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Wieczorek L, Chang D, Sanders-Buell E, Zemil M, Martinez E, Schoen J, Chenine AL, Molnar S, Barrows B, Poltavee K, Charurat ME, Abimiku A, Blattner W, Iroezindu M, Kokogho A, Michael NL, Crowell TA, Ake JA, Tovanabutra S, Polonis VR. Differences in neutralizing antibody sensitivities and envelope characteristics indicate distinct antigenic properties of Nigerian HIV-1 subtype G and CRF02_AG. Virol J 2024; 21:148. [PMID: 38951814 PMCID: PMC11218331 DOI: 10.1186/s12985-024-02394-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/19/2024] [Indexed: 07/03/2024] Open
Abstract
The magnitude of the HIV-1 epidemic in Nigeria is second only to the subtype C epidemic in South Africa, yet the subtypes prevalent in Nigeria require further characterization. A panel of 50 subtype G and 18 CRF02_AG Nigerian HIV-1 pseudoviruses (PSV) was developed and envelope coreceptor usage, neutralization sensitivity and cross-clade reactivity were characterized. These PSV were neutralized by some antibodies targeting major neutralizing determinants, but potentially important differences were observed in specific sensitivities (eg. to sCD4, MPER and V2/V3 monoclonal antibodies), as well as in properties such as variable loop lengths, number of potential N-linked glycans and charge, demonstrating distinct antigenic characteristics of CRF02_AG and subtype G. There was preferential neutralization of the matched CRF/subtype when PSV from subtype G or CRF02_AG were tested using pooled plasma. These novel Nigerian PSV will be useful to study HIV-1 CRF- or subtype-specific humoral immune responses for subtype G and CRF02_AG.
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Affiliation(s)
- Lindsay Wieczorek
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - David Chang
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Office of AIDS Research, National Institutes of Health, Rockville, MD, 20852, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth Martinez
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Jesse Schoen
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Integrated Biotherapeutics, Rockville, MD, 20850, USA
| | - Sebastian Molnar
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Brittani Barrows
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
- Present address: Lentigen Technology, Gaithersburg, MD, 20878, USA
| | - Kultida Poltavee
- SEARCH, Insititute of HIV Research and Innovation (IHRI), Bangkok, Thailand
| | - Man E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alash'le Abimiku
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - William Blattner
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michael Iroezindu
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Afoke Kokogho
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- HJF Medical Research International, Abuja, Nigeria
| | - Nelson L Michael
- Center for Infectious Disease Research, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Trevor A Crowell
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA
- Henry M. Jackson Foundation for Advancement of Military Medicine, Bethesda, MD, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Resarch, Silver Spring, MD, USA.
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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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Gräf T, Delatorre E, Bello G. Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences. Mem Inst Oswaldo Cruz 2020; 115:e190461. [PMID: 32187328 PMCID: PMC7098263 DOI: 10.1590/0074-02760190461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 12/14/2022] Open
Abstract
Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.
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Affiliation(s)
- Tiago Gräf
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil
| | - Edson Delatorre
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia, Alegre, ES, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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Delatorre E, Couto-Fernandez JC, Bello G. HIV-1 Genetic Diversity in Northeastern Brazil: High Prevalence of Non-B Subtypes. AIDS Res Hum Retroviruses 2017; 33:639-647. [PMID: 28325060 DOI: 10.1089/aid.2017.0045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The Northeastern Brazilian region has experienced a constant increase in the number of newly reported AIDS cases over the last decade, but the genetic diversity of HIV-1 strains currently disseminated in this region remains poorly explored. HIV-1 pol sequences were obtained from 140 patients followed at outpatient clinics from four Northeastern Brazilian states (Alagoas, Bahia, Ceará, and Piauí) between 2014 and 2015. Subtype B was the most prevalent HIV-1 clade (72%) detected in the Northeastern region, followed by subtypes F1 (6%), C (5%), and D (1%). The remaining strains (16%) displayed a recombinant structure and were classified as follows: BF1 (11%), BC (4%), BCF1 (1%), and CRF02_AG like (1%). The 20 HIV-1 BF1 and BC recombinant sequences detected were distributed among 11 lineages classified as follows: CRF28/29_BF like (n = 5), CRF39_BF like (n = 1), URF_BF (n = 9), and URF_BC (n = 5). Non-B subtypes were detected in all Northeastern Brazilian states, but with variable prevalence, ranging from 16% in Ceará to 55% in Alagoas. Phylogenetic analyses support that subtype D and CRF02_AG strains detected in the Northeastern region resulted from the expansion of autochthonous transmission networks, rather than from exogenous introductions from other countries. These results reveal that HIV-1 epidemic spreading in the Northeastern Brazilian region comprised by multiple subtypes and recombinant strains and the molecular epidemiologic pattern in this Brazilian region is much more complex than originally estimated.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Delatorre E, Silva-de-Jesus C, Couto-Fernandez JC, Pilotto JH, Morgado MG. High HIV-1 Diversity and Prevalence of Transmitted Drug Resistance Among Antiretroviral-Naive HIV-Infected Pregnant Women from Rio de Janeiro, Brazil. AIDS Res Hum Retroviruses 2017; 33:68-73. [PMID: 27392995 DOI: 10.1089/aid.2016.0159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antiretroviral (ARV) resistance mutations in human immunodeficiency virus type 1 (HIV-1) infection may reduce the efficacy of prophylactic therapy to prevent mother-to-child transmission (PMTCT) and future treatment options. This study evaluated the diversity and the prevalence of transmitted drug resistance (TDR) in protease (PR) and reverse transcriptase (RT) regions of HIV-1 pol gene among 87 ARV-naive HIV-1-infected pregnant women from Rio de Janeiro, Brazil, between 2012 and 2015. The viral diversity comprised HIV-1 subtypes B (67.8%), F1 (17.2%), and C (4.6%); the circulating recombinant forms 12_BF (2.3%), 28/29_BF, 39_BF, 02_AG (1.1% each) and unique recombinants forms (4.5%). The overall prevalence of any TDR was 17.2%, of which 5.7% for nucleoside RT inhibitors, 5.7% for non-nucleoside RT inhibitors, and 8% for PR inhibitors. The TDR prevalence found in this population may affect the virological outcome of the standard PMTCT ARV-regimens, reinforcing the importance of continuous monitoring.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–FIOCRUZ, Rio de Janeiro, Brazil
| | - Carlos Silva-de-Jesus
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz–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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Predominance of CRF63_02A1 and multiple patterns of unique recombinant forms of CRF63_A1 among individuals with newly diagnosed HIV-1 infection in Kemerovo Oblast, Russia. Arch Virol 2016; 162:379-390. [PMID: 27761744 DOI: 10.1007/s00705-016-3120-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/18/2022]
Abstract
Kemerovo Oblast (KO) has had the highest rate of HIV spread in Russia since 2011. The aim of this work was to study the genetic variation of HIV-1 in Kemerovo Oblast. Blood was sampled from a total of 91 HIV-positive antiretroviral-therapy-naïve individuals in 2013 (38) and 2015 (53). HIV-1 subtypes, pol gene drug resistance mutations, and viral tropism were analyzed. In 2013-2015, the prevalence of HIV-1 subtype A decreased in KO from 60.5 to 7.5 %. The samples collected in 2015 from the patients with newly diagnosed HIV demonstrate the current dominance of HIV-1 CRF63_02A1 (71.7 %) and HIV-1 URF63_A1 (20.8 %), their parental viruses being CRF63_02A1 and subtype A. The initially predominant genetic variant, HIV-1 subtype A, was replaced in KO. An unusually high incidence of HIV-1 unique recombinant forms is probably the result of HIV-1 CRF63_02A1 introduction in the group of injection drug users with the initial HIV-1 subtype A infection and the practice of risky behavior that promotes reinfection. HIV-1 CRF63_02A1, which recently emerged in Siberia, and its recombinant forms have an ever-increasing impact on the current HIV epidemic in Russia, making urgent the need for in-depth study of this HIV-1 genetic variant.
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Mir D, Jung M, Delatorre E, Vidal N, Peeters M, Bello G. Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global dissemination. INFECTION GENETICS AND EVOLUTION 2016; 46:190-199. [PMID: 27180893 DOI: 10.1016/j.meegid.2016.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 05/09/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022]
Abstract
The HIV-1 CRF02_AG clade is the most prevalent HIV variant in West and West-Central Africa and its detection outside Africa is increasingly common. Little is known, however, about the number and phylodynamics of major CRF02_AG lineages circulating worldwide. To this end, a total of 3170 HIV-1 CRF02_AG-like pol sequences isolated around the world, over a period of 25years (1989 to 2013), were analyzed using Maximum Likelihood and Bayesian coalescent-based methods. Our results suggest that most of the current CRF02_AG diversity comes from the dissemination of a few founder strains out of Central Africa into West Africa and Cameroon between the late 1960s and the middle 1980s. The CRF02_AG strain introduced into West Africa established a large regional epidemic with low phylogeographic structure. This strain was also successfully disseminated out of the West African region and originated at least three large secondary outbreaks in Cameroon at around the late 1970s, in the former Soviet Union (FSU) countries at around the late 1990s, and in Bulgaria/Germany at around the early 2000s. The CRF02_AG African lineages introduced into Cameroon remained mostly restricted to this country and its neighbors. Demographic reconstructions indicate that major CRF02_AG clades circulating in Africa exhibited a decline in growth rate since the middle 1980s/1990s, whereas CRF02_AG clades in Europe and the FSU countries continue to grow exponentially until the middle to late 2000s. Substantial differences in the median estimated growth rate of the same CRF02_AG clade circulating in different regions (0.63-2.00year-1), and of different CRF02_AG clades circulating in the same country (0.41-0.75year-1) were observed. Thus, the cause of the epidemic outcome of the different HIV-1 CRF02_AG lineages is probably multifactorial.
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Affiliation(s)
- Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Matthieu Jung
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicole Vidal
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and Université Montpellier, Montpellier, France; Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS - Université Montpellier, Montpellier, France
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
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