, GPGR, and GXGX groups, when compared to an HXB2 reference, were 0.72, 0.77, and 0.67, respectively. Seventy-six percent of the viruses studied were predicted to use the CCR5 coreceptor for cell entry (R5 viruses), while 24% were predicted to use the CXCR4 or were classified as dual tropic viruses. The prevalence of subtypes B' and recombinant B/F1 was shown to be lower than findings from previous studies performed both in Brazil (B') and in Bahia (B/F1). The association between subtype B' and a lengthy period of time since diagnosis can be correlated with a slower disease progression in infected patients, when compared with those infected with subtype B.
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Affiliation(s)
- Adriano Fernando Araujo
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil
| | | | - Joana Monteiro-Cunha
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil
| | - Luciane Amorim Santos
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil
| | - Bernardo Galvao–Castro
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil
- Bahia School of Medicine and Public Health/Foundation for Development of Science, Salvador, BA, Brazil
| | - Luiz Carlos Junior Alcantara
- Advanced Public Health Laboratory, Gonçalo Moniz Research Center, Oswaldo Cruz Foundation, Salvador, BA, Brazil
- Bahia School of Medicine and Public Health/Foundation for Development of Science, Salvador, BA, Brazil
- Animal Models and Retroviral Vaccines Section, NCI/NIH, Bethesda, Maryland
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18
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High genetic diversity of HIV-1 viruses in Macao, China. J Infect 2010; 61:164-72. [DOI: 10.1016/j.jinf.2010.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 02/06/2010] [Accepted: 04/30/2010] [Indexed: 11/21/2022]
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19
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Machado LF, Ishak MO, Vallinoto AC, Lemos JAR, Azevedo VN, Moreira MR, Souza MI, Fernandes LM, Souza LL, Ishak R. Molecular epidemiology of HIV type 1 in northern Brazil: identification of subtypes C and D and the introduction of CRF02_AG in the Amazon region of Brazil. AIDS Res Hum Retroviruses 2009; 25:961-6. [PMID: 19795985 DOI: 10.1089/aid.2009.0027] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular epidemiology of HIV-1 strains circulating in Belem-PA and Macapa-AP, in the Northern region of Brazil, is described using sequences of the C2V3 segment of the env and the pro gene of HIV-1 from patients of the Reference Unit for Special Infectious and Parasitary Diseases (URE-DIPE) in Belem-PA and the Central Laboratory (LACEN) in Macapa-AP. Subtype B was the most frequently found in relation to pro (88.3%) in Belem and in Macapa (97.1%) and env (88.3% in Belem and 100% in Macapa). Subtype F was also described in Belem (9.3% pro and 8.3% env) and Macapa (2.8% pro). Subtype D was described for the first time in the Northern region of the country as well as the recent entry of CRF02_AG. Furthermore, several possible recombinant forms among the various subtypes were found in both cities. The results support the hypothesis that HIV-1 infection is associated with the epidemic of the virus in the Southeast region of the country and that the city of Belem is the most important route for HIV-1 entry in the Northern region of Brazil.
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Affiliation(s)
- Luiz F.A. Machado
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Marluísa O.G. Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Antonio C.R. Vallinoto
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - José Alexandre R. Lemos
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
- Laboratory of Molecular Biology, State Blood Bank, Para, Brazil
| | - Vania N. Azevedo
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | | | - Maria I.M. Souza
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Luciana M. Fernandes
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
| | - Lia L.B. Souza
- Reference Unit for Special Infectious and Parasitary Diseases, Brazil
| | - Ricardo Ishak
- Virus Laboratory, Institute of Biological Sciences, Universidade Federal do Para, Para, Brazil
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