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Souto B, Triunfante V, Santos-Pereira A, Martins J, Araújo PMM, Osório NS. Evolutionary dynamics of HIV-1 subtype C in Brazil. Sci Rep 2021; 11:23060. [PMID: 34845263 PMCID: PMC8629974 DOI: 10.1038/s41598-021-02428-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/12/2021] [Indexed: 11/29/2022] Open
Abstract
The extensive genetic diversity of HIV-1 is a major challenge for the prevention and treatment of HIV-1 infections. Subtype C accounts for most of the HIV-1 infections in the world but has been mainly localized in Southern Africa, Ethiopia and India. For elusive reasons, South Brazil harbors the largest HIV-1 subtype C epidemic in the American continent that is elsewhere dominated by subtype B. To investigate this topic, we collected clinical data and viral sequences from 2611 treatment-naïve patients diagnosed with HIV-1 in Brazil. Molecular epidemiology analysis supported 35 well-delimited transmission clusters of subtype C highlighting transmission within South Brazil but also from the South to all other Brazilian regions and internationally. Individuals infected with subtype C had lower probability to be deficient in CD4+ T cells when compared to subtype B. The HIV-1 epidemics in the South was characterized by high female-to-male infection ratios and women-to-child transmission. Our results suggest that HIV-1 subtype C probably takes advantage of longer asymptomatic periods to maximize transmission and is unlikely to outcompete subtype B in settings where the infection of women is relatively less relevant. This study contributes to elucidate factors possibly underlying the geographical distribution and expansion patterns of the most spread HIV-1 subtypes.
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Affiliation(s)
- Bernardino Souto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.,Department of Medicine, Federal University of São Carlos, São Carlos, Brazil
| | - Vera Triunfante
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Ana Santos-Pereira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Joana Martins
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Pedro M M Araújo
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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Fritsch HM, Tanuri A, Pinto AR, Gräf T. Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil. INFECTION GENETICS AND EVOLUTION 2021; 92:104854. [PMID: 33839313 DOI: 10.1016/j.meegid.2021.104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
Abstract
The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent subtype, with a significant increase in prevalence over time. HIV-1B was observed to be associated with highly educated men, suggesting a compartmentalization from other subtypes. Such observation was confirmed by the high frequency of HIV-1B circulating in MSM transmission networks. Identified transmission clusters were majority composed by individuals living up to 25 km away and interstate linkages were mainly between southern neighbor states. In general, individuals between 25 and 40 years old and sequences sampled after 2014 were more likely to be in transmission chains, in agreement with the universal treatment protocol launched in 2014. The present study brings new insights about HIV-1 transmission dynamics in southern Brazil.
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Affiliation(s)
- Hegger M Fritsch
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aguinaldo R Pinto
- Laboratório de Imunologia Aplicada, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil.
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3
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Bahls LD, Canezin PH, Reiche EMV, Fernandez JCC, Dias JRC, Meneguetti VAF, Ueda LT, Bertolini DA. Moderate prevalence of HIV-1 transmitted drug resistance mutations in southern Brazil. AIDS Res Ther 2019; 16:4. [PMID: 30722787 PMCID: PMC6364409 DOI: 10.1186/s12981-019-0219-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/22/2019] [Indexed: 11/22/2022] Open
Abstract
Background Despite the advances in therapy, the occurrence of drug-resistant human immunodeficiency virus type 1 (HIV-1) is a major obstacle to successful treatment. This study aimed to characterize the genetic diversity and to determine the prevalence of transmitted drug resistance mutations (TDRM) between individuals recently or chronically diagnosed with HIV-1 from Paraná, Brazil. Methods A total of 260 HIV-1 positive antiretroviral therapy-naïve patients were recruited to participate on the study, of which 39 were recently diagnosed. HIV-1 genotyping was performed using sequencing reaction followed by phylogenetic analyses to determine the HIV-1 subtype. TDRM were defined using the Calibrated Population Resistance Tool program. Results The HIV-1 subtypes frequency found in the studied population were 54.0% of subtype B, 26.7% subtype C, 6.7% subtype F1 and 12.7% recombinant forms. The overall prevalence of TDRM was 6.7%, including 13.3% for recently diagnosed subjects and 5.9% for the chronic group. Conclusions The prevalence of resistance mutations found in this study is considered moderate, thus to perform genotyping tests before the initiation of antiretroviral therapy may be important to define the first line therapy and contribute for the improvement of regional prevention strategies for epidemic control. Electronic supplementary material The online version of this article (10.1186/s12981-019-0219-1) contains supplementary material, which is available to authorized users.
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Tanaka TSO, Leite TF, Freitas SZ, Cesar GA, de Rezende GR, Lindenberg ADSC, Guimarães ML, Motta-Castro ARC. HIV-1 Molecular Epidemiology, Transmission Clusters and Transmitted Drug Resistance Mutations in Central Brazil. Front Microbiol 2019; 10:20. [PMID: 30804893 PMCID: PMC6371026 DOI: 10.3389/fmicb.2019.00020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
We aimed to characterize HIV-1 molecular epidemiology and transmission clusters among heterosexual (HET) and men who have sex with men (MSM) individuals, as well as transmitted drug resistance mutations (TDRM) in Central-Western Brazil. This cross-sectional survey was conducted among 190 antiretroviral naïve HIV-1 infected individuals. Proviral DNA was extracted, and nested PCR amplified partial polymerase gene (PR/RT). After sequencing, subtypes were assigned, and the sequences were analyzed for the occurrence of possible transmission networks. Calibrated Population Resistance (CPR) tool from Stanford HIV Database was used to investigate the presence of TDRM. Among 150 individuals whose samples were successfully sequenced, the most prevalent HIV-1 subtype was B, followed by recombinant forms. The occurrence of twenty transmission clusters composed by at least two sequences was verified, suggesting the existence of transmission clusters among individuals from the same or distinct sexual orientations. Intermediate level of TDRM (12%) was found in the study population, and almost half of the subjects with TDRM had more than one resistance mutation. No correlations between sexual orientation and the presence of TDRM, HIV-1 subtypes/recombinants forms were verified. Taken together, the necessity of the continuous monitoring of the TDRM to verify the importance of pre-genotyping and to delineate future strategies in primary antiretroviral therapy. Likewise, the knowledge of the HIV-1 transmission networks in Brazil would allow the implementation of effective HIV-1 prevention strategies in local settings.
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Affiliation(s)
- Tayana Serpa Ortiz Tanaka
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Thaysse Ferreira Leite
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Solange Zacalusni Freitas
- Universitary Hospital Maria Aparecida Pedrossian, HUMAP, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Gabriela Alves Cesar
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Grazielli Rocha de Rezende
- Laboratory of Clinical Immunology, FACFAN, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | | | - Monick Lindenmeyer Guimarães
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Ana Rita Coimbra Motta-Castro
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Federal University of Mato Grosso do Sul, Campo Grande, Brazil.,Laboratory of Clinical Immunology, FACFAN, Federal University of Mato Grosso do Sul, Campo Grande, Brazil.,Laboratory of Molecular Virology, Oswaldo Cruz Foundation, Mato Grosso do Sul, Campo Grande, Brazil
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Mir D, Gräf T, Esteves de Matos Almeida S, Pinto AR, Delatorre E, Bello G. Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches. Sci Rep 2018; 8:8778. [PMID: 29884822 PMCID: PMC5993807 DOI: 10.1038/s41598-018-26824-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/18/2018] [Indexed: 12/01/2022] Open
Abstract
The subtype C Eastern Africa clade (CEA), a particularly successful HIV-1 subtype C lineage, has seeded several sub-epidemics in Eastern African countries and Southern Brazil during the 1960s and 1970s. Here, we characterized the past population dynamics of the major CEA sub-epidemics in Eastern Africa and Brazil by using Bayesian phylodynamic approaches based on coalescent and birth-death models. All phylodynamic models support similar epidemic dynamics and exponential growth rates until roughly the mid-1980s for all the CEA sub-epidemics. Divergent growth patterns, however, were supported afterwards. The Bayesian skygrid coalescent model (BSKG) and the birth-death skyline model (BDSKY) supported longer exponential growth phases than the Bayesian skyline coalescent model (BSKL). The BDSKY model uncovers patterns of a recent decline for the CEA sub-epidemics in Burundi/Rwanda and Tanzania (Re < 1) and a recent growth for Southern Brazil (Re > 1); whereas coalescent models infer an epidemic stabilization. To the contrary, the BSKG model captured a decline of Ethiopian CEA sub-epidemic between the mid-1990s and mid-2000s that was not uncovered by the BDSKY model. These results underscore that the joint use of different phylodynamic approaches may yield complementary insights into the past HIV population dynamics.
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Affiliation(s)
- Daiana Mir
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.
| | - Tiago Gräf
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sabrina Esteves de Matos Almeida
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Aguinaldo Roberto Pinto
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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Fritsch HM, Almeida SEM, Pinto AR, Gräf T. Spatiotemporal and demographic history of the HIV-1 circulating recombinant form CRF31_BC in Brazil. INFECTION GENETICS AND EVOLUTION 2018; 61:113-118. [PMID: 29601872 DOI: 10.1016/j.meegid.2018.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/19/2018] [Accepted: 03/25/2018] [Indexed: 10/17/2022]
Abstract
CRF31_BC is an HIVs-1 recombinant form very prevalent in the southernmost capital city of Brazil, Porto Alegre. Recent studies have been describing a growing number of cases of infection by CRF31_BC in other Brazilian cities and countries, suggesting a process of expansion of this strain. Aiming to describe the city of origin, dispersion routes and demographic history of CRF31_BC, this study analyzed all HIV-1 CRF31_BC and Brazilian BC mosaic publicly available sequences. CRF31_BC classification was performed by bootscanning and tree reconstruction methods. Bayesian phylogeographic and phylodynamic model approaches were used to reconstruct the spatiotemporal and demographic history of 95 sequences identified as CRF31_BC-like. Porto Alegre was estimated to be the origin and center of the dispersion of the CRF31_BC for most of the analyzed locations. However, some viral transitions independent from Porto Alegre were observed in other cities from the Rio Grande do Sul state and also in other Brazilian states. The estimated CRF31_BC epidemic growth rate was similar to subtype C and B in Brazil. Our findings suggest that CRF31_BC, although mostly prevalent in south region, is circulating nation-wide with some localities presenting autochthonous transmissions.
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Affiliation(s)
- Hegger M Fritsch
- Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; Centro de Desenvolvimento Científico e Tecnológico, Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Sabrina E M Almeida
- Centro de Desenvolvimento Científico e Tecnológico, Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil; Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Aguinaldo R Pinto
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Tiago Gräf
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Transmitted drug resistance in patients with acute/recent HIV infection in Brazil. Braz J Infect Dis 2017; 21:396-401. [PMID: 28539254 PMCID: PMC9427834 DOI: 10.1016/j.bjid.2017.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 11/20/2022] Open
Abstract
Introduction The widespread use of antiretroviral therapy increased the transmission of antiretroviral resistant HIV strains. Antiretroviral therapy initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance may jeopardize the early goals of early antiretroviral treatment among acute/recent HIV infected patients. Methods Patients with acute/recent HIV infection who underwent resistance test before antiretroviral treatment initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. Transmitted drug resistance was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without transmitted drug resistance was made using Kruskal–Wallis and Chi-square tests. Results Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall transmitted drug resistance prevalence was 16.3% (95% confidence interval [CI]: 8.1–30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1–24.5) was against non-nucleoside reverse transcriptase inhibitors, and K103N was the most frequently identified mutation. Conclusions The high prevalence of nonnucleoside reverse transcriptase inhibitors resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for antiretroviral naive individuals. Further studies on transmitted drug resistance among acutely/recently HIV-infected are needed to inform the predictors of transmitted resistance and the antiretroviral therapy outcomes among these population.
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A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012. PLoS One 2017; 12:e0170601. [PMID: 28489920 PMCID: PMC5425008 DOI: 10.1371/journal.pone.0170601] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/06/2017] [Indexed: 12/12/2022] Open
Abstract
Introduction Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. Methods The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster). Results HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008). Conclusion This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.
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Barral MF, Sousa AK, Santos AF, Abreu CM, Tanuri A, Soares MA, for the Brazilian Consortium for th. Identification of Novel Resistance-Related Polymorphisms in HIV-1 Subtype C RT Connection and RNase H Domains from Patients Under Virological Failure in Brazil. AIDS Res Hum Retroviruses 2017; 33:465-471. [PMID: 27875905 DOI: 10.1089/aid.2015.0376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mutations in the connection and RNase H C-terminal reverse transcriptase (RT) domains of HIV-1 have been shown to impact drug resistance to RT inhibitors. However, their impact in the context of non-B subtypes has been poorly assessed. This study aimed to characterize resistance-related mutations in the C-terminal portions of RT in treatment-failing patients from southern Brazil, a region with endemic HIV-1 subtype C (HIV-1C). Viral RNA was isolated and reverse transcribed from 280 infected subjects, and genomic regions were analyzed by polymerase chain reaction, DNA sequencing, and phylogenetic analysis. Two novel mutations, M357R and E529D, were evidenced in Brazilian HIV-1C strains from treatment-failing patients. In global viral isolates of subjects on treatment, M357R was selected in HIV-1C and CRF01_AE and E529D was selected in HIV-1 subtype B (HIV-1B). While most C-terminal RT mutations described for HIV-1B also occur in HIV-1C, this work pinpointed novel mutations that display subtype-specific predominance or occurrence.
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Affiliation(s)
- Maria F.M. Barral
- Departamento de Medicina, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Arielly K.P. Sousa
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - André F. Santos
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celina M. Abreu
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A. Soares
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, 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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Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS. J Virol 2016; 90:8160-8. [PMID: 27384663 DOI: 10.1128/jvi.00363-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1 env and pol genes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region. IMPORTANCE The AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our analyses showed distinct epidemic growth curves for the two epidemics, and we also found evidence suggesting that separate transmission chains may be impacting the viral phylodynamics and the emergence of new recombinant forms.
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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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Kannangai R, David S, Sundaresan VC, Sachithanandham J, Mani M, Abraham OC, Pulimood SA, Rupali P, Sridharan G. Frequency of transmitted drug resistance mutations among treatment-naïve HIV-1-infected individuals at a tertiary care centre in South India. Mol Diagn Ther 2016; 19:273-5. [PMID: 26296335 DOI: 10.1007/s40291-015-0160-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Morbidity and mortality among HIV-1-infected individuals has been dramatically reduced by the implementation of combinational antiretroviral therapy (ART). However, the efficiency of these therapies is compromised due to HIV-1 transmitted drug resistance mutations (TDRMs). METHODS We collected a total of 127 samples from ART-naïve HIV-infected individuals and sequenced the pol gene and analysed for drug resistance mutations using the Calibrated Population Resistance (CPR) tool in the Stanford database. RESULTS All the 127 clinical samples (100 %) were identified as HIV-1 subtype C. Based on the CPR tool, three strains (2.4 %) had TDRMs, and these were K101E, Y181C and G190A. Our findings correlated well with the WHO surveys conducted in Asia, including India, which consistently reported <5 % TDRM among the specific populations assessed. CONCLUSION In countries like India, regular monitoring of TDRMs will provide better information for clinical practice improvement and policy making.
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Affiliation(s)
- Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Shoba David
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India
| | - Vijayanand C Sundaresan
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India
| | | | - Monika Mani
- Department of Clinical Virology, Christian Medical College, Vellore, 632004, Tamil Nadu, India
| | | | | | - Priscilla Rupali
- Department of Internal Medicine, Christian Medical College, Vellore, India
| | - Gopalan Sridharan
- Sri Sakthi Amma Institute of Biomedical Research Institute, Vellore, India
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Lima K, de Souza Leal É, Cavalcanti AMS, Salustiano DM, de Medeiros LB, da Silva SP, Lacerda HR. Epidemiological, Clinical and Antiretroviral Susceptibility Characterization of Human Immunodeficiency Virus Subtypes B and Non-B in Pernambuco, Northeast Brazil. PLoS One 2016; 11:e0155854. [PMID: 27218259 PMCID: PMC4878750 DOI: 10.1371/journal.pone.0155854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background HIV-1 diversity causes important differences in the virus’ biological properties and their interactions with hosts, such as cell tropism, responses to antiretroviral therapy, drug-resistance, and disease progression. Objectives We evaluated the interrelationship of phylogenetic inference with epidemiological and laboratory data for HIV-1 isolates circulating in Pernambuco, Northeast Region—Brazil. Study design A total of 168 HIV-1 pol sequences were analysed, 64 were obtained from 2002–2003, and 104, from 2007–2009. Socio-demographic, clinical, and behavioural data were obtained from medical records. Laboratory testing enabled the determination of recent HIV-1 infections and co-infections with HBV, HCV, HTLV, or syphilis. Surveillance drug-resistance mutation analysis and antiretroviral susceptibility profiling were performed using HIV Drug-Resistance Database. Results HIV-1 non-B was associated with female, lower education, lower viral loads, and higher T cell counts mean. Frequencies of co-infection HIV-HBV, HIV-HCV, and HIV-syphilis were 27.8% (95% CI: 19.8–37.7), 1.04% (95% CI: 0.05–5.00) and 14.7% (95% CI: 8.6–23.0), respectively. Drug-resistant mutations rate was 2.98% (95% CI: 1.10–6.47). HIV-HBV subtype B co-infection was associated with men who have sex with men (MSM), higher education, higher viral loads and males. HIV-syphilis subtype non-B co-infection was associated with MSM status, lower T cell counts and males. Conclusions Data showed the importance of molecular characterisations of the HIV-1 epidemic and its relation with epidemiological and clinical characteristics of the population, as well as its association with other infectious diseases, so they can effort to improve preventive measures for health services and more information about the progress and effects of the epidemic in Northeastern–Brazil.
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Affiliation(s)
- Kledoaldo Lima
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
- * E-mail:
| | | | | | | | | | | | - Heloísa Ramos Lacerda
- Postgraduate at Department of Tropical Medicine, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Librelotto CS, Gräf T, Simon D, de Almeida SEM, Lunge VR. HIV-1 epidemiology and circulating subtypes in the countryside of South Brazil. Rev Soc Bras Med Trop 2016; 48:249-57. [PMID: 26108001 DOI: 10.1590/0037-8682-0083-2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Human immunodeficiency virus type 1 (HIV-1) has spread worldwide, with several subtypes and circulating recombinant forms. Brazil has an incidence of 20.5 HIV-1/acquired immunodeficiency syndrome (AIDS) patients per 100,000 inhabitants; however, the Southernmost State of Rio Grande do Sul (RS) has more than twice the number of HIV-1-infected people (41.3/100,000 inhabitants) and a different pattern of subtype frequencies, as previously reported in studies conducted in the capital (Porto Alegre) and its metropolitan region. This study examined HIV-1/AIDS epidemiological and molecular aspects in the countryside of Rio Grande do Sul. METHODS Socio-demographic, clinical and risk behavioral characteristics were obtained from HIV-1-positive adult patients using a structured questionnaire. HIV-1 subtypes were determined by nested-polymerase chain reaction (PCR) and sequencing of the pol and env genes. RESULTS The study sample included 149 (55% women) patients with a mean age of 41.8 ± 11.9 years. Most (73.8%) patients had a low education level and reported heterosexual practices as the most (91.9%) probable transmission route. HIV-1 subtypes were detected in 26 patients: 18 (69.2%) infected with subtype C, six (23.1%) infected with subtype B and two (7.7%) infected with BC recombinant forms. CONCLUSIONS These data highlight the increasing number of HIV-1 subtype C infections in the countryside of South Brazil.
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Affiliation(s)
- Carina Sperotto Librelotto
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Tiago Gräf
- Programa de Pós-Graduação em Biotecnologia e Biociências, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Daniel Simon
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
| | - Sabrina Esteves Matos de Almeida
- Centro de Desenvolvimento Técnico e Científico, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Rio Grande do Sul, Brazil
| | - Vagner Ricardo Lunge
- Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Universidade Luterana do Brasil, Canoas, Rio Grande do Sul, Brazil
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Delatorre E, Velasco-De-Castro CA, Pilotto JH, Couto-Fernandez JC, Bello G, Morgado MG. Short Communication: Reassessing the Origin of the HIV-1 CRF02_AG Lineages Circulating in Brazil. AIDS Res Hum Retroviruses 2015; 31:1230-7. [PMID: 26353079 DOI: 10.1089/aid.2015.0183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
HIV-1 CRF02_AG is responsible for at least 8% of the HIV-1 infections worldwide and is distributed mainly in West Africa. CRF02_AG has recently been reported in countries where it is not native, including Brazil. In a previous study including 10 CRF02_AG Brazilian samples, we found at least four independent introductions and two autochthonous transmission networks of this clade in Brazil. As more CRF02_AG samples have been identified in Brazil, we performed a new phylogeographic analysis using a larger dataset than before. A total of 20 Brazilian (18 from Rio de Janeiro and two from São Paulo) and 1,485 African HIV-1 CRF02_AG pol sequences were analyzed using maximum likelihood (ML). The ML tree showed that the Brazilian sequences were distributed in five different lineages. The Bayesian phylogeographic analysis of the Brazilian and their most closely related African sequences (n = 212) placed the origin of all Brazilian lineages in West Africa, probably Ghana, Senegal, and Nigeria. Two monophyletic clades were identified, comprising only sequences from Rio de Janeiro, and their date of origin was estimated at around 1985 (95% highest posterior density: 1979-1992). These results support the existence of at least five independent introductions of the CRF02_AG lineage from West Africa into Brazil and further indicate that at least two of these lineages have been locally disseminated in the Rio de Janeiro state over the past 30 years.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
| | - Carlos A. Velasco-De-Castro
- Laboratório de Virologia, Departamento de Patologia Clínica, Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–FIOCRUZ, Rio de Janeiro, Brazil
| | - José H. Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
- Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
| | | | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
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Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil. J Virol 2015; 89:12341-8. [PMID: 26423943 DOI: 10.1128/jvi.01681-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/22/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED The phylogeographic history of the Brazilian HIV-1 subtype C (HIV-1C) epidemic is still unclear. Previous studies have mainly focused on the capital cities of Brazilian federal states, and the fact that HIV-1C infections increase at a higher rate than subtype B infections in Brazil calls for a better understanding of the process of spatial spread. A comprehensive sequence data set sampled across 22 Brazilian locations was assembled and analyzed. A Bayesian phylogeographic generalized linear model approach was used to reconstruct the spatiotemporal history of HIV-1C in Brazil, considering several potential explanatory predictors of the viral diffusion process. Analyses were performed on several subsampled data sets in order to mitigate potential sample biases. We reveal a central role for the city of Porto Alegre, the capital of the southernmost state, in the Brazilian HIV-1C epidemic (HIV-1C_BR), and the northward expansion of HIV-1C_BR could be linked to source populations with higher HIV-1 burdens and larger proportions of HIV-1C infections. The results presented here bring new insights to the continuing discussion about the HIV-1C epidemic in Brazil and raise an alternative hypothesis for its spatiotemporal history. The current work also highlights how sampling bias can confound phylogeographic analyses and demonstrates the importance of incorporating external information to protect against this. IMPORTANCE Subtype C is responsible for the largest HIV infection burden worldwide, but our understanding of its transmission dynamics remains incomplete. Brazil witnessed a relatively recent introduction of HIV-1C compared to HIV-1B, but it swiftly spread throughout the south, where it now circulates as the dominant variant. The northward spread has been comparatively slow, and HIV-1B still prevails in that region. While epidemiological data and viral genetic analyses have both independently shed light on the dynamics of spread in isolation, their combination has not yet been explored. Here, we complement publically available sequences and new genetic data from 13 cities with epidemiological data to reconstruct the history of HIV-1C spread in Brazil. The combined approach results in more robust reconstructions and can protect against sampling bias. We found evidence for an alternative view of the HIV-1C spatiotemporal history in Brazil that, contrary to previous explanations, integrates seamlessly with other observational data.
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Moura MES, da Guarda Reis MN, Lima YAR, Eulálio KD, Cardoso LPV, Stefani MMA. HIV-1 transmitted drug resistance and genetic diversity among patients from Piauí State, Northeast Brazil. J Med Virol 2015; 87:798-806. [PMID: 25649362 DOI: 10.1002/jmv.24087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2014] [Indexed: 11/10/2022]
Abstract
HIV-1 transmitted-drug-resistance and genetic diversity are dynamic and may differ in distinct locations/risk groups. In Brazil, increased AIDS incidence and related mortality have been detected in the Northeast region, differently from the epicenter in the Southeast. This cross-sectional study describes transmitted-dru- resistance and HIV-1 subtypes in protease/PR and reverse transcriptase/RT regions among antiretroviral naïve patients from Piauí State, Northeast Brazil. Among 96 patients recruited 89 (92.7%) had HIV-1 PR/RT regions sequenced: 44 females and 45 males, 22 self-declared as men who have sex with men. Transmitted-drug-resistance was investigated by CPR tool (Stanford HIV-1 Drug Resistance/SDRM). HIV-1 subtypes were assigned by REGA and phylogenetic inference. Overall, transmitted-drug-resistance rate was 11.2% (10/89; CI 95%: 5.8-19.1%); 22.7% among men who have sex with men (5/22; CI 95%: 8.8-43.4%), 10% in heterosexual men (2/20; CI 95%: 1.7-29.3%) and 6.8% in women (3/44; CI 95%: 1.8-17.4%). Singleton mutations to protease-inhibitor/PI, nucleoside-reverse-transcriptase-inhibitor/NRTI or non-nucleoside-reverse-transcriptase-inhibitor/NNRTI predominated (8/10): PI mutations (M46L, V82F, L90M); NRTI mutations (M41L, D67N) and NNRTI mutations (K103N/S). Dual class resistance mutations to NRTI and NNRTI were observed: T215L (NRTI), Y188L (NNRTI) and T215N (NRTI), F227L (NNRTI). Subtype B prevailed (86.6%; 77/89), followed by subtype F1 (1.1%, 1/89) and subtype C (1.1%, 1/89). B/F1 and B/C intersubtype recombinants represented 11.2% (10/89). In Piauí State extensive testing of incidence and transmitted-drug-resistance in all populations with risk behaviors may help control AIDS epidemic locally.
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Junqueira DM, Medeiros RMD, Leite TCNF, Guimarães ML, Gräf T, Pinto AR, Almeida SEDM. Detection of the B"-GWGR variant in the southernmost region of Brazil: unveiling the complexity of the human immunodeficiency virus-1 subtype B epidemic. Mem Inst Oswaldo Cruz 2014; 108:735-40. [PMID: 24037196 PMCID: PMC3970682 DOI: 10.1590/0074-0276108062013010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/26/2013] [Indexed: 12/17/2022] Open
Abstract
Typical human immunodeficiency virus-1 subtype B (HIV-1B) sequences present a GPGR signature at the tip of the variable region 3 (V3) loop; however, unusual motifs harbouring a GWGR signature have also been isolated. Although epidemiological studies have detected this variant in approximately 17-50% of the total infections in Brazil, the prevalence of B"-GWGR in the southernmost region of Brazil is not yet clear. This study aimed to investigate the C2-V3 molecular diversity of the HIV-1B epidemic in southernmost Brazil. HIV-1 seropositive patients were ana-lysed at two distinct time points in the state of Rio Grande do Sul (RS98 and RS08) and at one time point in the state of Santa Catarina (SC08). Phylogenetic analysis classified 46 individuals in the RS98 group as HIV-1B and their molecular signatures were as follows: 26% B"-GWGR, 54% B-GPGR and 20% other motifs. In the RS08 group, HIV-1B was present in 32 samples: 22% B"-GWGR, 59% B-GPGR and 19% other motifs. In the SC08 group, 32 HIV-1B samples were found: 28% B"-GWGR, 59% B-GPGR and 13% other motifs. No association could be established between the HIV-1B V3 signatures and exposure categories in the HIV-1B epidemic in RS. However, B-GPGR seemed to be related to heterosexual individuals in the SC08 group. Our results suggest that the established B"-GWGR epidemics in both cities have similar patterns, which is likely due to their geographical proximity and cultural relationship.
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Affiliation(s)
- Dennis Maletich Junqueira
- Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em Saúde,, Porto AlegreRS, Brasil
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Prevalence of transmitted HIV-1 antiretroviral resistance among patients initiating antiretroviral therapy in Brazil: a surveillance study using dried blood spots. J Int AIDS Soc 2014; 17:19042. [PMID: 25249214 PMCID: PMC4172689 DOI: 10.7448/ias.17.1.19042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/28/2014] [Accepted: 08/20/2014] [Indexed: 11/09/2022] Open
Abstract
Introduction In Brazil, the use of antiretrovirals is widespread: more than 260,000 individuals are currently undergoing treatment. We conducted a survey targeting antiretroviral-naïve individuals who were initiating antiretroviral therapy (ART) according to local guidelines. This survey covered five Brazilian regions. Methods The HIV Threshold Survey methodology (HIV-THS) of the World Health Organization was utilized, and subjects were selected from seven highly populated cities representative of all Brazilian macro-regions. Dried blood spots (DBS) were collected on SS903 collection cards and were transported by regular mail at room temperature to a single central laboratory for genotyping. Results We analysed samples from 329 individuals initiating highly active antiretroviral therapy (HAART), 39 (11.8%) of whom were harbouring transmitted drug resistance (TDR). The mean CD4+ T cell count was 253 cells/µL, and the mean viral load was 142,044 copies/mL. The regional prevalence of resistance was 17.0% in the Northeast, 12.8% in the Southeast, 10.6% in the Central region, 8.5% in the North and 8.5% in the South. The inhibitor-specific TDR prevalence was 6.9% for nucleoside reverse transcriptase inhibitors, 4.9% for non-nucleoside reverse transcriptase inhibitors and 3.9% for protease inhibitors; 3.6% of individuals presented resistance to more than one class of inhibitors. Overall, there were trends towards higher prevalences of subtype C towards the South and subtype F towards the North. Of the DBS samples collected, 9.3% failed to provide reliable results. Discussion We identified variable TDR prevalence, ranging from intermediate to high levels, among individuals in whom HIV disease progressed, thus implying that resistance testing before initiating ART could be effective in Brazil. Our results also indicate that the use of DBS might be especially valuable for providing access to testing in resource-limited and remote settings.
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Baesi K, Ravanshad M, Ghanbarisafari M, Saberfar E, SeyedAlinaghi S, Volk JE. Antiretroviral drug resistance among antiretroviral-naïve and treatment experienced patients infected with HIV in Iran. J Med Virol 2014; 86:1093-8. [PMID: 24740443 DOI: 10.1002/jmv.23898] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2014] [Indexed: 02/05/2023]
Affiliation(s)
- Kazem Baesi
- Iranian Research Center for HIV/AIDS; Iranian Institute for Reduction of High Risk Behaviors; Tehran University of Medical Sciences; Tehran Iran
| | - Mehrdad Ravanshad
- Department of Virology, Faculty of Medical Sciences; Tarbiat Modares University; Tehran Iran
| | - Maryam Ghanbarisafari
- Iranian Research Center for HIV/AIDS; Iranian Institute for Reduction of High Risk Behaviors; Tehran University of Medical Sciences; Tehran Iran
| | - Esmaeil Saberfar
- Research and Development Department; Bayerpaul Group; Tehran Iran
| | - SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS; Iranian Institute for Reduction of High Risk Behaviors; Tehran University of Medical Sciences; Tehran Iran
| | - Jonathan E. Volk
- Center for AIDS Prevention Studies; University of California; San Francisco California
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Velasco-de-Castro CA, Grinsztejn B, Veloso VG, Bastos FI, Pilotto JH, Fernandes N, Morgado MG. HIV-1 diversity and drug resistance mutations among people seeking HIV diagnosis in voluntary counseling and testing sites in Rio de Janeiro, Brazil. PLoS One 2014; 9:e87622. [PMID: 24498155 PMCID: PMC3907471 DOI: 10.1371/journal.pone.0087622] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022] Open
Abstract
The remarkable viral diversity remains a big challenge to the development of HIV vaccines and optimal therapy worldwide. In the latest years, as a consequence of the large expansion of highly active antiretroviral therapy (HAART) availability worldwide, an increase in transmitted drug resistance mutations (TDRM) has been observed, varying according the region. This study assessed HIV-1 diversity and TDRM profile over time among newly HIV-1 diagnosed individuals from Rio de Janeiro, Brazil. Blood samples were collected from individuals seeking HIV diagnosis in four voluntary counseling and testing (VCTs) sites located in the Rio de Janeiro Metropolitan Area, in 2005-2007. Recent (RS) and long-term (LTS) HIV-1 seroconverters were distinguished using BED-CEIA. Pol viral sequences were obtained for 102 LTS identified in 2005 and 144 RS from 2005-2007. HIV-1 subtype and pol recombinant genomes were determined using Rega HIV-1 Subtyping Tool and by phylogenetic inferences and bootscanning analyses. Surveillance of HIV-1 TDRM to protease and reverse transcriptase inhibitors were performed according to the Calibrated Population Resistance (CPR) Tool 6.0. Overall, subtype B remains the most prevalent in Rio de Janeiro in both LTS and RS HIV-1 infected individuals. An increased proportion of recombinant samples was detected over time, especially in RS heterosexual men, due to the emergence of CRF02_AG and URF samples bearing a subtype K fragment. The prevalence of HIV-1 samples carrying TDRM was high and similar between LTS and RS (15.7% vs 14.6%) or age (<25yo 17.9% vs >25yo 16.6%) along the study period. The high resistance levels detected in both populations are of concern, especially considering the dynamics of HIV-1 diversity over time. Our results suggest that the incorporation of resistance testing prior to HAART initiation should be highly considered, as well as permanent surveillance, aiming to carefully monitoring HIV-1 diversity, with focus on CRF/URF emergence and putative transmission.
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Affiliation(s)
- Carlos A. Velasco-de-Castro
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Laboratório de Virologia, Departamento de Patologia Clínica, Instituto Fernandes Figueira, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- * E-mail: (MGM); (CAVdC)
| | - Beatriz Grinsztejn
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Valdiléa G. Veloso
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Francisco I. Bastos
- Instituto de Comunicação e Informação Científica e Tecnológica em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Laboratório de Informação em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brasil, and Imperial College London (CAPES visiting researcher # 17551-12-8), London, United Kingdom
| | - José H. Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- Hospital Geral de Nova Iguaçu, Nova Iguaçu, RJ, Brasil
| | - Nilo Fernandes
- Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Mariza G. Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
- * E-mail: (MGM); (CAVdC)
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Prellwitz IM, Alves BM, Ikeda MLR, Kuhleis D, Picon PD, Jarczewski CA, Osório MR, Sánchez A, Seuánez HN, Larouzé B, Soares MA, Soares EA. HIV behind bars: human immunodeficiency virus cluster analysis and drug resistance in a reference correctional unit from southern Brazil. PLoS One 2013; 8:e69033. [PMID: 23874857 PMCID: PMC3706441 DOI: 10.1371/journal.pone.0069033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 06/05/2013] [Indexed: 02/06/2023] Open
Abstract
People deprived of liberty in prisons are at higher risk of infection by the human immunodeficiency virus (HIV) due to their increased exposure through intravenous drug use, unprotected sexual activity, tattooing in prison and blood exposure in fights and rebellions. Yet, the contribution of intramural HIV transmission to the epidemic is scarcely known, especially in low- and middle-income settings. In this study, we surveyed 1,667 inmates incarcerated at Presídio Central de Porto Alegre, located in southern Brazil, for HIV infection and molecular characterization. The HIV seroprevalence was 6.6% (110/1,667). Further analyses were carried out on 40 HIV-seropositive inmates to assess HIV transmission clusters and drug resistance within the facility with the use of molecular and phylogenetic techniques. The molecular epidemiology of HIV-1 subtypes observed was similar to the one reported for the general population in southern Brazil, with the predominance of HIV-1 subtypes C, B, CRF31_BC and unique BC recombinants. In particular, the high rate (24%) of URF_BC found here may reflect multiple exposures of the population investigated to HIV infection. We failed to find HIV-infected inmates sharing transmission clusters with each other. Importantly, the analysis of HIV-1 pol genomic fragments evidenced high rates of HIV primary and secondary (acquired) drug resistance and an alarming proportion of virologic failure among patients under treatment, unveiling suboptimal access to antiretroviral therapy (ARV), low ARV adherence and dissemination of drug resistant HIV strains in primary infections. Our results call for immediate actions of public authority to implement preventive measures, serological screening and, for HIV-seropositive subjects, clinical and treatment follow-up in order to control HIV infection and limit the spread of drug resistance strains in Brazilian prisons.
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Affiliation(s)
| | - Brunna M. Alves
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria Letícia R. Ikeda
- Secretaria de Saúde de Viamão, Prefeitura de Viamão, Viamão, Brazil
- Departamento de Ensino e Pesquisa, Hospital Sanatório Partenon, Porto Alegre, Brazil
| | - Daniele Kuhleis
- Secretaria de Segurança Pública, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Pedro D. Picon
- Secretaria de Segurança Pública, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla A. Jarczewski
- Departamento de Ensino e Pesquisa, Hospital Sanatório Partenon, Porto Alegre, Brazil
| | - Marta R. Osório
- Fundação Estadual de Produção e Pesquisa em Saúde, Governo do Estado do Rio Grande do Sul, Porto Alegre, Brazil
| | - Alexandra Sánchez
- Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Secretaria de Estado de Administração Penitenciária, Governo do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N. Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bernard Larouzé
- Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- INSERM U707, Paris, France
- Université Pierre et Marie Curie - Paris 6, Paris, France
| | - Marcelo A. Soares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A. Soares
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- * E-mail:
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Transmitted Drug Resistance among People Living with HIV/Aids at Major Cities of Sao Paulo State, Brazil. Adv Virol 2013; 2013:878237. [PMID: 23401688 PMCID: PMC3562575 DOI: 10.1155/2013/878237] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 12/18/2012] [Indexed: 11/21/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) transmitted drug resistance (TDR) is an important public health issue. In Brazil, low to intermediate resistance levels have been described. We assessed 225 HIV-1 infected, antiretroviral naïve individuals, from HIV Reference Centers at two major metropolitan areas of Sao Paulo (Sao Paulo and Campinas), the state that concentrates most of the Brazilian Aids cases. TDR was analyzed by Stanford Calibrated Population Resistance criteria (CPR), and mutations were observed in 17 individuals (7.6%, 95% CI: 4.5%–11.9%). Seventy-six percent of genomes (13/17) with TDR carried a nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, mostly K103N/S (9/13, 69%), potentially compromising the preferential first-line therapy suggested by the Brazilian HIV Treatment Guideline that recommends efavirenz-based combinations. Moreover, 6/17 (35%) had multiple mutations associated with resistance to one or more classes. HIV-1 B was the prevalent subtype (80%); other subtypes include HIV-1 F and C, mosaics BC, BF, and single cases of subtype A1 and CRF02_AG. The HIV Reference Center of Campinas presented more cases with TDR, with a significant association of TDR with clade B infection (P < 0.05).
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Côrtes FH, Bello G, Vorsatz C, Pilotto JH, Guimarães ML, Grinsztejn B, Veloso VG, Pinto AR, Morgado MG. Higher cross-subtype IFN-γ ELISpot responses to Gag and Nef peptides in Brazilian HIV-1 subtype B- and F1- than in C-infected subjects. Vaccine 2012; 31:1106-12. [PMID: 23261042 DOI: 10.1016/j.vaccine.2012.12.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 11/19/2012] [Accepted: 12/08/2012] [Indexed: 02/06/2023]
Abstract
HIV-1 diversity has been considered a huge challenge for the HIV-1 vaccine development. To overcome it, immunogens based on centralized sequences, as consensus, have been tested. In Brazil, the co-circulation of three subtypes offers a suitable scenario to test T cell cross-subtype responses to consensus sequences. Furthermore, we included peptides based on closest viral isolates (CVI) from each subtype analyzed to compare with T cell responses detected against the consensus sequences. The study included 32 subjects infected with HIV-1 subtype B (n=13),C (n=11), and F1 (n=8). Gag and Nef-specific T cell responses were evaluated by IFN-γ-ELISpot assay. Peptides based on CVI sequences were similar to consensus in both reducing genetic distance and detecting T cell responses. A high cross-subtype response between B and F1 in both regions was observed in HIV-1 subtype B and F1-infected subjects. We also found no significant difference in responses to subtype B and C consensus peptides among subtype B-infected subjects. In contrast, the magnitude of T cell responses to consensus C peptides in the Gag region was higher than to consensus B peptides among HIV-1 subtype C-infected subjects. Regarding Nef, subtype C-infected subjects showed higher values to consensus C than to consensus F1 peptides. Moreover, subtype F1-infected subjects presented lower responses to subtype C peptides than to subtype F1 and B. A similar level of responses was detected with group M based peptides in subtype B and F1 infected subjects. However, among subtype C infected subjects, this set of peptides detected lower levels of response than consensus C. Overall, the level of cross-subtype response between subtypes B and F1 was higher than between subtype C and B or C and F1. Our data suggests that the barrier of genetic diversity in HIV-1 group M for vaccine design may be dependent on the subtypes involved.
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Affiliation(s)
- Fernanda Heloise Côrtes
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ 21040-360, Brazil
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Temporal dynamics of HIV-1 circulating subtypes in distinct exposure categories in southern Brazil. Virol J 2012; 9:306. [PMID: 23234345 PMCID: PMC3547702 DOI: 10.1186/1743-422x-9-306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 12/07/2012] [Indexed: 11/29/2022] Open
Abstract
Background The HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal dynamics of HIV-1 subtypes circulating in patients from distinct exposure categories in Southern Brazil. For this purpose 166 HIV-1 samples collected at the years of 1998 (group I) and 2005–2008 (group II) were analyzed. Results Analysis of group I revealed statistically significant (p < 0.05) associations between MSM and subtype B as well as between IDU and subtype C; while no statistical significant association between HIV-1 subtypes and exposure category was verified for group II. An overall temporal increase in the prevalence of subtype C and BC recombinants was observed in both HET and MSM populations, accompanied by a proportional decrease in the prevalence of the pure subtype B. Conclusions The present study shows an association between HIV subtypes and exposure categories at the middle 1990s in Southern Brazil. Our findings suggest that MSM and IDU populations might have played a major role in the introduction and initial dissemination of subtypes B and C, respectively, in Southern Brazil. This study also suggests a trend towards homogenization of HIV-1 strains across distinct exposure categories as a consequence of an overall increase in the prevalence of subtype C and BC recombinants in both HET and MSM populations.
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Alcântara KC, Reis MNG, Cardoso LPV, Bello G, Stefani MMA. Increasing heterosexual transmission of HIV-1 subtype C in Inland Central Western Brazil. J Med Virol 2012; 85:396-404. [DOI: 10.1002/jmv.23474] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2012] [Indexed: 11/09/2022]
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Gräf T, Pinto AR. The increasing prevalence of HIV-1 subtype C in Southern Brazil and its dispersion through the continent. Virology 2012; 435:170-8. [PMID: 22999094 DOI: 10.1016/j.virol.2012.08.048] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/29/2012] [Accepted: 08/30/2012] [Indexed: 01/15/2023]
Abstract
The HIV-1 has evolved swiftly and the scenario of HIV-1 genetic diversity is constantly changing. In South America, recombinant forms of subtypes B, F1, and BF1 have historically driven the HIV-1 epidemic. In recent years, however, infection with subtype C has gained prominence as its prevalence increased in Southern Brazil as well as neighboring countries. Current studies point to a single introduction of closely related strains as the beginning of the Brazilian subtype C epidemic. However, the place of origin of these strains, date, and route of introduction are under continuous debate as well as the clinical outcomes of the emergence of subtype C. Therefore, this paper reviews the history of the HIV-1 subtype C in Brazil, particularly in the Southern region, covering its demographic and evolutionary history and the possible implications to the Brazilian AIDS epidemic as well as to neighboring countries.
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Affiliation(s)
- Tiago Gräf
- Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC, Brazil
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Monno L, Brindicci G, Lai A, Punzi G, Altamura M, Simonetti FR, Ladisa N, Saracino A, Balotta C, Angarano G. An outbreak of HIV-1 BC recombinants in Southern Italy. J Clin Virol 2012; 55:370-3. [PMID: 22981618 DOI: 10.1016/j.jcv.2012.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 08/11/2012] [Accepted: 08/16/2012] [Indexed: 12/01/2022]
Abstract
BACKGROUND In Western Europe, a previously subtype B HIV-1 restricted area, BC recombinants have been rarely reported. OBJECTIVE To describe an outbreak of HIV-1 BC recombinants in southern Italy. STUDY DESIGN We analyzed pol (protease/reverse transcriptase) sequences from 135 newly diagnosed HIV-1-infected patients during the years 2009-2011. For phylogenetic relationships, sequences were aligned to the most recent reference data set from the Los Alamos database using BioEdit (version 7.1.3). The resulting alignment was analyzed with the Phylip package (version 3.67) building a neighbor-joining tree based on the Kimura two-parameter substitution model. The reliability of the tree topology was assessed through bootstrapping using 1000 replicates. The recombination pattern was characterized using SimPlot 3.5.1 and SplitsTree 4. RESULTS At phylogenetic analysis, 22 (16.2%) isolates whose sequences were not unequivocally assigned to a pure subtype or known CRF, formed a distinct monophyletic clade (100% of bootstrap value). For these isolates, the recombination analysis identified a BC mosaic pattern with two breakpoints at positions 2778±5 and 3162±8 (HXB2 numbering) which differed from those of known BC CRFs. All patients from whom these sequences were derived were highly educated youth Italians, 91% males and 82% MSM. Sequences of pol integrase, gp120 and gp41 from these same patients were classified as C subtype. CONCLUSIONS This outbreak which further reflects the increasing heterogeneity of HIV epidemic in our country is the first report of an Italian outbreak of a BC recombinant, possibly a novel candidate CRF.
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Affiliation(s)
- Laura Monno
- Clinic of Infectious Diseases, University of Bari, Bari, Italy.
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Murphey-Corb M, Rajakumar P, Michael H, Nyaundi J, Didier PJ, Reeve AB, Mitsuya H, Sarafianos SG, Parniak MA. Response of simian immunodeficiency virus to the novel nucleoside reverse transcriptase inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine in vitro and in vivo. Antimicrob Agents Chemother 2012; 56:4707-12. [PMID: 22713337 PMCID: PMC3421895 DOI: 10.1128/aac.00723-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/05/2012] [Indexed: 01/13/2023] Open
Abstract
Nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) are essential components in first-line therapy for human immunodeficiency virus (HIV) infection. However, long-term treatment with existing NRTIs can be associated with significant toxic side effects and the emergence of drug-resistant strains. The identification of new NRTIs for the continued management of HIV-infected people therefore is paramount. In this report, we describe the response of a primary isolate of simian immunodeficiency virus (SIV) to 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) both in vitro and in vivo. EFdA was 3 orders of magnitude better than tenofovir (TFV), zidovudine (AZT), and emtricitabine (FTC) in blocking replication of SIV in monkey peripheral blood mononuclear cells (PBMCs) in vitro, and in a preliminary study using two SIV-infected macaques with advanced AIDS, it was highly effective at treating SIV infection and AIDS symptoms in vivo. Both animals had 3- to 4-log decreases in plasma virus burden within 1 week of EFdA therapy (0.4 mg/kg of body weight, delivered subcutaneously twice a day) that eventually became undetectable. Clinical signs of disease (diarrhea, weight loss, and poor activity) also resolved within the first month of treatment. No detectable clinical or pathological signs of drug toxicity were observed within 6 months of continuous therapy. Virus suppression was sustained until drug treatment was discontinued, at which time virus levels rebounded. Although the rebound virus contained the M184V/I mutation in the viral reverse transcriptase, EFdA was fully effective in maintaining suppression of mutant virus throughout the drug treatment period. These results suggest that expanded studies with EFdA are warranted.
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Affiliation(s)
- Michael Murphey-Corb
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Phylogeographic analysis of HIV-1 subtype C dissemination in Southern Brazil. PLoS One 2012; 7:e35649. [PMID: 22530062 PMCID: PMC3329557 DOI: 10.1371/journal.pone.0035649] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/19/2012] [Indexed: 12/26/2022] Open
Abstract
The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Paraná). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianópolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Paraná state). This analysis further suggested that Florianópolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r2 = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades.
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Analysis of transmitted resistance to raltegravir and selective pressure among HIV-1-infected patients on a failing HAART in Sao Paulo, Brazil. J Clin Microbiol 2012; 50:2122-5. [PMID: 22403424 DOI: 10.1128/jcm.00539-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We studied the presence of primary resistance to raltegravir (RAL), natural polymorphisms, and selection pressure on HIV-1 integrase. We found a high frequency of integrase polymorphisms related to the resistance to RAL and sequence stability. Further studies are needed to determine the importance of these polymorphisms to RAL resistance.
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Silveira J, Santos AF, Martínez AMB, Góes LR, Mendoza-Sassi R, Muniz CP, Tupinambás U, Soares MA, Greco DB. Heterosexual transmission of human immunodeficiency virus type 1 subtype C in southern Brazil. J Clin Virol 2012; 54:36-41. [PMID: 22326760 DOI: 10.1016/j.jcv.2012.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 01/06/2012] [Accepted: 01/23/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) subtype B predominates in Brazil, but in the southern region subtype C is the most frequent, followed by subtypes B, F1 and recombinant forms. In southern Brazil, these subtypes co-circulate in subjects with homogeneous demographic and clinical features, enabling a better understanding of the role of HIV-1 subtypes on the characteristics of infection. OBJECTIVES To evaluate the prevalence of different HIV-1 subtypes in subjects with recent diagnosis for HIV infection in the extreme south of Brazil, and to study their association with demographic, behavioral, clinical and laboratorial characteristics. STUDY DESIGN We have determined the genetic sequence of viral protease and reverse transcriptase (polymerase, connection and RNase H domains) isolated from studied subjects. Viral subtype was inferred by comparison with reference HIV sequences, and recombination was determined with Simplot analysis. The association of HIV-1 subtypes with studied characteristics was evaluated by chi-square, Fisher's exact, Student's t and Kruskal-Wallis tests. RESULTS Two hundred and forty-five HIV isolates were molecularly characterized, and the association with variables was studied for 233 (95.1%) patients. Of those, 46.8% followed AIDS defining criteria. HIV-1C was responsible for 56.3% of infections, and was associated with heterosexual transmission (p=0.001) and with higher CD4(+) T-cell counts (p=0.02). CONCLUSIONS The molecular epidemiology of HIV-1 in the southernmost Brazil is currently steady with predominance of HIV-1C. This is the first study showing a robust association of the infection by this subtype and heterosexual transmission in the state of Rio Grande do Sul, Brazil.
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Affiliation(s)
- Jussara Silveira
- Faculdade de Medicina, Universidade Federal de Rio Grande, Rio Grande, Brazil
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