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Oliveira RC, Souza JSMD, Alcântara LCJ, Guimarães ML, Brites C, Monteiro-Cunha JP. Molecular and Phylogenetic Analysis of HIV-1 Subtype C in Bahia State, Northeastern Brazil. AIDS Res Hum Retroviruses 2024; 40:37-41. [PMID: 37312563 DOI: 10.1089/aid.2023.0038] [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] [Indexed: 06/15/2023] Open
Abstract
HIV-1 subtype C is associated with more than half of infections in southern Brazil and has been increasing in other regions of the country. In a previous study carried out in northeastern Brazil, we found a prevalence of 4.1% of subtype C. This work investigates the origin of subtype C in the state of Bahia based on five new viral sequences. The phylogenetic analysis showed that subtype C viruses found in Bahia descend from the main lineage that circulates in other Brazilian regions.
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Affiliation(s)
- Rodrigo Cunha Oliveira
- Departamento de Bioquímica e Biofísica, Núcleo de Bioinformática, Universidade Federal da Bahia, Salvador, Brasil
| | | | | | | | - Carlos Brites
- Laboratório de Pesquisa em Infectologia, Complexo Hospitalar Prof. Edgard Santos, Universidade Federal da Bahia, Salvador, Brasil
| | - Joana Paixão Monteiro-Cunha
- Departamento de Bioquímica e Biofísica, Núcleo de Bioinformática, Universidade Federal da Bahia, Salvador, Brasil
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2
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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 Azevedo SSD, Delatorre E, Gaido CM, Silva-de-Jesus C, Guimarães ML, Couto-Fernandez JC, Morgado MG. HIV-1 Diversity and Drug Resistance in Treatment-Naïve Children and Adolescents from Rio de Janeiro, Brazil. Viruses 2022; 14:v14081761. [PMID: 36016383 PMCID: PMC9413768 DOI: 10.3390/v14081761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/02/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) can be transmitted via parenteral, sexual, or vertical exposure routes. The number of HIV-1 cases detected yearly in children and adolescents in Brazil did not decrease over the last decade, representing ~5% of total cases described in the country. In recent years, the HIV-1 diversity and the prevalence of transmitted drug resistance mutations (TDRM) are moving toward a marked increase. In this study, we retrospectively evaluated the diversity of HIV-1 subtypes and the TDRM prevalence in 135 treatment-naïve HIV-1 vertically infected children and adolescents born in between 1993 and 2012. These children were assessed in either 2001–2007 or 2008–2012 when they were 0 to 17 years old. The individuals assessed in 2001–2007 (n = 38) had median CD4+ T cell counts of 1218 cells/mm3 (IQR: 738–2.084) and median HIV-1 plasma viral load of 4.18 log10 copies/mL (IQR: 3.88–4.08). The individuals (n = 97) evaluated in 2008–2012 showed median CD4+ T cell counts of 898.5 cells/mm3 (IQR: 591.3–1.821) and median HIV-1 plasma viral load of 4.69 log10 copies/mL (IQR: 4.26–5.33). A steady decrease in the median CD4 T+ cell counts was observed with age progression, as expected. The majority HIV-1 pol sequences (87%) were classified as pure HIV-1 subtypes (77% subtype B, 9% subtype F1 and 1.5% subtype C), while 13% of sequences were classified as recombinants (CRF45_cpx, n = 4; CRF28/29_BF1, n = 2; CRF02_AG, n = 1; CRF40_BF1, n = 1, CRF99_BF1, n = 1, URF_BF1, n = 8). The overall prevalence of TDRM was 14% (19/135), conferring resistance to the nucleoside reverse transcriptase inhibitors (NRTI, 13/135–9.6%), non-nucleoside reverse transcriptase inhibitors (NNRTI, 8/135–5.9%), and protease inhibitors (PI, 2/135–1.5%). The main TDRM observed for NNRTI was the K103N (n = 8), while the mutations T215I/Y/D/E (n = 7) and M184V (n = 4) were the main TDRM for NRTI. Only two TDRM were observed for PI in one individual each (M46I and V82A). Most TDRM were found in the HIV-1 subtype B (84%) sequences. This study reveals an HIV-1 epidemic with high diversity and moderate prevalence of TDRM in the pediatric population of Rio de Janeiro, indicating the existence of possible problems in the clinical management of prophylactic therapy to prevent mother-to-child transmission and future treatment options for the affected children.
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Affiliation(s)
- Suwellen Sardinha Dias de Azevedo
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
- Correspondence: or ; Tel.: +55-21-3865-8147; Fax: +55-21-3865-8173
| | - Edson Delatorre
- Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia—Universidade Federal do Espírito Santo—UFES, Espírito Santo 29500-000, Brazil
| | - Cibele Marina Gaido
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Carlos Silva-de-Jesus
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | | | - José Carlos Couto-Fernandez
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21045-900, Brazil
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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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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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Bello G, Delatorre E, Lacoste V, Darcissac E, Herrmann-Storck C, Tressières B, Cabras O, Lamaury I, Cabié A, Visseaux B, Chaix ML, Descamps D, Césaire R, Nacher M, Dos Santos G. Increasing prevalence and local transmission of non-B HIV-1 subtypes in the French Antilles and French Guiana between 1995 and 2018. Virus Evol 2020; 6:veaa081. [PMID: 33324493 PMCID: PMC7724245 DOI: 10.1093/ve/veaa081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Caribbean and South American French Overseas Territories (CSAFOT) are the regions most heavily affected by the Human Immunodeficiency Virus type 1 (HIV-1) epidemic in France. Although dominated by HIV-1 subtype B, the detection of non-B subtypes and the great proportion of HIV-positive persons born abroad demonstrated the potential for local spread of non-B subtype strains in CSAFOT. To reconstruct the epidemiologic dynamics of major non-B subtype clusters spreading in CSAFOT, we conducted phylogenetic and evolutionary analyses of 2,523 HIV-1 pol sequences collected from patients living in Martinique, Guadeloupe, and French Guiana from 1995 to 2018. A large variety of HIV-1 non-B subtype strains (eight subtypes, twelve CRFs, and multiple URFs) have been introduced in CSAFOT and their prevalence significantly increases over time in Martinique and Guadeloupe. We identified twelve major transmission networks of non-B subtypes (CRF02_AG and subtypes A3, C, D, and F1) that probably arose in Guadeloupe, Martinique, French Guiana, and mainland France between the late 1970s and the middle 2000s. Phylogeographic analyses support frequent non-B subtype viral transmissions within CSAFOT as well as transatlantic transmission between CSAFOT and mainland France. Domestic transmission networks of non-B subtype variants in CSAFOT comprise both men having sex with men and heterosexual individuals from different age groups. Different HIV-1 non-B subtype variants were sequentially introduced in CSAFOT between the late 1970s and the middle 2000s and are currently spreading through domestic, regional, and/or transatlantic networks of individuals from different age and risk groups.
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Affiliation(s)
- Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Edson Delatorre
- Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Brazil
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, Guyane Française
| | - Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, Guyane Française
| | | | - Benoit Tressières
- INSERM Centre d'Investigation Clinique 1424, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, Guadeloupe
| | - Ornella Cabras
- Service de Maladies Infectieuses et Tropicales, Martinique University Hospital, Université des Antilles, Fort-de-France EA 7524, Martinique
| | - Isabelle Lamaury
- Department of Infectious and Tropical Diseases, Dermatology, Internal Medicine, University Hospital Guadeloupe, Pointe-à-Pitre, Guadeloupe
| | - André Cabié
- Service de Maladies Infectieuses et Tropicales, Martinique University Hospital, Université des Antilles, Fort-de-France EA 7524, Martinique
| | - Benoit Visseaux
- Université de Paris, INSERM UMR 1137 IAME, Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, Paris, France
| | - Marie-Laure Chaix
- Université de Paris, INSERM U944, Laboratoire de Virologie, AP-HP, Hôpital Saint-Louis, Paris, France
| | - Diane Descamps
- Université de Paris, INSERM UMR 1137 IAME, Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, Paris, France
| | - Raymond Césaire
- Service de Virologie, Martinique University Hospital, Université des Antilles, Fort-de-France EA 7524, Martinique
| | - Mathieu Nacher
- Coordination Régionale de la lutte contre le VIH (COREVIH) and Centre d'Investigation Clinique - CIC INSERM 1424, Centre Hospitalier de Cayenne "Andrée Rosemon", Cayenne, Guyane Française
| | - Georges Dos Santos
- Service de Virologie, Martinique University Hospital, Université des Antilles, Fort-de-France EA 7524, Martinique
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Silva CMD, Peder LDD, Thomazella MV, Teixeira JJV, Bertolini DA. PROFILE OF HCV GENOTYPES AND HIV-SUBTYPES AMONG HIV-COINFECTED PATIENTS IN SOUTHERN BRAZIL. ARQUIVOS DE GASTROENTEROLOGIA 2020; 56:344-350. [PMID: 31800733 DOI: 10.1590/s0004-2803.201900000-68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/07/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Hepatitis B and C virus (HBV and HCV) are the two most common infections among human immunodeficiency virus (HIV)-infected patients. OBJECTIVE To identify the frequency of HIV subtypes and HCV genotypes in HIV-coinfected patients. METHODS A cross-sectional and retrospective study was carried out into two reference centers in Southern Brazil between January 1, 2002 and June 30, 2016. The Abbott Real Time HCV Genotype II system was used for routine diagnostics to determine the HCV genotype based on dual-target real-time PCR. Proviral HIV-1 RNA was extracted from serum samples and fragments of the pol gene were generated by PCR. The HIV-1 PT and RT gene sequences were submitted to Maximum Likelihood Phylogenetic analysis by collecting reference sequences from the HIV-1 group M subtype of the Los Alamos database. RESULTS During the study period, 3340 patients with HIV were diagnosed at both referral centers, of which 4.97% (166/3340) had HBV and/or HCV coinfection. Seroprevalence of HIV-HBV, HIV-HCV and HIV-HBV-HCV was 37.4%, 58.4%, and 4.2%, respectively. HIV-HCV-coinfected patients had a lower median nadir CD4+ T-cell count when compared to HIV-HBV-coinfected patients (P=0.01). Among those coinfected with HCV, HCV-1 (HCV-1) and HCV-3 (HCV-3) genotypes were the most prevalent, being detected in 73.8% and 21.4%, respectively. Among the HCV-1 coinfected patients, 79.3% and 20.1% had subtypes 1a and 1b, respectively. HIV subtype B was the most prevalent in HIV-coinfected patients. There was no significant difference regarding nadir CD4+ T-cell count and HIV viral load when compared to coinfected with HCV-1 with HCV-3, as well as those co-infected with HCV-1a with HCV-1b. CONCLUSION In the present study, a higher frequency of subtype B of HIV and HCV-1 were found in HIV-coinfected patients. Further larger-scale and long-term studies are needed to better understand the effect of HCV genotypes in HIV-infected patients.
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Affiliation(s)
| | - Leyde Daiane de Peder
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
| | - Mateus Vailant Thomazella
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
| | | | - Dennis Armando Bertolini
- Universidade Estadual de Maringá, Departamento de Análises Clínicas e Biomedicina, Maringá, PR, Brasil
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Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 2019; 15:e1007976. [PMID: 31809523 PMCID: PMC6897401 DOI: 10.1371/journal.ppat.1007976] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.
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Crispim MAE, Reis MNDG, Abrahim C, Kiesslich D, Fraiji N, Bello G, Stefani MMA. Homogenous HIV-1 subtype B from the Brazilian Amazon with infrequent diverse BF1 recombinants, subtypes F1 and C among blood donors. PLoS One 2019; 14:e0221151. [PMID: 31498798 PMCID: PMC6733458 DOI: 10.1371/journal.pone.0221151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 07/31/2019] [Indexed: 11/18/2022] Open
Abstract
In the last decade a growing HIV/AIDS epidemic with increased incidence and AIDS-related mortality has been reported in Northern Brazil from which molecular data are scarce. Also, apparently healthy, adult blood donors, recently diagnosed with HIV-1 represent important sentinel populations for molecular studies. This cross-sectional study describes HIV-1 subtypes in blood donors from three reference public blood centers located in three States in Northern Brazil. HIV-1 pol sequencing (protease/PR, reverse transcriptase/RT) was performed on plasma samples of HIV-1 positive donors from HEMOAM, Manaus, Amazonas (n = 198), HEMERON, Porto Velho, Rondônia (n = 20) and HEMORAIMA, Boa Vista, Roraima (n = 9) collected from 2011-2017. HIV-1 subtypes were identified by REGA, phylogenetic inference; recombinant viruses were characterized by SIMPLOT. Young, single, males predominated, around half was first-time donors. Syphilis co-infection was detected in 17% (39 out of 227), 8% (18 out of 227) was anti-HBc positive. Subtype B represented ≥ 90% in Amazonas, Rondônia and Roraima, subtype C (3.1%) was found in Amazonas and Rondônia; subtype F1 (0.9%) and BF1 recombinants (5.3%) were only detected in Amazonas. Subtype B sequences from Amazonas (n = 179), Rondônia (n = 18) and Roraima (n = 9) were combined with viral strains representative of the BPANDEMIC (n = 300) and BCARIBBEAN/BCAR (n = 200) lineages. The BPANDEMIC lineage predominated (78%) although BCAR lineages were frequent in Roraima (56%) and Amazonas (22%). Subtype C and subtype F1 sequences identified here clustered within Brazilian CBR and F1BR lineages, respectively. Twelve BF1 mosaics showed 11 different recombination profiles: six were singleton unique-recombinant-forms/URFs, one displays a CRF28/29_BF-like recombinant pattern and the remaining four BF1 isolates branched with other Brazilian BF1 viruses previously described and may represent putative new CRF_BF1 from Northern Brazil. Our study shows a highly homogeneous molecular pattern with prevalent subtype B, followed by BF1, and sporadic subtype C and F1 in blood donors from the Northern region. Surveillance studies are important to monitor HIV-1 diversity which can reveal patterns of viral dissemination, especially in a highly endemic, remote and geographically isolated region as Northern Brazil.
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Affiliation(s)
| | - Mônica Nogueira da Guarda Reis
- Instituto de Patologia Tropical e Saúde Pública, Laboratório de Imunologia da AIDS e da Hanseniase, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Claudia Abrahim
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Dagmar Kiesslich
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Nelson Fraiji
- Fundação de Hematologia e Hemoterapia do Amazonas/HEMOAM, Amazonas, Manaus, Brazil
| | - Gonzalo Bello
- Instituto Oswaldo Cruz, FIOCRUZ, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariane Martins Araújo Stefani
- Instituto de Patologia Tropical e Saúde Pública, Laboratório de Imunologia da AIDS e da Hanseniase, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
- * E-mail:
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11
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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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13
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de Almeida DV, Macieira KV, Grinsztejn BGJ, Veloso dos Santos VG, Guimarães ML. Cross-Neutralizing Antibodies in HIV-1 Individuals Infected by Subtypes B, F1, C or the B/Bbr Variant in Relation to the Genetics and Biochemical Characteristics of the env Gene. PLoS One 2016; 11:e0167690. [PMID: 27936047 PMCID: PMC5147934 DOI: 10.1371/journal.pone.0167690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/21/2016] [Indexed: 11/18/2022] Open
Abstract
Various HIV-1 env genetic and biochemical features impact the elicitation of cross-reactive neutralizing antibodies in natural infections. Thus, we aimed to investigate cross-neutralizing antibodies in individuals infected with HIV-1 env subtypes B, F1, C or the B/Bbr variant as well as env characteristics. Therefore, plasma samples from Brazilian chronically HIV-1 infected individuals were submitted to the TZM-bl neutralization assay. We also analyzed putative N-glycosylation sites (PNGLs) and the size of gp120 variable domains in the context of HIV-1 subtypes prevalent in Brazil. We observed a greater breadth and potency of the anti-Env neutralizing response in individuals infected with the F1 or B HIV-1 subtypes compared with the C subtype and the variant B/Bbr. We observed greater V1 B/Bbr and smaller V4 F1 than those of other subtypes (p<0.005), however neither was there a correlation verified between the variable region length and neutralization potency, nor between PNLG and HIV-1 subtypes. The enrichment of W at top of V3 loop in weak neutralizing response viruses and the P in viruses with higher neutralization susceptibility was statistically significant (p = 0.013). Some other signatures sites were associated to HIV-1 subtype-specific F1 and B/Bbr samples might influence in the distinct neutralizing response. These results indicate that a single amino acid substitution may lead to a distinct conformational exposure or load in the association domain of the trimer of gp120 and interfere with the induction power of the neutralizing response, which affects the sensitivity of the neutralizing antibody and has significant implications for vaccine design.
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Affiliation(s)
| | - Karine Venegas Macieira
- Laboratory of AIDS and Molecular Immunology, Oswaldo Cruz Institute - FIOCRUZ, Rio de Janeiro, 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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15
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Fernandes-Cardoso J, Süffert TA, Correa MDG, Jobim LFJ, Jobim M, Salim PH, Arruda MB, Boullosa LT, Tanuri A, Porto LC, Ferreira OC. Association between KIR genotypes and HLA-B alleles on viral load in Southern Brazilian individuals infected by HIV-1 subtypes B and C. Hum Immunol 2016; 77:854-860. [PMID: 27346697 DOI: 10.1016/j.humimm.2016.06.013] [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] [Received: 01/15/2015] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/15/2022]
Abstract
There is a great variety of HIV-1 subtypes circulating in Brazil, including subtype C, whose prevalence is on the rise, particularly in the southern region. Many host and viral genetic factors may be involved in this trend. We evaluated the influence of human leukocyte antigen (HLA) class I alleles and killer-cell immunoglobulin-like receptor (KIR) genotypes on viral set point and T-CD4(+) parameters in 84 treatment-naïve HIV-1-positive individuals. Frequency data in the infected group were compared to data of 548 healthy control subjects. Individuals with the KIR AA genotype had a higher viral load (VL) than individuals with the KIR Bx genotype. The HIV-1 group was subdivided into three subgroups according to HLA-B allele presence: those with protection to disease alleles (HLA-B(+)), accelerated disease progression alleles (HLA-B(-)), or neither (HLA-B(o)) were grouped. We observed a significant effect of the HLA-B allele presence on VL. The HLA-B(+) group had significantly lower VL than the HLA-B(-) group and trended toward a lower VL than the HLA-B(o) group. There were significant differences between groups expressing extreme VL values: KIR-AA+HLA-B(-) vs. KIR Bx+HLA-B(+) and KIR-AA+HLA-B(o)vs. KIR Bx+HLA-B(+). The relationship of KIR/HLA host genetics with slow HIV disease progression in southern Brazil may be useful for vaccine developers, epidemiologists, and clinicians.
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Affiliation(s)
- Juliana Fernandes-Cardoso
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Theodoro Armando Süffert
- Serviço de Assistência Especializada em DST/AIDS, Prefeitura Municipal de Porto Alegre, Porto Alegre, Brazil
| | - Maria da Gloria Correa
- Serviço de Assistência Especializada em DST/AIDS, Prefeitura Municipal de Porto Alegre, Porto Alegre, Brazil
| | | | - Mariana Jobim
- Departamento de Imunologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Monica Barcelos Arruda
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lidia Theodoro Boullosa
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luis Cristóvão Porto
- Laboratório de Histocompatibilidade e Criopreservação, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Orlando C Ferreira
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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16
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Delatorre E, de Azevedo SSD, Rodrigues-Pedro A, Velasco-de-Castro CA, Couto-Fernandez JC, Pilotto JH, Morgado MG. Tracing the origin of a singular HIV-1 CRF45_cpx clade identified in Brazil. INFECTION GENETICS AND EVOLUTION 2016; 46:223-232. [PMID: 27259365 DOI: 10.1016/j.meegid.2016.05.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 01/10/2023]
Abstract
The HIV-1 epidemiology has changed over the past decade toward a marked increase in the circulation of strains previously restricted to local epidemics. Recent molecular epidemiological surveys identified some HIV-1 strains of probable African origin circulating in Brazil, including the Circulating Recombinant Form (CRF) 45_cpx, a complex A1/K/U recombinant that circulates in Central Africa. Here, we characterize partial genomic sequences and reconstruct the evolutionary history of HIV-1 CRF45_cpx-related recombinant samples identified in independent studies carried out with HIV+ individuals in Brazil. The sequences were obtained by overlapping PCR amplifications followed by direct sequencing. Recombination profiles were determined by phylogenetic and bootscaning analyses. The evolutionary history was estimated by a Bayesian coalescent-based method using datasets representing the gag, pol and env gene fragments. Six of the 10 samples isolated in Rio de Janeiro showed a CRF45_cpx-like pattern throughout the sequenced genome. The remaining were classified as second-generation recombinants, showing the mosaic patterns: CRF45_cpx/B/D/F1/U, CRF45_cpx/B/F1/U, CRF45_cpx/B/U and CRF45_cpx/F1. All Brazilian CRF45_cpx sequences, except one, formed a monophyletic clade (CRF45-BR), which seems to be the result of a single introduction event that has spread to the Rio de Janeiro, São Paulo and Minas Gerais states and is related to sequences from Argentina, Italy and Belgium. The Bayesian analyses pointed out quite consistent onset dates for CRF45-BR clade (~1984: 1976-1996) in the three gene datasets. These results indicate that the CRF45-BR clade has been circulating in the Southeastern Brazilian region for about 30years, although its presence was not detected until recently due to its very low prevalence. This reinforces the relevance of large-scale molecular surveillance data to identify the emergence of new HIV variants and their impact on local epidemics.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Suwellen S D de Azevedo
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Adriana Rodrigues-Pedro
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Carlos Augusto 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
| | | | - Jose H Pilotto
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil; Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
| | - Mariza G Morgado
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 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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Cabello M, Mendoza Y, Bello G. Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 subtype B clades in the Caribbean region. PLoS One 2014; 9:e106045. [PMID: 25148215 PMCID: PMC4141835 DOI: 10.1371/journal.pone.0106045] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/29/2014] [Indexed: 11/18/2022] Open
Abstract
The Human immunodeficiency virus type-1 (HIV-1) epidemic in the Caribbean region is mostly driven by subtype B; but information about the pattern of viral spread in this geographic region is scarce and different studies point to quite divergent models of viral dissemination. In this study, we reconstructed the spatiotemporal and population dynamics of the HIV-1 subtype B epidemic in the Caribbean. A total of 1,806 HIV-1 subtype B pol sequences collected from 17 different Caribbean islands between 1996 and 2011 were analyzed together with sequences from the United States (n = 525) and France (n = 340) included as control. Maximum Likelihood phylogenetic analyses revealed that HIV-1 subtype B infections in the Caribbean are driven by dissemination of the pandemic clade (BPANDEMIC) responsible for most subtype B infections across the world, and older non-pandemic lineages (BCAR) characteristics of the Caribbean region. The non-pandemic BCAR strains account for >40% of HIV-1 infections in most Caribbean islands; with exception of Cuba and Puerto Rico. Bayesian phylogeographic analyses indicate that BCAR strains probably arose in the island of Hispaniola (Haiti/Dominican Republic) around the middle 1960s and were later disseminated to Trinidad and Tobago and to Jamaica between the late 1960s and the early 1970s. In the following years, the BCAR strains were also disseminated from Hispaniola and Trinidad and Tobago to other Lesser Antilles islands at multiple times. The BCAR clades circulating in Hispaniola, Jamaica and Trinidad and Tobago appear to have experienced an initial phase of exponential growth, with mean estimated growth rates of 0.35-0.45 year(-1), followed by a more recent stabilization since the middle 1990s. These results demonstrate that non-pandemic subtype B lineages have been widely disseminated through the Caribbean since the late 1960s and account for an important fraction of current HIV-1 infections in the region.
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Affiliation(s)
- Marina Cabello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Yaxelis Mendoza
- Department of Genomics and Proteomics, Gorgas Memorial Institute for Health Studies, Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur City, Andhra Pradesh, India
- Department of Genetics and Molecular Biology, University of Panama, Panama City, Panama
- INDICASAT-AIP, City of Knowledge, Clayton, Panama City, Panama
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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